Starting phenix.real_space_refine on Thu Mar 5 22:46:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7soe_25268/03_2026/7soe_25268.cif Found real_map, /net/cci-nas-00/data/ceres_data/7soe_25268/03_2026/7soe_25268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7soe_25268/03_2026/7soe_25268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7soe_25268/03_2026/7soe_25268.map" model { file = "/net/cci-nas-00/data/ceres_data/7soe_25268/03_2026/7soe_25268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7soe_25268/03_2026/7soe_25268.cif" } resolution = 2.8 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= 0.060 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 126 5.16 5 C 16305 2.51 5 N 4473 2.21 5 O 5043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25947 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 7222 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 251} Link IDs: {'PTRANS': 56, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 902 Unresolved non-hydrogen angles: 1157 Unresolved non-hydrogen dihedrals: 742 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 18, 'ASN:plan1': 24, 'PHE:plan': 15, 'ASP:plan': 18, 'GLU:plan': 15, 'ARG:plan': 12, 'TRP:plan': 3, 'TYR:plan': 12, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 539 Chain: "L" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 530 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 355 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'TYR:plan': 6, 'GLU:plan': 5, 'GLN:plan1': 8, 'ASP:plan': 5, 'TRP:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 158 Chain: "B" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 631 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 7, 'TRANS': 117} Unresolved non-hydrogen bonds: 352 Unresolved non-hydrogen angles: 465 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'PHE:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 5, 'ARG:plan': 2, 'TYR:plan': 4, 'ASP:plan': 7, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 171 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Restraints were copied for chains: C, F, D, G, E, H, J, K Time building chain proxies: 7.69, per 1000 atoms: 0.30 Number of scatterers: 25947 At special positions: 0 Unit cell: (202.32, 187.146, 171.972, 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 126 16.00 O 5043 8.00 N 4473 7.00 C 16305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS C 985 " distance=2.00 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.11 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=2.01 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=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.14 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.12 Simple disulfide: pdb=" SG CYS A 985 " - pdb=" SG CYS F 383 " distance=2.00 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 97 " distance=2.07 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS F 985 " distance=2.00 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.11 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.11 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS F 538 " - pdb=" SG CYS F 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.14 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.14 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.12 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.12 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 87 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.07 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.07 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 BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A1074 " " NAG A1305 " - " ASN A1098 " " NAG A1306 " - " ASN A1134 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 801 " " NAG A1310 " - " ASN A 717 " " NAG A1311 " - " ASN A 61 " " NAG A1312 " - " ASN A 282 " " NAG A1313 " - " ASN A 165 " " NAG A1314 " - " ASN A 234 " " NAG A1315 " - " ASN A 149 " " NAG A1316 " - " ASN A 17 " " NAG A1317 " - " ASN A 343 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C1098 " " NAG C1306 " - " ASN C1134 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 801 " " NAG C1310 " - " ASN C 717 " " NAG C1311 " - " ASN C 61 " " NAG C1312 " - " ASN C 282 " " NAG C1313 " - " ASN C 165 " " NAG C1314 " - " ASN C 234 " " NAG C1315 " - " ASN C 149 " " NAG C1316 " - " ASN C 17 " " NAG C1317 " - " ASN C 343 " " NAG F1301 " - " ASN F 331 " " NAG F1302 " - " ASN F 603 " " NAG F1303 " - " ASN F 657 " " NAG F1304 " - " ASN F1074 " " NAG F1305 " - " ASN F1098 " " NAG F1306 " - " ASN F1134 " " NAG F1307 " - " ASN F 616 " " NAG F1308 " - " ASN F 709 " " NAG F1309 " - " ASN F 801 " " NAG F1310 " - " ASN F 717 " " NAG F1311 " - " ASN F 61 " " NAG F1312 " - " ASN F 282 " " NAG F1313 " - " ASN F 165 " " NAG F1314 " - " ASN F 234 " " NAG F1315 " - " ASN F 149 " " NAG F1316 " - " ASN F 17 " " NAG F1317 " - " ASN F 343 " " NAG I 1 " - " ASN A 122 " " NAG J 1 " - " ASN C 122 " " NAG K 1 " - " ASN F 122 " Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.0 seconds 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7056 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 54 sheets defined 21.3% alpha, 26.6% 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 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.595A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.655A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.758A 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 853 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.104A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.754A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (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: 4.000A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.823A pdb=" N GLU L 82 " --> pdb=" O THR L 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.595A 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: 3.655A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.758A 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 853 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.104A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.754A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) 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 removed outlier: 4.000A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 removed outlier: 3.823A pdb=" N GLU D 82 " --> pdb=" O THR D 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 67 No H-bonds generated for 'chain 'E' and resid 65 through 67' Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'F' and resid 294 through 304 Processing helix chain 'F' and resid 338 through 343 Processing helix chain 'F' and resid 365 through 370 Processing helix chain 'F' and resid 386 through 389 Processing helix chain 'F' and resid 405 through 410 removed outlier: 4.595A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 422 Processing helix chain 'F' and resid 438 through 443 removed outlier: 3.654A pdb=" N SER F 443 " --> pdb=" O ASN F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 616 through 620 Processing helix chain 'F' and resid 737 through 744 Processing helix chain 'F' and resid 746 through 754 Processing helix chain 'F' and resid 755 through 757 No H-bonds generated for 'chain 'F' and resid 755 through 757' Processing helix chain 'F' and resid 758 through 783 removed outlier: 3.758A pdb=" N ASP F 775 " --> pdb=" O ALA F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 826 Processing helix chain 'F' and resid 853 through 856 Processing helix chain 'F' and resid 866 through 885 Processing helix chain 'F' and resid 897 through 908 Processing helix chain 'F' and resid 912 through 919 removed outlier: 4.105A pdb=" N LEU F 916 " --> pdb=" O THR F 912 " (cutoff:3.500A) Processing helix chain 'F' and resid 919 through 940 Processing helix chain 'F' and resid 945 through 965 removed outlier: 3.754A pdb=" N VAL F 951 " --> pdb=" O LYS F 947 " (cutoff:3.500A) Processing helix chain 'F' and resid 966 through 968 No H-bonds generated for 'chain 'F' and resid 966 through 968' Processing helix chain 'F' and resid 976 through 984 Processing helix chain 'F' and resid 985 through 1033 removed outlier: 4.000A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN F 992 " --> pdb=" O GLU F 988 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP F 994 " --> pdb=" O GLU F 990 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 82 removed outlier: 3.824A pdb=" N GLU G 82 " --> pdb=" O THR G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 88 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.231A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 10.378A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.713A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 through 85 current: chain 'A' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 126 through 132 current: chain 'A' and resid 151 through 158 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 151 through 158 current: chain 'B' and resid 48 through 54 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 59 through 61 current: chain 'B' and resid 108 through 115 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.362A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.232A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.874A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.538A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.684A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.963A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.394A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.000A pdb=" N ILE A 788 " --> pdb=" O ASN F 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.648A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.563A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AC1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'C' and resid 27 through 31 removed outlier: 8.231A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 10.378A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.713A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 83 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 85 current: chain 'C' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 126 through 132 current: chain 'C' and resid 151 through 158 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 151 through 158 current: chain 'E' and resid 48 through 54 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 59 through 61 current: chain 'E' and resid 108 through 115 Processing sheet with id=AC5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.362A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.232A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.873A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.537A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 702 through 704 Processing sheet with id=AD4, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.684A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.963A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.394A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.648A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 9 through 11 removed outlier: 6.564A pdb=" N TRP D 34 " --> pdb=" O VAL D 46 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AE1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'F' and resid 27 through 31 removed outlier: 8.230A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE F 201 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP F 228 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE F 203 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N HIS F 207 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 10.378A pdb=" N ALA F 222 " --> pdb=" O HIS F 207 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL F 36 " --> pdb=" O LEU F 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 47 through 55 removed outlier: 3.714A pdb=" N ASP F 287 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 83 through 85 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 83 through 85 current: chain 'F' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 126 through 132 current: chain 'F' and resid 151 through 158 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 151 through 158 current: chain 'H' and resid 48 through 54 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 59 through 61 current: chain 'H' and resid 108 through 115 Processing sheet with id=AE5, first strand: chain 'F' and resid 311 through 319 removed outlier: 5.362A pdb=" N ILE F 312 " --> pdb=" O THR F 599 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR F 599 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN F 314 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL F 597 " --> pdb=" O GLN F 314 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER F 316 " --> pdb=" O VAL F 595 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY F 594 " --> pdb=" O GLN F 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 324 through 328 removed outlier: 4.232A pdb=" N GLU F 324 " --> pdb=" O CYS F 538 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ASP F 574 " --> pdb=" O ILE F 587 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA F 575 " --> pdb=" O GLY F 566 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 354 through 358 Processing sheet with id=AE8, first strand: chain 'F' and resid 361 through 362 removed outlier: 6.873A pdb=" N CYS F 361 " --> pdb=" O CYS F 525 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'F' and resid 654 through 655 removed outlier: 6.537A pdb=" N ILE F 670 " --> pdb=" O ILE F 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 711 through 715 removed outlier: 3.684A pdb=" N ALA F1078 " --> pdb=" O PHE F1095 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE F1095 " --> pdb=" O ALA F1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 718 through 728 removed outlier: 5.963A pdb=" N TYR F1067 " --> pdb=" O HIS F1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS F1048 " --> pdb=" O TYR F1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 733 through 736 removed outlier: 4.394A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 1120 through 1125 removed outlier: 4.648A pdb=" N ALA F1087 " --> pdb=" O SER F1123 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 9 through 11 removed outlier: 6.563A pdb=" N TRP G 34 " --> pdb=" O VAL G 46 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 7 1180 hydrogen bonds defined for protein. 3180 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: 7.40 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4778 1.32 - 1.45: 6499 1.45 - 1.57: 15015 1.57 - 1.70: 3 1.70 - 1.83: 150 Bond restraints: 26445 Sorted by residual: bond pdb=" C PRO C 986 " pdb=" O PRO C 986 " ideal model delta sigma weight residual 1.240 1.202 0.038 1.12e-02 7.97e+03 1.18e+01 bond pdb=" C PRO A 986 " pdb=" O PRO A 986 " ideal model delta sigma weight residual 1.240 1.202 0.038 1.12e-02 7.97e+03 1.17e+01 bond pdb=" C PRO F 986 " pdb=" O PRO F 986 " ideal model delta sigma weight residual 1.240 1.202 0.038 1.12e-02 7.97e+03 1.16e+01 bond pdb=" N CYS A 985 " pdb=" CA CYS A 985 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.25e-02 6.40e+03 9.81e+00 bond pdb=" N CYS F 985 " pdb=" CA CYS F 985 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.25e-02 6.40e+03 9.74e+00 ... (remaining 26440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 34647 2.57 - 5.14: 1232 5.14 - 7.71: 411 7.71 - 10.28: 19 10.28 - 12.85: 3 Bond angle restraints: 36312 Sorted by residual: angle pdb=" N PRO F 986 " pdb=" CA PRO F 986 " pdb=" C PRO F 986 " ideal model delta sigma weight residual 110.70 123.55 -12.85 1.22e+00 6.72e-01 1.11e+02 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 123.53 -12.83 1.22e+00 6.72e-01 1.11e+02 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 123.51 -12.81 1.22e+00 6.72e-01 1.10e+02 angle pdb=" C LEU F 861 " pdb=" N PRO F 862 " pdb=" CA PRO F 862 " ideal model delta sigma weight residual 119.66 126.23 -6.57 7.20e-01 1.93e+00 8.33e+01 angle pdb=" C LEU C 861 " pdb=" N PRO C 862 " pdb=" CA PRO C 862 " ideal model delta sigma weight residual 119.66 126.20 -6.54 7.20e-01 1.93e+00 8.25e+01 ... (remaining 36307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 15942 17.50 - 34.99: 393 34.99 - 52.49: 60 52.49 - 69.99: 42 69.99 - 87.48: 18 Dihedral angle restraints: 16455 sinusoidal: 5547 harmonic: 10908 Sorted by residual: dihedral pdb=" C ASN A 540 " pdb=" N ASN A 540 " pdb=" CA ASN A 540 " pdb=" CB ASN A 540 " ideal model delta harmonic sigma weight residual -122.60 -111.84 -10.76 0 2.50e+00 1.60e-01 1.85e+01 dihedral pdb=" C ASN F 540 " pdb=" N ASN F 540 " pdb=" CA ASN F 540 " pdb=" CB ASN F 540 " ideal model delta harmonic sigma weight residual -122.60 -111.84 -10.76 0 2.50e+00 1.60e-01 1.85e+01 dihedral pdb=" C ASN C 540 " pdb=" N ASN C 540 " pdb=" CA ASN C 540 " pdb=" CB ASN C 540 " ideal model delta harmonic sigma weight residual -122.60 -111.86 -10.74 0 2.50e+00 1.60e-01 1.85e+01 ... (remaining 16452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 4080 0.104 - 0.208: 327 0.208 - 0.312: 60 0.312 - 0.416: 15 0.416 - 0.519: 9 Chirality restraints: 4491 Sorted by residual: chirality pdb=" C1 NAG C1317 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG C1317 " pdb=" O5 NAG C1317 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.75e+00 chirality pdb=" C1 NAG F1317 " pdb=" ND2 ASN F 343 " pdb=" C2 NAG F1317 " pdb=" O5 NAG F1317 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.74e+00 chirality pdb=" C1 NAG A1317 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1317 " pdb=" O5 NAG A1317 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.68e+00 ... (remaining 4488 not shown) Planarity restraints: 4857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1074 " 0.043 2.00e-02 2.50e+03 4.47e-02 2.49e+01 pdb=" CG ASN A1074 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A1074 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A1074 " -0.069 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " -0.043 2.00e-02 2.50e+03 4.46e-02 2.49e+01 pdb=" CG ASN C1074 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " 0.069 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F1074 " -0.043 2.00e-02 2.50e+03 4.45e-02 2.47e+01 pdb=" CG ASN F1074 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN F1074 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN F1074 " 0.068 2.00e-02 2.50e+03 pdb=" C1 NAG F1304 " -0.053 2.00e-02 2.50e+03 ... (remaining 4854 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 10940 2.91 - 3.41: 22424 3.41 - 3.91: 40963 3.91 - 4.40: 44555 4.40 - 4.90: 76032 Nonbonded interactions: 194914 Sorted by model distance: nonbonded pdb=" O GLU A 988 " pdb=" OE1 GLU A 988 " model vdw 2.416 3.040 nonbonded pdb=" O GLU C 988 " pdb=" OE1 GLU C 988 " model vdw 2.417 3.040 nonbonded pdb=" O GLU F 988 " pdb=" OE1 GLU F 988 " model vdw 2.417 3.040 nonbonded pdb=" ND2 ASN C 540 " pdb=" OG1 THR C 549 " model vdw 2.539 3.120 nonbonded pdb=" ND2 ASN A 540 " pdb=" OG1 THR A 549 " model vdw 2.539 3.120 ... (remaining 194909 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'L' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.040 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 27.580 Find NCS groups from input model: 0.380 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: 0.010 Load rotamer database and sin/cos tables:8.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 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 : 0.011 0.112 26553 Z= 0.606 Angle : 1.312 12.846 36585 Z= 0.881 Chirality : 0.073 0.519 4491 Planarity : 0.005 0.030 4803 Dihedral : 9.440 87.485 9246 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.15 % Allowed : 0.89 % Favored : 98.96 % 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: 0.29 (0.13), residues: 3717 helix: 0.36 (0.18), residues: 675 sheet: 1.07 (0.16), residues: 981 loop : -0.25 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 34 TYR 0.036 0.004 TYR F1067 PHE 0.025 0.004 PHE A 329 TRP 0.021 0.005 TRP A1102 HIS 0.006 0.001 HIS C1071 Details of bonding type rmsd covalent geometry : bond 0.01045 (26445) covalent geometry : angle 1.29081 (36312) SS BOND : bond 0.04217 ( 51) SS BOND : angle 3.11550 ( 102) hydrogen bonds : bond 0.18565 ( 1180) hydrogen bonds : angle 8.04955 ( 3180) link_BETA1-4 : bond 0.00698 ( 3) link_BETA1-4 : angle 5.13152 ( 9) link_NAG-ASN : bond 0.05287 ( 54) link_NAG-ASN : angle 2.77902 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 401 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 780 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7253 (tp30) outliers start: 3 outliers final: 0 residues processed: 401 average time/residue: 0.5302 time to fit residues: 249.7642 Evaluate side-chains 265 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 0.0010 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 0.0470 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.7980 overall best weight: 0.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A 607 GLN A 641 ASN A 644 GLN A 658 ASN A 779 GLN A 901 GLN A 935 GLN A 955 ASN A1010 GLN C 540 ASN C 544 ASN C 606 ASN C 607 GLN C 641 ASN C 658 ASN C 779 GLN C 901 GLN C 935 GLN C 955 ASN C1002 GLN C1005 GLN C1010 GLN F 540 ASN F 544 ASN F 641 ASN F 644 GLN F 658 ASN F 779 GLN F 901 GLN F 935 GLN F 955 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.234401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.200749 restraints weight = 29347.024| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 1.86 r_work: 0.3938 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3896 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26553 Z= 0.123 Angle : 0.561 7.553 36585 Z= 0.296 Chirality : 0.046 0.207 4491 Planarity : 0.004 0.032 4803 Dihedral : 4.265 27.582 5118 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.79 % Allowed : 7.99 % Favored : 90.23 % 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: 1.09 (0.13), residues: 3717 helix: 2.20 (0.21), residues: 648 sheet: 1.29 (0.15), residues: 1017 loop : -0.01 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 319 TYR 0.020 0.001 TYR A1067 PHE 0.017 0.001 PHE F 192 TRP 0.007 0.001 TRP A 353 HIS 0.005 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00248 (26445) covalent geometry : angle 0.53844 (36312) SS BOND : bond 0.00183 ( 51) SS BOND : angle 0.98267 ( 102) hydrogen bonds : bond 0.05384 ( 1180) hydrogen bonds : angle 6.01254 ( 3180) link_BETA1-4 : bond 0.00449 ( 3) link_BETA1-4 : angle 2.92322 ( 9) link_NAG-ASN : bond 0.00457 ( 54) link_NAG-ASN : angle 2.23663 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 287 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7890 (tt0) cc_final: 0.7493 (tt0) REVERT: C 773 GLU cc_start: 0.7924 (tt0) cc_final: 0.7721 (tt0) outliers start: 36 outliers final: 16 residues processed: 298 average time/residue: 0.5359 time to fit residues: 189.1846 Evaluate side-chains 252 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain F residue 432 CYS Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 810 SER Chi-restraints excluded: chain F residue 988 GLU Chi-restraints excluded: chain F residue 1001 LEU Chi-restraints excluded: chain F residue 1005 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 152 optimal weight: 1.9990 chunk 325 optimal weight: 0.9990 chunk 241 optimal weight: 30.0000 chunk 213 optimal weight: 1.9990 chunk 313 optimal weight: 0.0970 chunk 332 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 226 optimal weight: 0.5980 chunk 224 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A 644 GLN A 779 GLN A1002 GLN C 607 GLN C 764 ASN C 935 GLN C1002 GLN C1010 GLN F 644 GLN F 856 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.232258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.198333 restraints weight = 29147.913| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 1.86 r_work: 0.3911 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3864 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26553 Z= 0.133 Angle : 0.538 6.408 36585 Z= 0.280 Chirality : 0.046 0.204 4491 Planarity : 0.004 0.035 4803 Dihedral : 4.019 23.365 5118 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.73 % Allowed : 8.13 % Favored : 89.14 % 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: 1.05 (0.13), residues: 3717 helix: 2.29 (0.21), residues: 645 sheet: 1.39 (0.16), residues: 993 loop : -0.14 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 319 TYR 0.022 0.001 TYR A1067 PHE 0.016 0.002 PHE F 55 TRP 0.005 0.001 TRP C1102 HIS 0.005 0.001 HIS F 655 Details of bonding type rmsd covalent geometry : bond 0.00292 (26445) covalent geometry : angle 0.51881 (36312) SS BOND : bond 0.00246 ( 51) SS BOND : angle 1.23657 ( 102) hydrogen bonds : bond 0.05061 ( 1180) hydrogen bonds : angle 5.61041 ( 3180) link_BETA1-4 : bond 0.00657 ( 3) link_BETA1-4 : angle 2.42372 ( 9) link_NAG-ASN : bond 0.00384 ( 54) link_NAG-ASN : angle 1.96618 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 242 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7966 (tt0) cc_final: 0.7422 (tt0) REVERT: A 935 GLN cc_start: 0.7365 (tp40) cc_final: 0.7118 (tt0) REVERT: C 773 GLU cc_start: 0.8040 (tt0) cc_final: 0.7771 (tt0) REVERT: C 935 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7264 (tt0) REVERT: F 319 ARG cc_start: 0.7308 (ttm110) cc_final: 0.6913 (mtt-85) outliers start: 55 outliers final: 29 residues processed: 264 average time/residue: 0.5498 time to fit residues: 171.5552 Evaluate side-chains 253 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 432 CYS Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 780 GLU Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 810 SER Chi-restraints excluded: chain F residue 902 MET Chi-restraints excluded: chain F residue 1001 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 176 optimal weight: 3.9990 chunk 287 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 41 optimal weight: 30.0000 chunk 120 optimal weight: 50.0000 chunk 37 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A 644 GLN A 779 GLN C 607 GLN C 658 ASN C1002 GLN C1010 GLN F 935 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.226561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.174515 restraints weight = 27862.171| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 5.85 r_work: 0.3081 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 26553 Z= 0.250 Angle : 0.646 7.518 36585 Z= 0.335 Chirality : 0.050 0.194 4491 Planarity : 0.005 0.041 4803 Dihedral : 4.577 23.453 5118 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.47 % Allowed : 8.09 % Favored : 88.44 % 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: 0.57 (0.13), residues: 3717 helix: 1.63 (0.20), residues: 651 sheet: 1.08 (0.15), residues: 1050 loop : -0.40 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F1107 TYR 0.025 0.002 TYR A1067 PHE 0.019 0.002 PHE A 898 TRP 0.007 0.001 TRP F1102 HIS 0.008 0.002 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00587 (26445) covalent geometry : angle 0.62686 (36312) SS BOND : bond 0.00352 ( 51) SS BOND : angle 1.25267 ( 102) hydrogen bonds : bond 0.06420 ( 1180) hydrogen bonds : angle 5.85561 ( 3180) link_BETA1-4 : bond 0.00533 ( 3) link_BETA1-4 : angle 2.06191 ( 9) link_NAG-ASN : bond 0.00401 ( 54) link_NAG-ASN : angle 2.24580 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 247 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 618 THR cc_start: 0.8125 (OUTLIER) cc_final: 0.7691 (m) REVERT: A 780 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8470 (tp30) REVERT: C 380 TYR cc_start: 0.7287 (m-80) cc_final: 0.6999 (m-80) REVERT: C 704 SER cc_start: 0.8139 (t) cc_final: 0.7866 (p) REVERT: C 773 GLU cc_start: 0.8797 (tt0) cc_final: 0.8431 (tt0) REVERT: C 785 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8233 (m) REVERT: F 759 PHE cc_start: 0.8292 (m-10) cc_final: 0.7825 (m-10) REVERT: F 1005 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8765 (mm-40) outliers start: 70 outliers final: 42 residues processed: 283 average time/residue: 0.5145 time to fit residues: 172.8387 Evaluate side-chains 273 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 227 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 780 GLU Chi-restraints excluded: chain F residue 785 VAL Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 810 SER Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 988 GLU Chi-restraints excluded: chain F residue 1005 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 226 optimal weight: 0.6980 chunk 233 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 202 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 353 optimal weight: 0.0670 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 350 optimal weight: 0.1980 chunk 154 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 779 GLN A 935 GLN C 52 GLN C 607 GLN C 804 GLN C1002 GLN C1010 GLN F 607 GLN F 644 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.229176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.182341 restraints weight = 28183.132| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 5.13 r_work: 0.3159 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 26553 Z= 0.114 Angle : 0.531 6.842 36585 Z= 0.270 Chirality : 0.046 0.295 4491 Planarity : 0.004 0.037 4803 Dihedral : 4.260 24.943 5118 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.88 % Allowed : 9.03 % Favored : 88.10 % 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: 0.87 (0.13), residues: 3717 helix: 2.21 (0.20), residues: 645 sheet: 1.17 (0.15), residues: 1044 loop : -0.27 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 319 TYR 0.016 0.001 TYR F1067 PHE 0.018 0.001 PHE C 65 TRP 0.006 0.001 TRP C 436 HIS 0.004 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00242 (26445) covalent geometry : angle 0.50992 (36312) SS BOND : bond 0.00215 ( 51) SS BOND : angle 1.16648 ( 102) hydrogen bonds : bond 0.04706 ( 1180) hydrogen bonds : angle 5.46792 ( 3180) link_BETA1-4 : bond 0.00629 ( 3) link_BETA1-4 : angle 1.96258 ( 9) link_NAG-ASN : bond 0.00348 ( 54) link_NAG-ASN : angle 2.09285 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 236 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.8561 (tt0) cc_final: 0.7916 (tt0) REVERT: A 933 LYS cc_start: 0.8376 (mttt) cc_final: 0.8168 (mttp) REVERT: A 947 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8066 (mtmt) REVERT: C 704 SER cc_start: 0.8090 (t) cc_final: 0.7800 (p) REVERT: C 773 GLU cc_start: 0.8451 (tt0) cc_final: 0.8130 (tt0) REVERT: C 935 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7168 (tt0) REVERT: C 1038 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7978 (mmtm) REVERT: F 780 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8476 (tp30) outliers start: 58 outliers final: 28 residues processed: 262 average time/residue: 0.5599 time to fit residues: 172.6936 Evaluate side-chains 263 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 432 CYS Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 780 GLU Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 859 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 202 optimal weight: 0.9980 chunk 158 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 244 optimal weight: 50.0000 chunk 140 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 254 optimal weight: 4.9990 chunk 326 optimal weight: 1.9990 chunk 138 optimal weight: 0.0870 chunk 190 optimal weight: 1.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN A 935 GLN C 52 GLN C 607 GLN C 658 ASN C1002 GLN C1010 GLN F 607 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.227550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.176040 restraints weight = 28201.059| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 5.84 r_work: 0.3113 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26553 Z= 0.162 Angle : 0.566 7.195 36585 Z= 0.288 Chirality : 0.047 0.242 4491 Planarity : 0.004 0.039 4803 Dihedral : 4.240 23.246 5118 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.17 % Allowed : 9.62 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.76 (0.13), residues: 3717 helix: 2.18 (0.20), residues: 645 sheet: 1.12 (0.16), residues: 1020 loop : -0.35 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.023 0.002 TYR A1067 PHE 0.021 0.002 PHE F 643 TRP 0.005 0.001 TRP F1102 HIS 0.006 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00376 (26445) covalent geometry : angle 0.54402 (36312) SS BOND : bond 0.00298 ( 51) SS BOND : angle 1.23068 ( 102) hydrogen bonds : bond 0.05290 ( 1180) hydrogen bonds : angle 5.48578 ( 3180) link_BETA1-4 : bond 0.00429 ( 3) link_BETA1-4 : angle 1.79994 ( 9) link_NAG-ASN : bond 0.00344 ( 54) link_NAG-ASN : angle 2.19997 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 234 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.8730 (tt0) cc_final: 0.8060 (tt0) REVERT: A 933 LYS cc_start: 0.8398 (mttt) cc_final: 0.8185 (mttp) REVERT: A 947 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8101 (mtmt) REVERT: C 704 SER cc_start: 0.8125 (OUTLIER) cc_final: 0.7853 (p) REVERT: C 773 GLU cc_start: 0.8757 (tt0) cc_final: 0.8362 (tt0) REVERT: C 785 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8369 (m) REVERT: C 935 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7337 (tt0) REVERT: C 1038 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7942 (mmtm) REVERT: F 577 ARG cc_start: 0.7834 (ttm-80) cc_final: 0.7619 (ttm-80) REVERT: F 580 GLN cc_start: 0.8442 (mt0) cc_final: 0.8207 (mt0) REVERT: F 1005 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8778 (mm-40) outliers start: 64 outliers final: 37 residues processed: 268 average time/residue: 0.5672 time to fit residues: 178.9263 Evaluate side-chains 270 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 227 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 432 CYS Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 780 GLU Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 810 SER Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 902 MET Chi-restraints excluded: chain F residue 988 GLU Chi-restraints excluded: chain F residue 1005 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 164 optimal weight: 10.0000 chunk 115 optimal weight: 0.0470 chunk 364 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 107 optimal weight: 50.0000 chunk 122 optimal weight: 50.0000 chunk 69 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 136 optimal weight: 30.0000 overall best weight: 2.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN A1135 ASN C 52 GLN C 607 GLN C 613 GLN C1002 GLN C1010 GLN C1135 ASN F 607 GLN F1135 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.224176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.172350 restraints weight = 27986.998| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 5.61 r_work: 0.3060 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 26553 Z= 0.339 Angle : 0.734 9.047 36585 Z= 0.377 Chirality : 0.053 0.250 4491 Planarity : 0.005 0.045 4803 Dihedral : 5.129 30.754 5118 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.32 % Allowed : 10.12 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.18 (0.13), residues: 3717 helix: 1.30 (0.20), residues: 654 sheet: 0.87 (0.16), residues: 999 loop : -0.65 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1107 TYR 0.025 0.003 TYR A1067 PHE 0.028 0.003 PHE F 643 TRP 0.010 0.002 TRP F1102 HIS 0.010 0.002 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00817 (26445) covalent geometry : angle 0.71268 (36312) SS BOND : bond 0.00472 ( 51) SS BOND : angle 1.38671 ( 102) hydrogen bonds : bond 0.07174 ( 1180) hydrogen bonds : angle 5.97568 ( 3180) link_BETA1-4 : bond 0.00734 ( 3) link_BETA1-4 : angle 1.63861 ( 9) link_NAG-ASN : bond 0.00465 ( 54) link_NAG-ASN : angle 2.52742 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 248 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 TYR cc_start: 0.7289 (m-80) cc_final: 0.6880 (m-80) REVERT: A 521 PRO cc_start: 0.7881 (Cg_exo) cc_final: 0.7657 (Cg_endo) REVERT: C 380 TYR cc_start: 0.7299 (m-80) cc_final: 0.6957 (m-80) REVERT: C 521 PRO cc_start: 0.7938 (Cg_exo) cc_final: 0.7682 (Cg_endo) REVERT: C 773 GLU cc_start: 0.8846 (tt0) cc_final: 0.8488 (tt0) REVERT: C 935 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7423 (tt0) REVERT: F 521 PRO cc_start: 0.7956 (Cg_exo) cc_final: 0.7729 (Cg_endo) REVERT: F 567 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.6917 (mtt-85) REVERT: F 580 GLN cc_start: 0.8314 (mt0) cc_final: 0.8093 (mt0) REVERT: F 618 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7844 (m) REVERT: F 1005 GLN cc_start: 0.9008 (mt0) cc_final: 0.8794 (mm-40) REVERT: F 1073 LYS cc_start: 0.8877 (mttm) cc_final: 0.8611 (mmtm) outliers start: 67 outliers final: 44 residues processed: 291 average time/residue: 0.5572 time to fit residues: 190.7942 Evaluate side-chains 283 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 236 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 432 CYS Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 780 GLU Chi-restraints excluded: chain F residue 785 VAL Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 810 SER Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 988 GLU Chi-restraints excluded: chain F residue 1001 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 176 optimal weight: 0.5980 chunk 253 optimal weight: 0.7980 chunk 125 optimal weight: 8.9990 chunk 219 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 326 optimal weight: 0.8980 chunk 314 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 236 optimal weight: 9.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN A 935 GLN A 955 ASN C 52 GLN C 607 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN F 607 GLN F 644 GLN ** F 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 935 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.227305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.178467 restraints weight = 28056.376| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 5.35 r_work: 0.3130 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26553 Z= 0.127 Angle : 0.554 9.282 36585 Z= 0.280 Chirality : 0.046 0.234 4491 Planarity : 0.004 0.040 4803 Dihedral : 4.431 32.284 5118 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.33 % Allowed : 11.41 % Favored : 86.26 % 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: 0.54 (0.14), residues: 3717 helix: 2.00 (0.21), residues: 651 sheet: 0.92 (0.16), residues: 1017 loop : -0.47 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 995 TYR 0.017 0.001 TYR F1067 PHE 0.021 0.002 PHE A 392 TRP 0.007 0.001 TRP C 436 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00280 (26445) covalent geometry : angle 0.53169 (36312) SS BOND : bond 0.00278 ( 51) SS BOND : angle 1.18309 ( 102) hydrogen bonds : bond 0.04973 ( 1180) hydrogen bonds : angle 5.51072 ( 3180) link_BETA1-4 : bond 0.00545 ( 3) link_BETA1-4 : angle 1.60561 ( 9) link_NAG-ASN : bond 0.00368 ( 54) link_NAG-ASN : angle 2.20016 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 237 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7519 (mtmm) REVERT: A 773 GLU cc_start: 0.8666 (tt0) cc_final: 0.8027 (tt0) REVERT: A 780 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: A 947 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8101 (mtmt) REVERT: C 773 GLU cc_start: 0.8692 (tt0) cc_final: 0.8316 (tt0) REVERT: C 935 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7291 (tt0) REVERT: C 1038 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8040 (mmtm) REVERT: F 392 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8281 (m-80) REVERT: F 567 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6960 (mtt-85) REVERT: F 780 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8512 (tp30) REVERT: F 1073 LYS cc_start: 0.8852 (mttm) cc_final: 0.8561 (mmtm) outliers start: 47 outliers final: 32 residues processed: 262 average time/residue: 0.5646 time to fit residues: 173.4221 Evaluate side-chains 266 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 226 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain F residue 392 PHE Chi-restraints excluded: chain F residue 432 CYS Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 780 GLU Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 988 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 135 optimal weight: 3.9990 chunk 296 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 222 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 299 optimal weight: 5.9990 chunk 43 optimal weight: 0.0070 chunk 97 optimal weight: 0.9990 chunk 320 optimal weight: 0.0010 overall best weight: 0.4806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN C 52 GLN C 607 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1010 GLN F 607 GLN ** F 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.227961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.177927 restraints weight = 28140.595| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 5.58 r_work: 0.3129 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26553 Z= 0.114 Angle : 0.534 7.795 36585 Z= 0.271 Chirality : 0.045 0.233 4491 Planarity : 0.004 0.039 4803 Dihedral : 4.165 26.241 5118 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.33 % Allowed : 11.66 % Favored : 86.01 % 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: 0.68 (0.14), residues: 3717 helix: 2.24 (0.21), residues: 651 sheet: 0.95 (0.16), residues: 1020 loop : -0.39 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 995 TYR 0.018 0.001 TYR F1067 PHE 0.020 0.002 PHE F 65 TRP 0.007 0.001 TRP C 436 HIS 0.004 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00253 (26445) covalent geometry : angle 0.51616 (36312) SS BOND : bond 0.00262 ( 51) SS BOND : angle 1.20387 ( 102) hydrogen bonds : bond 0.04630 ( 1180) hydrogen bonds : angle 5.35882 ( 3180) link_BETA1-4 : bond 0.00538 ( 3) link_BETA1-4 : angle 1.57287 ( 9) link_NAG-ASN : bond 0.00383 ( 54) link_NAG-ASN : angle 1.90949 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 233 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7346 (mtmm) REVERT: A 773 GLU cc_start: 0.8612 (tt0) cc_final: 0.7938 (tt0) REVERT: A 780 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: C 603 ASN cc_start: 0.6855 (t0) cc_final: 0.6629 (t0) REVERT: C 773 GLU cc_start: 0.8688 (tt0) cc_final: 0.8305 (tt0) REVERT: C 935 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: C 1038 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8075 (mmtm) REVERT: F 392 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.8078 (m-80) REVERT: F 780 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8368 (tp30) outliers start: 47 outliers final: 33 residues processed: 260 average time/residue: 0.5583 time to fit residues: 170.8141 Evaluate side-chains 269 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 230 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain F residue 392 PHE Chi-restraints excluded: chain F residue 432 CYS Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 780 GLU Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 810 SER Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 902 MET Chi-restraints excluded: chain F residue 988 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 170 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 308 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 278 optimal weight: 5.9990 chunk 229 optimal weight: 30.0000 chunk 202 optimal weight: 0.8980 chunk 235 optimal weight: 2.9990 chunk 262 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN C 52 GLN C 607 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1010 GLN F 607 GLN ** F 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.225310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.173630 restraints weight = 27875.358| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 5.69 r_work: 0.3086 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 26553 Z= 0.234 Angle : 0.633 7.734 36585 Z= 0.324 Chirality : 0.049 0.251 4491 Planarity : 0.004 0.041 4803 Dihedral : 4.511 25.131 5118 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.03 % Allowed : 12.15 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.43 (0.14), residues: 3717 helix: 1.79 (0.20), residues: 654 sheet: 0.86 (0.16), residues: 1014 loop : -0.50 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1000 TYR 0.025 0.002 TYR A1067 PHE 0.027 0.002 PHE F 541 TRP 0.007 0.001 TRP F1102 HIS 0.007 0.002 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00555 (26445) covalent geometry : angle 0.61467 (36312) SS BOND : bond 0.00349 ( 51) SS BOND : angle 1.34003 ( 102) hydrogen bonds : bond 0.06054 ( 1180) hydrogen bonds : angle 5.60966 ( 3180) link_BETA1-4 : bond 0.00608 ( 3) link_BETA1-4 : angle 1.48492 ( 9) link_NAG-ASN : bond 0.00433 ( 54) link_NAG-ASN : angle 2.11242 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 235 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7501 (mtmm) REVERT: A 773 GLU cc_start: 0.8796 (tt0) cc_final: 0.8152 (tt0) REVERT: A 780 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: C 521 PRO cc_start: 0.7894 (Cg_exo) cc_final: 0.7677 (Cg_endo) REVERT: C 773 GLU cc_start: 0.8772 (tt0) cc_final: 0.8393 (tt0) REVERT: C 935 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7410 (tt0) REVERT: F 378 LYS cc_start: 0.6813 (mmtp) cc_final: 0.6020 (ttpt) REVERT: F 1073 LYS cc_start: 0.8885 (mttm) cc_final: 0.8619 (mmtm) outliers start: 41 outliers final: 36 residues processed: 262 average time/residue: 0.5689 time to fit residues: 175.4303 Evaluate side-chains 270 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain F residue 432 CYS Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 780 GLU Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 810 SER Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 902 MET Chi-restraints excluded: chain F residue 988 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 174 optimal weight: 3.9990 chunk 343 optimal weight: 0.5980 chunk 336 optimal weight: 0.9980 chunk 202 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 252 optimal weight: 0.0980 chunk 222 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 237 optimal weight: 30.0000 chunk 330 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN C 52 GLN C 607 GLN C 762 GLN C1002 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN F 607 GLN ** F 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.227369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.176842 restraints weight = 27919.506| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 5.60 r_work: 0.3119 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26553 Z= 0.126 Angle : 0.547 8.503 36585 Z= 0.276 Chirality : 0.046 0.236 4491 Planarity : 0.004 0.041 4803 Dihedral : 4.200 26.158 5118 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.03 % Allowed : 12.20 % Favored : 85.76 % 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: 0.62 (0.14), residues: 3717 helix: 2.06 (0.21), residues: 660 sheet: 0.92 (0.16), residues: 1014 loop : -0.40 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 995 TYR 0.018 0.001 TYR F1067 PHE 0.027 0.002 PHE F 541 TRP 0.007 0.001 TRP C 436 HIS 0.004 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00286 (26445) covalent geometry : angle 0.52808 (36312) SS BOND : bond 0.00266 ( 51) SS BOND : angle 1.20531 ( 102) hydrogen bonds : bond 0.04813 ( 1180) hydrogen bonds : angle 5.35971 ( 3180) link_BETA1-4 : bond 0.00566 ( 3) link_BETA1-4 : angle 1.48645 ( 9) link_NAG-ASN : bond 0.00372 ( 54) link_NAG-ASN : angle 1.97680 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9007.00 seconds wall clock time: 153 minutes 26.92 seconds (9206.92 seconds total)