Starting phenix.real_space_refine on Tue Sep 15 21:50:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6kg7_9975/09_2026/6kg7_9975.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kg7_9975/09_2026/6kg7_9975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6kg7_9975/09_2026/6kg7_9975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kg7_9975/09_2026/6kg7_9975.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6kg7_9975/09_2026/6kg7_9975.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6kg7_9975/09_2026/6kg7_9975.cif" model { file = "/net/cci-nas-00/data/ceres_data/6kg7_9975/09_2026/6kg7_9975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kg7_9975/09_2026/6kg7_9975.cif" } resolution = 3.8 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= 0.078 sd= 1.367 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 303 5.16 5 C 29862 2.51 5 N 7143 2.21 5 O 7584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 345 residue(s): 0.27s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 44892 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 14908 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1817, 14900 Classifications: {'peptide': 1817} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 64, 'TRANS': 1752} Chain breaks: 15 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'ASP:plan': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 48 Conformer: "B" Number of residues, atoms: 1817, 14900 Classifications: {'peptide': 1817} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 64, 'TRANS': 1752} Chain breaks: 15 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'ASP:plan': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 48 bond proxies already assigned to first conformer: 15299 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: B, C Time building chain proxies: 34.44, per 1000 atoms: 0.77 Number of scatterers: 44892 At special positions: 0 Unit cell: (264.789, 250.779, 180.729, 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 303 16.00 O 7584 8.00 N 7143 7.00 C 29862 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A1031 " - pdb=" SG CYS A1209 " distance=2.03 Simple disulfide: pdb=" SG CYS B1031 " - pdb=" SG CYS B1209 " distance=2.03 Simple disulfide: pdb=" SG CYS C1031 " - pdb=" SG CYS C1209 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A3001 " - " ASN A 769 " " NAG A3002 " - " ASN A1030 " " NAG A3003 " - " ASN A1037 " " NAG A3004 " - " ASN A2642 " " NAG B3001 " - " ASN B 769 " " NAG B3002 " - " ASN B1030 " " NAG B3003 " - " ASN B1037 " " NAG B3004 " - " ASN B2642 " " NAG C3001 " - " ASN C 769 " " NAG C3002 " - " ASN C1030 " " NAG C3003 " - " ASN C1037 " " NAG C3004 " - " ASN C2642 " Time building additional restraints: 3.87 Conformation dependent library (CDL) restraints added in 3.4 seconds 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10464 Finding SS restraints... Secondary structure from input PDB file: 234 helices and 9 sheets defined 68.4% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 13 through 24 Processing helix chain 'A' and resid 28 through 41 removed outlier: 4.315A pdb=" N VAL A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 51 through 77 removed outlier: 4.062A pdb=" N PHE A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 142 removed outlier: 4.161A pdb=" N ILE A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 238 removed outlier: 4.020A pdb=" N SER A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 222 " --> pdb=" O MET A 218 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LYS A 224 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 259 removed outlier: 4.102A pdb=" N TYR A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 287 removed outlier: 3.504A pdb=" N PHE A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 356 removed outlier: 3.745A pdb=" N LEU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 515 removed outlier: 3.560A pdb=" N ILE A 496 " --> pdb=" O VAL A 492 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER A 512 " --> pdb=" O MET A 508 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE A 513 " --> pdb=" O MET A 509 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR A 514 " --> pdb=" O ALA A 510 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR A 515 " --> pdb=" O TRP A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.570A pdb=" N MET A 532 " --> pdb=" O CYS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 561 removed outlier: 3.870A pdb=" N TYR A 539 " --> pdb=" O ASN A 535 " (cutoff:3.500A) Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 583 through 615 removed outlier: 4.040A pdb=" N THR A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 691 Processing helix chain 'A' and resid 691 through 704 removed outlier: 3.684A pdb=" N PHE A 699 " --> pdb=" O CYS A 695 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE A 700 " --> pdb=" O GLY A 696 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 701 " --> pdb=" O GLY A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 729 removed outlier: 3.587A pdb=" N MET A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 758 removed outlier: 3.634A pdb=" N PHE A 740 " --> pdb=" O ILE A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 771 removed outlier: 4.350A pdb=" N GLN A 768 " --> pdb=" O PRO A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 780 Processing helix chain 'A' and resid 789 through 812 removed outlier: 3.802A pdb=" N THR A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) Proline residue: A 798 - end of helix removed outlier: 3.520A pdb=" N TYR A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 820 Processing helix chain 'A' and resid 936 through 958 Processing helix chain 'A' and resid 959 through 974 Processing helix chain 'A' and resid 979 through 989 Processing helix chain 'A' and resid 992 through 996 Processing helix chain 'A' and resid 997 through 1017 removed outlier: 3.705A pdb=" N SER A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N CYS A1003 " --> pdb=" O ALA A 999 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS A1008 " --> pdb=" O THR A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1100 removed outlier: 3.821A pdb=" N MET A1080 " --> pdb=" O ASN A1076 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1122 removed outlier: 3.909A pdb=" N ASP A1122 " --> pdb=" O HIS A1119 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1119 through 1122' Processing helix chain 'A' and resid 1123 through 1139 removed outlier: 6.787A pdb=" N PHE A1136 " --> pdb=" O VAL A1132 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N TYR A1137 " --> pdb=" O ASN A1133 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A1138 " --> pdb=" O TYR A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1156 removed outlier: 3.879A pdb=" N LEU A1146 " --> pdb=" O GLU A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1173 removed outlier: 4.213A pdb=" N ARG A1173 " --> pdb=" O GLY A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1180 removed outlier: 3.585A pdb=" N ILE A1179 " --> pdb=" O ARG A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1202 Processing helix chain 'A' and resid 1222 through 1229 Processing helix chain 'A' and resid 1239 through 1241 No H-bonds generated for 'chain 'A' and resid 1239 through 1241' Processing helix chain 'A' and resid 1242 through 1263 removed outlier: 4.085A pdb=" N ASP A1246 " --> pdb=" O PHE A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1270 Processing helix chain 'A' and resid 1303 through 1312 Processing helix chain 'A' and resid 1314 through 1325 Processing helix chain 'A' and resid 1333 through 1347 removed outlier: 4.249A pdb=" N TYR A1337 " --> pdb=" O PHE A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1354 Processing helix chain 'A' and resid 1355 through 1380 removed outlier: 4.406A pdb=" N ILE A1359 " --> pdb=" O PRO A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1447 removed outlier: 3.550A pdb=" N MET A1447 " --> pdb=" O ARG A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1464 removed outlier: 4.261A pdb=" N HIS A1453 " --> pdb=" O TYR A1449 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL A1454 " --> pdb=" O TYR A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1513 removed outlier: 4.229A pdb=" N GLY A1468 " --> pdb=" O LEU A1464 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A1469 " --> pdb=" O ALA A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1558 through 1564 removed outlier: 3.948A pdb=" N ARG A1564 " --> pdb=" O ALA A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1567 through 1571 Processing helix chain 'A' and resid 1669 through 1687 Processing helix chain 'A' and resid 1688 through 1712 Processing helix chain 'A' and resid 1718 through 1725 Processing helix chain 'A' and resid 1961 through 1973 removed outlier: 3.713A pdb=" N GLU A1965 " --> pdb=" O ASP A1961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1978 through 1991 Processing helix chain 'A' and resid 1991 through 2007 Processing helix chain 'A' and resid 2010 through 2023 Proline residue: A2016 - end of helix Processing helix chain 'A' and resid 2024 through 2026 No H-bonds generated for 'chain 'A' and resid 2024 through 2026' Processing helix chain 'A' and resid 2031 through 2052 removed outlier: 3.521A pdb=" N TRP A2035 " --> pdb=" O SER A2031 " (cutoff:3.500A) Processing helix chain 'A' and resid 2086 through 2106 removed outlier: 3.704A pdb=" N HIS A2106 " --> pdb=" O ILE A2102 " (cutoff:3.500A) Processing helix chain 'A' and resid 2237 through 2250 removed outlier: 3.925A pdb=" N ILE A2241 " --> pdb=" O ILE A2237 " (cutoff:3.500A) Processing helix chain 'A' and resid 2259 through 2277 Processing helix chain 'A' and resid 2278 through 2280 No H-bonds generated for 'chain 'A' and resid 2278 through 2280' Processing helix chain 'A' and resid 2301 through 2323 removed outlier: 3.871A pdb=" N VAL A2305 " --> pdb=" O GLY A2301 " (cutoff:3.500A) Processing helix chain 'A' and resid 2326 through 2347 removed outlier: 3.616A pdb=" N PHE A2338 " --> pdb=" O VAL A2334 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A2347 " --> pdb=" O TRP A2343 " (cutoff:3.500A) Processing helix chain 'A' and resid 2355 through 2358 Processing helix chain 'A' and resid 2359 through 2383 Processing helix chain 'A' and resid 2398 through 2410 Processing helix chain 'A' and resid 2414 through 2425 removed outlier: 3.562A pdb=" N TRP A2425 " --> pdb=" O MET A2421 " (cutoff:3.500A) Processing helix chain 'A' and resid 2431 through 2458 Processing helix chain 'A' and resid 2467 through 2488 removed outlier: 3.663A pdb=" N PHE A2488 " --> pdb=" O CYS A2484 " (cutoff:3.500A) Processing helix chain 'A' and resid 2489 through 2491 No H-bonds generated for 'chain 'A' and resid 2489 through 2491' Processing helix chain 'A' and resid 2535 through 2546 removed outlier: 3.751A pdb=" N PHE A2546 " --> pdb=" O PHE A2542 " (cutoff:3.500A) Processing helix chain 'A' and resid 2552 through 2557 removed outlier: 3.510A pdb=" N LEU A2556 " --> pdb=" O ALA A2552 " (cutoff:3.500A) Processing helix chain 'A' and resid 2580 through 2593 removed outlier: 3.715A pdb=" N THR A2592 " --> pdb=" O ILE A2588 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP A2593 " --> pdb=" O GLN A2589 " (cutoff:3.500A) Processing helix chain 'A' and resid 2628 through 2640 Processing helix chain 'A' and resid 2740 through 2761 removed outlier: 3.518A pdb=" N GLU A2757 " --> pdb=" O LYS A2753 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE A2758 " --> pdb=" O PHE A2754 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE A2759 " --> pdb=" O VAL A2755 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY A2761 " --> pdb=" O GLU A2757 " (cutoff:3.500A) Processing helix chain 'A' and resid 2763 through 2767 removed outlier: 3.647A pdb=" N ILE A2766 " --> pdb=" O SER A2763 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N MET A2767 " --> pdb=" O HIS A2764 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2763 through 2767' Processing helix chain 'A' and resid 2774 through 2791 Processing helix chain 'A' and resid 2792 through 2808 Processing helix chain 'A' and resid 2809 through 2817 Processing helix chain 'B' and resid 13 through 24 Processing helix chain 'B' and resid 28 through 41 removed outlier: 4.315A pdb=" N VAL B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 51 through 77 removed outlier: 4.062A pdb=" N PHE B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 142 removed outlier: 4.161A pdb=" N ILE B 127 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 238 removed outlier: 4.021A pdb=" N SER B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 222 " --> pdb=" O MET B 218 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LYS B 224 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 259 removed outlier: 4.102A pdb=" N TYR B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 287 removed outlier: 3.505A pdb=" N PHE B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 356 removed outlier: 3.746A pdb=" N LEU B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 515 removed outlier: 3.560A pdb=" N ILE B 496 " --> pdb=" O VAL B 492 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER B 512 " --> pdb=" O MET B 508 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE B 513 " --> pdb=" O MET B 509 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR B 514 " --> pdb=" O ALA B 510 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR B 515 " --> pdb=" O TRP B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 532 removed outlier: 3.570A pdb=" N MET B 532 " --> pdb=" O CYS B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 561 removed outlier: 3.870A pdb=" N TYR B 539 " --> pdb=" O ASN B 535 " (cutoff:3.500A) Proline residue: B 545 - end of helix Processing helix chain 'B' and resid 583 through 615 removed outlier: 4.040A pdb=" N THR B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE B 593 " --> pdb=" O PHE B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 691 Processing helix chain 'B' and resid 691 through 704 removed outlier: 3.684A pdb=" N PHE B 699 " --> pdb=" O CYS B 695 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE B 700 " --> pdb=" O GLY B 696 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 701 " --> pdb=" O GLY B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 729 removed outlier: 3.587A pdb=" N MET B 716 " --> pdb=" O LYS B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 758 removed outlier: 3.634A pdb=" N PHE B 740 " --> pdb=" O ILE B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 771 removed outlier: 4.351A pdb=" N GLN B 768 " --> pdb=" O PRO B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 780 Processing helix chain 'B' and resid 789 through 812 removed outlier: 3.802A pdb=" N THR B 793 " --> pdb=" O ALA B 789 " (cutoff:3.500A) Proline residue: B 798 - end of helix removed outlier: 3.520A pdb=" N TYR B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 820 Processing helix chain 'B' and resid 936 through 958 Processing helix chain 'B' and resid 959 through 974 Processing helix chain 'B' and resid 979 through 989 Processing helix chain 'B' and resid 992 through 996 Processing helix chain 'B' and resid 997 through 1017 removed outlier: 3.706A pdb=" N SER B1001 " --> pdb=" O ARG B 997 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N CYS B1003 " --> pdb=" O ALA B 999 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS B1008 " --> pdb=" O THR B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1100 removed outlier: 3.821A pdb=" N MET B1080 " --> pdb=" O ASN B1076 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL B1088 " --> pdb=" O LEU B1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 1119 through 1122 removed outlier: 3.908A pdb=" N ASP B1122 " --> pdb=" O HIS B1119 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1119 through 1122' Processing helix chain 'B' and resid 1123 through 1139 removed outlier: 6.788A pdb=" N PHE B1136 " --> pdb=" O VAL B1132 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N TYR B1137 " --> pdb=" O ASN B1133 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS B1138 " --> pdb=" O TYR B1134 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1156 removed outlier: 3.879A pdb=" N LEU B1146 " --> pdb=" O GLU B1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 1157 through 1173 removed outlier: 4.213A pdb=" N ARG B1173 " --> pdb=" O GLY B1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 1175 through 1180 removed outlier: 3.585A pdb=" N ILE B1179 " --> pdb=" O ARG B1175 " (cutoff:3.500A) Processing helix chain 'B' and resid 1182 through 1202 Processing helix chain 'B' and resid 1222 through 1229 Processing helix chain 'B' and resid 1239 through 1241 No H-bonds generated for 'chain 'B' and resid 1239 through 1241' Processing helix chain 'B' and resid 1242 through 1263 removed outlier: 4.085A pdb=" N ASP B1246 " --> pdb=" O PHE B1242 " (cutoff:3.500A) Processing helix chain 'B' and resid 1265 through 1270 Processing helix chain 'B' and resid 1303 through 1312 Processing helix chain 'B' and resid 1314 through 1325 Processing helix chain 'B' and resid 1333 through 1347 removed outlier: 4.249A pdb=" N TYR B1337 " --> pdb=" O PHE B1333 " (cutoff:3.500A) Processing helix chain 'B' and resid 1350 through 1354 Processing helix chain 'B' and resid 1355 through 1380 removed outlier: 4.406A pdb=" N ILE B1359 " --> pdb=" O PRO B1355 " (cutoff:3.500A) Processing helix chain 'B' and resid 1430 through 1447 removed outlier: 3.550A pdb=" N MET B1447 " --> pdb=" O ARG B1443 " (cutoff:3.500A) Processing helix chain 'B' and resid 1449 through 1464 removed outlier: 4.262A pdb=" N HIS B1453 " --> pdb=" O TYR B1449 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL B1454 " --> pdb=" O TYR B1450 " (cutoff:3.500A) Processing helix chain 'B' and resid 1464 through 1513 removed outlier: 4.229A pdb=" N GLY B1468 " --> pdb=" O LEU B1464 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA B1469 " --> pdb=" O ALA B1465 " (cutoff:3.500A) Processing helix chain 'B' and resid 1558 through 1564 removed outlier: 3.949A pdb=" N ARG B1564 " --> pdb=" O ALA B1560 " (cutoff:3.500A) Processing helix chain 'B' and resid 1567 through 1571 Processing helix chain 'B' and resid 1669 through 1687 Processing helix chain 'B' and resid 1688 through 1712 Processing helix chain 'B' and resid 1718 through 1725 Processing helix chain 'B' and resid 1961 through 1973 removed outlier: 3.713A pdb=" N GLU B1965 " --> pdb=" O ASP B1961 " (cutoff:3.500A) Processing helix chain 'B' and resid 1978 through 1991 Processing helix chain 'B' and resid 1991 through 2007 Processing helix chain 'B' and resid 2010 through 2023 Proline residue: B2016 - end of helix Processing helix chain 'B' and resid 2024 through 2026 No H-bonds generated for 'chain 'B' and resid 2024 through 2026' Processing helix chain 'B' and resid 2031 through 2052 removed outlier: 3.521A pdb=" N TRP B2035 " --> pdb=" O SER B2031 " (cutoff:3.500A) Processing helix chain 'B' and resid 2086 through 2106 removed outlier: 3.704A pdb=" N HIS B2106 " --> pdb=" O ILE B2102 " (cutoff:3.500A) Processing helix chain 'B' and resid 2237 through 2250 removed outlier: 3.924A pdb=" N ILE B2241 " --> pdb=" O ILE B2237 " (cutoff:3.500A) Processing helix chain 'B' and resid 2259 through 2277 Processing helix chain 'B' and resid 2278 through 2280 No H-bonds generated for 'chain 'B' and resid 2278 through 2280' Processing helix chain 'B' and resid 2301 through 2323 removed outlier: 3.871A pdb=" N VAL B2305 " --> pdb=" O GLY B2301 " (cutoff:3.500A) Processing helix chain 'B' and resid 2326 through 2347 removed outlier: 3.616A pdb=" N PHE B2338 " --> pdb=" O VAL B2334 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B2347 " --> pdb=" O TRP B2343 " (cutoff:3.500A) Processing helix chain 'B' and resid 2355 through 2358 Processing helix chain 'B' and resid 2359 through 2383 Processing helix chain 'B' and resid 2398 through 2410 Processing helix chain 'B' and resid 2414 through 2425 removed outlier: 3.561A pdb=" N TRP B2425 " --> pdb=" O MET B2421 " (cutoff:3.500A) Processing helix chain 'B' and resid 2431 through 2458 Processing helix chain 'B' and resid 2467 through 2488 removed outlier: 3.663A pdb=" N PHE B2488 " --> pdb=" O CYS B2484 " (cutoff:3.500A) Processing helix chain 'B' and resid 2489 through 2491 No H-bonds generated for 'chain 'B' and resid 2489 through 2491' Processing helix chain 'B' and resid 2535 through 2546 removed outlier: 3.752A pdb=" N PHE B2546 " --> pdb=" O PHE B2542 " (cutoff:3.500A) Processing helix chain 'B' and resid 2552 through 2557 removed outlier: 3.510A pdb=" N LEU B2556 " --> pdb=" O ALA B2552 " (cutoff:3.500A) Processing helix chain 'B' and resid 2580 through 2593 removed outlier: 3.715A pdb=" N THR B2592 " --> pdb=" O ILE B2588 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP B2593 " --> pdb=" O GLN B2589 " (cutoff:3.500A) Processing helix chain 'B' and resid 2628 through 2640 Processing helix chain 'B' and resid 2740 through 2761 removed outlier: 3.518A pdb=" N GLU B2757 " --> pdb=" O LYS B2753 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE B2758 " --> pdb=" O PHE B2754 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE B2759 " --> pdb=" O VAL B2755 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY B2761 " --> pdb=" O GLU B2757 " (cutoff:3.500A) Processing helix chain 'B' and resid 2763 through 2767 removed outlier: 3.647A pdb=" N ILE B2766 " --> pdb=" O SER B2763 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N MET B2767 " --> pdb=" O HIS B2764 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2763 through 2767' Processing helix chain 'B' and resid 2774 through 2791 Processing helix chain 'B' and resid 2792 through 2808 Processing helix chain 'B' and resid 2809 through 2817 Processing helix chain 'C' and resid 13 through 24 Processing helix chain 'C' and resid 28 through 41 removed outlier: 4.315A pdb=" N VAL C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 44 No H-bonds generated for 'chain 'C' and resid 42 through 44' Processing helix chain 'C' and resid 51 through 77 removed outlier: 4.062A pdb=" N PHE C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 142 removed outlier: 4.161A pdb=" N ILE C 127 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 238 removed outlier: 4.021A pdb=" N SER C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 222 " --> pdb=" O MET C 218 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LYS C 224 " --> pdb=" O THR C 220 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL C 225 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL C 226 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 259 removed outlier: 4.102A pdb=" N TYR C 246 " --> pdb=" O THR C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 287 removed outlier: 3.504A pdb=" N PHE C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 356 removed outlier: 3.745A pdb=" N LEU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 515 removed outlier: 3.560A pdb=" N ILE C 496 " --> pdb=" O VAL C 492 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER C 512 " --> pdb=" O MET C 508 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE C 513 " --> pdb=" O MET C 509 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR C 514 " --> pdb=" O ALA C 510 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 515 " --> pdb=" O TRP C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 532 removed outlier: 3.570A pdb=" N MET C 532 " --> pdb=" O CYS C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 561 removed outlier: 3.870A pdb=" N TYR C 539 " --> pdb=" O ASN C 535 " (cutoff:3.500A) Proline residue: C 545 - end of helix Processing helix chain 'C' and resid 583 through 615 removed outlier: 4.040A pdb=" N THR C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE C 593 " --> pdb=" O PHE C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 691 Processing helix chain 'C' and resid 691 through 704 removed outlier: 3.684A pdb=" N PHE C 699 " --> pdb=" O CYS C 695 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE C 700 " --> pdb=" O GLY C 696 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE C 701 " --> pdb=" O GLY C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 729 removed outlier: 3.586A pdb=" N MET C 716 " --> pdb=" O LYS C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 758 removed outlier: 3.634A pdb=" N PHE C 740 " --> pdb=" O ILE C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 771 removed outlier: 4.351A pdb=" N GLN C 768 " --> pdb=" O PRO C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 780 Processing helix chain 'C' and resid 789 through 812 removed outlier: 3.802A pdb=" N THR C 793 " --> pdb=" O ALA C 789 " (cutoff:3.500A) Proline residue: C 798 - end of helix removed outlier: 3.520A pdb=" N TYR C 811 " --> pdb=" O LEU C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 820 Processing helix chain 'C' and resid 936 through 958 Processing helix chain 'C' and resid 959 through 974 Processing helix chain 'C' and resid 979 through 989 Processing helix chain 'C' and resid 992 through 996 Processing helix chain 'C' and resid 997 through 1017 removed outlier: 3.705A pdb=" N SER C1001 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N CYS C1003 " --> pdb=" O ALA C 999 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS C1008 " --> pdb=" O THR C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1100 removed outlier: 3.821A pdb=" N MET C1080 " --> pdb=" O ASN C1076 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL C1088 " --> pdb=" O LEU C1084 " (cutoff:3.500A) Processing helix chain 'C' and resid 1119 through 1122 removed outlier: 3.909A pdb=" N ASP C1122 " --> pdb=" O HIS C1119 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1119 through 1122' Processing helix chain 'C' and resid 1123 through 1139 removed outlier: 6.787A pdb=" N PHE C1136 " --> pdb=" O VAL C1132 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N TYR C1137 " --> pdb=" O ASN C1133 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS C1138 " --> pdb=" O TYR C1134 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1156 removed outlier: 3.879A pdb=" N LEU C1146 " --> pdb=" O GLU C1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 1157 through 1173 removed outlier: 4.213A pdb=" N ARG C1173 " --> pdb=" O GLY C1169 " (cutoff:3.500A) Processing helix chain 'C' and resid 1175 through 1180 removed outlier: 3.585A pdb=" N ILE C1179 " --> pdb=" O ARG C1175 " (cutoff:3.500A) Processing helix chain 'C' and resid 1182 through 1202 Processing helix chain 'C' and resid 1222 through 1229 Processing helix chain 'C' and resid 1239 through 1241 No H-bonds generated for 'chain 'C' and resid 1239 through 1241' Processing helix chain 'C' and resid 1242 through 1263 removed outlier: 4.085A pdb=" N ASP C1246 " --> pdb=" O PHE C1242 " (cutoff:3.500A) Processing helix chain 'C' and resid 1265 through 1270 Processing helix chain 'C' and resid 1303 through 1312 Processing helix chain 'C' and resid 1314 through 1325 Processing helix chain 'C' and resid 1333 through 1347 removed outlier: 4.249A pdb=" N TYR C1337 " --> pdb=" O PHE C1333 " (cutoff:3.500A) Processing helix chain 'C' and resid 1350 through 1354 Processing helix chain 'C' and resid 1355 through 1380 removed outlier: 4.406A pdb=" N ILE C1359 " --> pdb=" O PRO C1355 " (cutoff:3.500A) Processing helix chain 'C' and resid 1430 through 1447 removed outlier: 3.549A pdb=" N MET C1447 " --> pdb=" O ARG C1443 " (cutoff:3.500A) Processing helix chain 'C' and resid 1449 through 1464 removed outlier: 4.262A pdb=" N HIS C1453 " --> pdb=" O TYR C1449 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL C1454 " --> pdb=" O TYR C1450 " (cutoff:3.500A) Processing helix chain 'C' and resid 1464 through 1513 removed outlier: 4.229A pdb=" N GLY C1468 " --> pdb=" O LEU C1464 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA C1469 " --> pdb=" O ALA C1465 " (cutoff:3.500A) Processing helix chain 'C' and resid 1558 through 1564 removed outlier: 3.949A pdb=" N ARG C1564 " --> pdb=" O ALA C1560 " (cutoff:3.500A) Processing helix chain 'C' and resid 1567 through 1571 Processing helix chain 'C' and resid 1669 through 1687 Processing helix chain 'C' and resid 1688 through 1712 Processing helix chain 'C' and resid 1718 through 1725 Processing helix chain 'C' and resid 1961 through 1973 removed outlier: 3.714A pdb=" N GLU C1965 " --> pdb=" O ASP C1961 " (cutoff:3.500A) Processing helix chain 'C' and resid 1978 through 1991 Processing helix chain 'C' and resid 1991 through 2007 Processing helix chain 'C' and resid 2010 through 2023 Proline residue: C2016 - end of helix Processing helix chain 'C' and resid 2024 through 2026 No H-bonds generated for 'chain 'C' and resid 2024 through 2026' Processing helix chain 'C' and resid 2031 through 2052 removed outlier: 3.521A pdb=" N TRP C2035 " --> pdb=" O SER C2031 " (cutoff:3.500A) Processing helix chain 'C' and resid 2086 through 2106 removed outlier: 3.704A pdb=" N HIS C2106 " --> pdb=" O ILE C2102 " (cutoff:3.500A) Processing helix chain 'C' and resid 2237 through 2250 removed outlier: 3.925A pdb=" N ILE C2241 " --> pdb=" O ILE C2237 " (cutoff:3.500A) Processing helix chain 'C' and resid 2259 through 2277 Processing helix chain 'C' and resid 2278 through 2280 No H-bonds generated for 'chain 'C' and resid 2278 through 2280' Processing helix chain 'C' and resid 2301 through 2323 removed outlier: 3.871A pdb=" N VAL C2305 " --> pdb=" O GLY C2301 " (cutoff:3.500A) Processing helix chain 'C' and resid 2326 through 2347 removed outlier: 3.616A pdb=" N PHE C2338 " --> pdb=" O VAL C2334 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE C2347 " --> pdb=" O TRP C2343 " (cutoff:3.500A) Processing helix chain 'C' and resid 2355 through 2358 Processing helix chain 'C' and resid 2359 through 2383 Processing helix chain 'C' and resid 2398 through 2410 Processing helix chain 'C' and resid 2414 through 2425 removed outlier: 3.561A pdb=" N TRP C2425 " --> pdb=" O MET C2421 " (cutoff:3.500A) Processing helix chain 'C' and resid 2431 through 2458 Processing helix chain 'C' and resid 2467 through 2488 removed outlier: 3.663A pdb=" N PHE C2488 " --> pdb=" O CYS C2484 " (cutoff:3.500A) Processing helix chain 'C' and resid 2489 through 2491 No H-bonds generated for 'chain 'C' and resid 2489 through 2491' Processing helix chain 'C' and resid 2535 through 2546 removed outlier: 3.751A pdb=" N PHE C2546 " --> pdb=" O PHE C2542 " (cutoff:3.500A) Processing helix chain 'C' and resid 2552 through 2557 removed outlier: 3.511A pdb=" N LEU C2556 " --> pdb=" O ALA C2552 " (cutoff:3.500A) Processing helix chain 'C' and resid 2580 through 2593 removed outlier: 3.715A pdb=" N THR C2592 " --> pdb=" O ILE C2588 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP C2593 " --> pdb=" O GLN C2589 " (cutoff:3.500A) Processing helix chain 'C' and resid 2628 through 2640 Processing helix chain 'C' and resid 2740 through 2761 removed outlier: 3.518A pdb=" N GLU C2757 " --> pdb=" O LYS C2753 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE C2758 " --> pdb=" O PHE C2754 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE C2759 " --> pdb=" O VAL C2755 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY C2761 " --> pdb=" O GLU C2757 " (cutoff:3.500A) Processing helix chain 'C' and resid 2763 through 2767 removed outlier: 3.647A pdb=" N ILE C2766 " --> pdb=" O SER C2763 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N MET C2767 " --> pdb=" O HIS C2764 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2763 through 2767' Processing helix chain 'C' and resid 2774 through 2791 Processing helix chain 'C' and resid 2792 through 2808 Processing helix chain 'C' and resid 2809 through 2817 Processing sheet with id=AA1, first strand: chain 'A' and resid 2522 through 2526 Processing sheet with id=AA2, first strand: chain 'A' and resid 2531 through 2533 Processing sheet with id=AA3, first strand: chain 'A' and resid 2651 through 2654 Processing sheet with id=AA4, first strand: chain 'B' and resid 2522 through 2526 Processing sheet with id=AA5, first strand: chain 'B' and resid 2531 through 2533 Processing sheet with id=AA6, first strand: chain 'B' and resid 2651 through 2654 Processing sheet with id=AA7, first strand: chain 'C' and resid 2522 through 2526 Processing sheet with id=AA8, first strand: chain 'C' and resid 2531 through 2533 Processing sheet with id=AA9, first strand: chain 'C' and resid 2651 through 2654 2721 hydrogen bonds defined for protein. 8052 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: 10.87 Time building geometry restraints manager: 5.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13255 1.34 - 1.46: 8465 1.46 - 1.58: 23919 1.58 - 1.69: 0 1.69 - 1.81: 486 Bond restraints: 46125 Sorted by residual: bond pdb=" C1 NAG A3004 " pdb=" O5 NAG A3004 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C1 NAG C3004 " pdb=" O5 NAG C3004 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C1 NAG B3004 " pdb=" O5 NAG B3004 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C1 NAG B3003 " pdb=" O5 NAG B3003 " ideal model delta sigma weight residual 1.406 1.502 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C1 NAG B3002 " pdb=" O5 NAG B3002 " ideal model delta sigma weight residual 1.406 1.502 -0.096 2.00e-02 2.50e+03 2.31e+01 ... (remaining 46120 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 59964 1.32 - 2.64: 2099 2.64 - 3.96: 376 3.96 - 5.28: 119 5.28 - 6.60: 25 Bond angle restraints: 62583 Sorted by residual: angle pdb=" O LEU C 773 " pdb=" C LEU C 773 " pdb=" N LYS C 774 " ideal model delta sigma weight residual 123.27 127.38 -4.11 1.16e+00 7.43e-01 1.26e+01 angle pdb=" O LEU A 773 " pdb=" C LEU A 773 " pdb=" N LYS A 774 " ideal model delta sigma weight residual 123.27 127.36 -4.09 1.16e+00 7.43e-01 1.25e+01 angle pdb=" O LEU B 773 " pdb=" C LEU B 773 " pdb=" N LYS B 774 " ideal model delta sigma weight residual 123.27 127.35 -4.08 1.16e+00 7.43e-01 1.24e+01 angle pdb=" CA ASN B1047 " pdb=" C ASN B1047 " pdb=" N LYS B1048 " ideal model delta sigma weight residual 117.96 113.63 4.33 1.23e+00 6.61e-01 1.24e+01 angle pdb=" CA ASN A1047 " pdb=" C ASN A1047 " pdb=" N LYS A1048 " ideal model delta sigma weight residual 117.96 113.64 4.32 1.23e+00 6.61e-01 1.23e+01 ... (remaining 62578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 24644 17.50 - 34.99: 1842 34.99 - 52.49: 241 52.49 - 69.98: 48 69.98 - 87.48: 39 Dihedral angle restraints: 26814 sinusoidal: 10671 harmonic: 16143 Sorted by residual: dihedral pdb=" CA PRO C 299 " pdb=" C PRO C 299 " pdb=" N PRO C 300 " pdb=" CA PRO C 300 " ideal model delta harmonic sigma weight residual -180.00 -152.90 -27.10 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA PRO B 299 " pdb=" C PRO B 299 " pdb=" N PRO B 300 " pdb=" CA PRO B 300 " ideal model delta harmonic sigma weight residual -180.00 -152.93 -27.07 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA PRO A 299 " pdb=" C PRO A 299 " pdb=" N PRO A 300 " pdb=" CA PRO A 300 " ideal model delta harmonic sigma weight residual -180.00 -152.93 -27.07 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 26811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 7081 0.137 - 0.274: 26 0.274 - 0.411: 0 0.411 - 0.548: 0 0.548 - 0.685: 3 Chirality restraints: 7110 Sorted by residual: chirality pdb=" C1 NAG C3001 " pdb=" ND2 ASN C 769 " pdb=" C2 NAG C3001 " pdb=" O5 NAG C3001 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" C1 NAG A3001 " pdb=" ND2 ASN A 769 " pdb=" C2 NAG A3001 " pdb=" O5 NAG A3001 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" C1 NAG B3001 " pdb=" ND2 ASN B 769 " pdb=" C2 NAG B3001 " pdb=" O5 NAG B3001 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.17e+01 ... (remaining 7107 not shown) Planarity restraints: 7581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C3002 " -0.113 2.00e-02 2.50e+03 9.58e-02 1.15e+02 pdb=" C7 NAG C3002 " 0.022 2.00e-02 2.50e+03 pdb=" C8 NAG C3002 " 0.030 2.00e-02 2.50e+03 pdb=" N2 NAG C3002 " 0.153 2.00e-02 2.50e+03 pdb=" O7 NAG C3002 " -0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A3002 " 0.113 2.00e-02 2.50e+03 9.57e-02 1.14e+02 pdb=" C7 NAG A3002 " -0.022 2.00e-02 2.50e+03 pdb=" C8 NAG A3002 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG A3002 " -0.152 2.00e-02 2.50e+03 pdb=" O7 NAG A3002 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B3002 " 0.113 2.00e-02 2.50e+03 9.54e-02 1.14e+02 pdb=" C7 NAG B3002 " -0.022 2.00e-02 2.50e+03 pdb=" C8 NAG B3002 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG B3002 " -0.152 2.00e-02 2.50e+03 pdb=" O7 NAG B3002 " 0.091 2.00e-02 2.50e+03 ... (remaining 7578 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 8138 2.76 - 3.29: 46016 3.29 - 3.83: 73982 3.83 - 4.36: 81153 4.36 - 4.90: 138137 Nonbonded interactions: 347426 Sorted by model distance: nonbonded pdb=" O GLY A2517 " pdb=" OG SER B2525 " model vdw 2.223 3.040 nonbonded pdb=" O GLY B2517 " pdb=" OG SER C2525 " model vdw 2.227 3.040 nonbonded pdb=" OG SER A2525 " pdb=" O GLY C2517 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR C2518 " pdb=" OE1 GLU C2590 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR A2518 " pdb=" OE1 GLU A2590 " model vdw 2.248 3.040 ... (remaining 347421 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: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 0.910 Check model and map are aligned: 0.140 Set scattering table: 0.130 Process input model: 70.770 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.100 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 46140 Z= 0.185 Angle : 0.599 6.599 62625 Z= 0.339 Chirality : 0.042 0.685 7110 Planarity : 0.004 0.096 7569 Dihedral : 12.765 87.477 16341 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % 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: -1.77 (0.11), residues: 5358 helix: 0.06 (0.08), residues: 3426 sheet: -1.92 (0.28), residues: 216 loop : -3.67 (0.13), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C2608 TYR 0.014 0.001 TYR B2050 PHE 0.012 0.001 PHE A2602 TRP 0.014 0.001 TRP B 986 HIS 0.010 0.001 HIS A1727 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.18 (46125) covalent geometry : angle 0.59623 / 0.34 (62583) SS BOND : bond 0.00021 / 0.01 ( 3) SS BOND : angle 0.94355 / 0.49 ( 6) hydrogen bonds : bond 0.09634 / 6.19 ( 2721) hydrogen bonds : angle 4.57183 / 3.28 ( 8052) link_NAG-ASN : bond 0.01342 / 0.97 ( 12) link_NAG-ASN : angle 2.31110 / 1.38 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 543 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 ILE cc_start: 0.8812 (mm) cc_final: 0.8557 (mm) REVERT: A 532 MET cc_start: 0.8833 (ptm) cc_final: 0.8606 (ptm) REVERT: A 698 MET cc_start: 0.9255 (tpp) cc_final: 0.9053 (tpp) REVERT: A 983 LEU cc_start: 0.8747 (tt) cc_final: 0.8482 (tt) REVERT: A 1147 MET cc_start: 0.9521 (tpp) cc_final: 0.9304 (mmp) REVERT: A 1202 ILE cc_start: 0.9234 (tp) cc_final: 0.8991 (tt) REVERT: A 1271 MET cc_start: 0.8410 (ptm) cc_final: 0.7952 (ptp) REVERT: A 1462 GLN cc_start: 0.8952 (tp40) cc_final: 0.8679 (tt0) REVERT: A 1704 MET cc_start: 0.8924 (ttm) cc_final: 0.8447 (tmm) REVERT: A 1716 THR cc_start: 0.7169 (m) cc_final: 0.6881 (p) REVERT: A 2039 ILE cc_start: 0.9418 (mt) cc_final: 0.9174 (mt) REVERT: A 2331 ILE cc_start: 0.9209 (mm) cc_final: 0.9008 (mm) REVERT: A 2344 MET cc_start: 0.9210 (mmm) cc_final: 0.8743 (tpt) REVERT: A 2513 ILE cc_start: 0.9486 (mp) cc_final: 0.9212 (tp) REVERT: A 2655 LYS cc_start: 0.7258 (mttt) cc_final: 0.6861 (mmtt) REVERT: A 2690 ARG cc_start: 0.8323 (ptm160) cc_final: 0.7974 (ptt90) REVERT: A 2807 TYR cc_start: 0.9353 (m-80) cc_final: 0.9118 (m-10) REVERT: B 218 MET cc_start: 0.8810 (tpt) cc_final: 0.8442 (tpp) REVERT: B 698 MET cc_start: 0.9289 (tpp) cc_final: 0.9024 (tpp) REVERT: B 749 MET cc_start: 0.7838 (ttp) cc_final: 0.7598 (ttp) REVERT: B 1376 MET cc_start: 0.8457 (mmm) cc_final: 0.8008 (mpp) REVERT: B 1716 THR cc_start: 0.7569 (m) cc_final: 0.7235 (p) REVERT: B 2317 ASP cc_start: 0.9298 (t0) cc_final: 0.9084 (t0) REVERT: B 2344 MET cc_start: 0.9263 (mmm) cc_final: 0.8866 (mmm) REVERT: B 2485 ILE cc_start: 0.9179 (mt) cc_final: 0.8893 (mt) REVERT: B 2553 MET cc_start: 0.8551 (mtp) cc_final: 0.8177 (mpp) REVERT: B 2682 MET cc_start: 0.2922 (tpp) cc_final: 0.2513 (tpp) REVERT: B 2690 ARG cc_start: 0.8332 (ptm160) cc_final: 0.7896 (ttp80) REVERT: B 2716 GLN cc_start: 0.8698 (tt0) cc_final: 0.8236 (mp10) REVERT: C 218 MET cc_start: 0.8818 (tpt) cc_final: 0.8562 (tpt) REVERT: C 698 MET cc_start: 0.9296 (tpp) cc_final: 0.9064 (tpp) REVERT: C 1147 MET cc_start: 0.9605 (tpp) cc_final: 0.9370 (mmt) REVERT: C 1376 MET cc_start: 0.8653 (mmm) cc_final: 0.8282 (mpp) REVERT: C 1491 MET cc_start: 0.8969 (mmp) cc_final: 0.8754 (mmp) REVERT: C 1716 THR cc_start: 0.7544 (m) cc_final: 0.7285 (p) REVERT: C 2344 MET cc_start: 0.9218 (mmm) cc_final: 0.8767 (tpt) REVERT: C 2481 LEU cc_start: 0.9323 (tp) cc_final: 0.9111 (tt) REVERT: C 2485 ILE cc_start: 0.8960 (mt) cc_final: 0.8614 (mp) REVERT: C 2513 ILE cc_start: 0.9528 (mp) cc_final: 0.9288 (tp) REVERT: C 2553 MET cc_start: 0.8525 (mtp) cc_final: 0.8042 (mpp) REVERT: C 2590 GLU cc_start: 0.8748 (pt0) cc_final: 0.8536 (pt0) REVERT: C 2741 MET cc_start: 0.7238 (tpp) cc_final: 0.6973 (mmp) REVERT: C 2769 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8856 (mm-30) outliers start: 0 outliers final: 0 residues processed: 543 average time/residue: 0.2442 time to fit residues: 232.9697 Evaluate side-chains 379 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 394 optimal weight: 0.6980 chunk 430 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 3.9990 chunk 523 optimal weight: 7.9990 chunk 497 optimal weight: 2.9990 chunk 414 optimal weight: 0.5980 chunk 310 optimal weight: 0.9990 chunk 488 optimal weight: 0.0870 chunk 366 optimal weight: 9.9990 chunk 223 optimal weight: 1.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 GLN A 357 GLN A 558 GLN A 600 HIS ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 GLN A 785 GLN ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 GLN A1076 ASN A1094 GLN A1150 ASN A1222 ASN A1370 ASN A1727 HIS A2053 GLN A2310 GLN A2460 GLN A2674 GLN B 53 GLN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 357 GLN B 558 GLN B 600 HIS ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN B 785 GLN B1018 GLN B1076 ASN B1094 GLN B1154 GLN B1222 ASN B1370 ASN B1727 HIS B2053 GLN B2310 GLN B2460 GLN C 53 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN C 357 GLN C 558 GLN C 600 HIS ** C 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 759 GLN C 785 GLN C1018 GLN C1076 ASN C1094 GLN C1154 GLN C1222 ASN C1727 HIS C2053 GLN C2460 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.075181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.058245 restraints weight = 196108.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.059836 restraints weight = 93689.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.060893 restraints weight = 59904.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.061535 restraints weight = 45582.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.061985 restraints weight = 38902.342| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 46140 Z= 0.126 Angle : 0.596 9.354 62625 Z= 0.299 Chirality : 0.040 0.211 7110 Planarity : 0.004 0.063 7569 Dihedral : 4.314 27.405 5910 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.07 % Allowed : 8.47 % Favored : 90.47 % 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: -0.42 (0.12), residues: 5358 helix: 1.09 (0.09), residues: 3486 sheet: -1.27 (0.30), residues: 216 loop : -3.24 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C2690 TYR 0.022 0.001 TYR B 501 PHE 0.033 0.001 PHE A1977 TRP 0.017 0.001 TRP A2604 HIS 0.007 0.001 HIS C1727 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (46125) covalent geometry : angle 0.59548 / 0.30 (62583) SS BOND : bond 0.00156 / 0.09 ( 3) SS BOND : angle 0.04881 / 0.03 ( 6) hydrogen bonds : bond 0.03974 / 2.58 ( 2721) hydrogen bonds : angle 3.91714 / 2.80 ( 8052) link_NAG-ASN : bond 0.00363 / 0.23 ( 12) link_NAG-ASN : angle 1.44155 / 0.89 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 432 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 TRP cc_start: 0.7267 (OUTLIER) cc_final: 0.6444 (t60) REVERT: A 1147 MET cc_start: 0.9348 (tpp) cc_final: 0.9133 (mmp) REVERT: A 1202 ILE cc_start: 0.9276 (tp) cc_final: 0.9017 (tt) REVERT: A 1271 MET cc_start: 0.8076 (ptm) cc_final: 0.7627 (ptp) REVERT: A 1462 GLN cc_start: 0.8814 (tp40) cc_final: 0.8591 (tt0) REVERT: A 1704 MET cc_start: 0.8914 (ttm) cc_final: 0.8616 (tmm) REVERT: A 1716 THR cc_start: 0.6833 (m) cc_final: 0.6547 (p) REVERT: A 2513 ILE cc_start: 0.9462 (mp) cc_final: 0.9229 (tp) REVERT: A 2655 LYS cc_start: 0.7316 (mttt) cc_final: 0.6918 (mmtt) REVERT: A 2656 ILE cc_start: 0.8727 (mm) cc_final: 0.8482 (mp) REVERT: A 2690 ARG cc_start: 0.8360 (ptm160) cc_final: 0.7898 (ptt90) REVERT: A 2813 MET cc_start: 0.9199 (ttp) cc_final: 0.8976 (ttt) REVERT: B 218 MET cc_start: 0.8455 (tpt) cc_final: 0.8096 (tpp) REVERT: B 698 MET cc_start: 0.9211 (tpp) cc_final: 0.8947 (tpp) REVERT: B 749 MET cc_start: 0.7808 (ttp) cc_final: 0.7517 (ttp) REVERT: B 1376 MET cc_start: 0.8445 (mmm) cc_final: 0.8073 (mpp) REVERT: B 1704 MET cc_start: 0.8598 (ppp) cc_final: 0.8389 (ppp) REVERT: B 1716 THR cc_start: 0.7148 (m) cc_final: 0.6828 (p) REVERT: B 2317 ASP cc_start: 0.9181 (t0) cc_final: 0.8981 (t0) REVERT: B 2485 ILE cc_start: 0.9241 (mt) cc_final: 0.8944 (mp) REVERT: B 2553 MET cc_start: 0.8563 (mtp) cc_final: 0.8252 (mpp) REVERT: B 2682 MET cc_start: 0.3273 (tpp) cc_final: 0.2908 (tpp) REVERT: B 2716 GLN cc_start: 0.8625 (tt0) cc_final: 0.8209 (mp10) REVERT: C 218 MET cc_start: 0.8444 (tpt) cc_final: 0.8213 (tpt) REVERT: C 597 LEU cc_start: 0.9523 (tp) cc_final: 0.9303 (tp) REVERT: C 698 MET cc_start: 0.9227 (tpp) cc_final: 0.9004 (tpp) REVERT: C 716 MET cc_start: 0.8968 (tpp) cc_final: 0.8703 (tpp) REVERT: C 980 TYR cc_start: 0.8530 (t80) cc_final: 0.8079 (t80) REVERT: C 1147 MET cc_start: 0.9498 (tpp) cc_final: 0.9118 (mmt) REVERT: C 1376 MET cc_start: 0.8605 (mmm) cc_final: 0.8328 (mpp) REVERT: C 1716 THR cc_start: 0.7132 (m) cc_final: 0.6906 (p) REVERT: C 2314 MET cc_start: 0.8820 (mtm) cc_final: 0.8467 (mtt) REVERT: C 2344 MET cc_start: 0.8953 (mmm) cc_final: 0.8513 (tpt) REVERT: C 2470 VAL cc_start: 0.9532 (m) cc_final: 0.9136 (p) REVERT: C 2481 LEU cc_start: 0.9298 (tp) cc_final: 0.9089 (tt) REVERT: C 2485 ILE cc_start: 0.9010 (mt) cc_final: 0.8669 (mt) REVERT: C 2508 ASP cc_start: 0.8685 (t0) cc_final: 0.8453 (t0) REVERT: C 2513 ILE cc_start: 0.9541 (mp) cc_final: 0.9298 (tp) REVERT: C 2553 MET cc_start: 0.8542 (mtp) cc_final: 0.8054 (mpp) REVERT: C 2590 GLU cc_start: 0.8856 (pt0) cc_final: 0.8431 (pt0) REVERT: C 2690 ARG cc_start: 0.7277 (ptm-80) cc_final: 0.6852 (ptm-80) REVERT: C 2741 MET cc_start: 0.7287 (tpp) cc_final: 0.7020 (mmp) REVERT: C 2769 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8623 (mm-30) outliers start: 52 outliers final: 28 residues processed: 453 average time/residue: 0.2281 time to fit residues: 183.2476 Evaluate side-chains 429 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 400 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1433 SER Chi-restraints excluded: chain A residue 2019 ILE Chi-restraints excluded: chain A residue 2310 GLN Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2760 SER Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1670 TRP Chi-restraints excluded: chain B residue 2019 ILE Chi-restraints excluded: chain B residue 2310 GLN Chi-restraints excluded: chain B residue 2601 VAL Chi-restraints excluded: chain B residue 2760 SER Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 518 TRP Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 1193 ILE Chi-restraints excluded: chain C residue 1433 SER Chi-restraints excluded: chain C residue 1977 PHE Chi-restraints excluded: chain C residue 2013 LEU Chi-restraints excluded: chain C residue 2019 ILE Chi-restraints excluded: chain C residue 2272 ILE Chi-restraints excluded: chain C residue 2304 LEU Chi-restraints excluded: chain C residue 2601 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 477 optimal weight: 1.9990 chunk 539 optimal weight: 0.8980 chunk 437 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 490 optimal weight: 0.8980 chunk 236 optimal weight: 0.8980 chunk 405 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 515 optimal weight: 7.9990 chunk 169 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 ASN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 979 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.075527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.058392 restraints weight = 211160.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.060067 restraints weight = 97877.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.061092 restraints weight = 61455.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.061840 restraints weight = 46798.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.062224 restraints weight = 39403.005| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 46140 Z= 0.117 Angle : 0.570 9.437 62625 Z= 0.285 Chirality : 0.040 0.285 7110 Planarity : 0.004 0.064 7569 Dihedral : 4.194 26.286 5910 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.84 % Allowed : 11.03 % Favored : 88.13 % 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: 0.03 (0.12), residues: 5358 helix: 1.42 (0.09), residues: 3501 sheet: -1.06 (0.32), residues: 216 loop : -3.07 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C2690 TYR 0.023 0.001 TYR A 501 PHE 0.029 0.001 PHE A1977 TRP 0.013 0.001 TRP B 986 HIS 0.005 0.001 HIS A1559 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (46125) covalent geometry : angle 0.56949 / 0.28 (62583) SS BOND : bond 0.00049 / 0.03 ( 3) SS BOND : angle 0.11384 / 0.06 ( 6) hydrogen bonds : bond 0.03733 / 2.43 ( 2721) hydrogen bonds : angle 3.78376 / 2.71 ( 8052) link_NAG-ASN : bond 0.00175 / 0.12 ( 12) link_NAG-ASN : angle 1.23013 / 0.74 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 435 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 MET cc_start: 0.8019 (tpp) cc_final: 0.7690 (tpt) REVERT: A 518 TRP cc_start: 0.7249 (OUTLIER) cc_final: 0.6530 (t60) REVERT: A 1147 MET cc_start: 0.9312 (tpp) cc_final: 0.9072 (mmp) REVERT: A 1271 MET cc_start: 0.8153 (ptm) cc_final: 0.7849 (ptp) REVERT: A 1462 GLN cc_start: 0.8770 (tp40) cc_final: 0.8562 (tt0) REVERT: A 1704 MET cc_start: 0.8849 (ttm) cc_final: 0.8547 (tmm) REVERT: A 1716 THR cc_start: 0.6762 (m) cc_final: 0.6513 (p) REVERT: A 2421 MET cc_start: 0.8677 (mmp) cc_final: 0.8414 (mmp) REVERT: A 2513 ILE cc_start: 0.9484 (mp) cc_final: 0.9249 (tp) REVERT: A 2610 MET cc_start: 0.5059 (mmm) cc_final: 0.4792 (mmm) REVERT: A 2655 LYS cc_start: 0.7339 (mttt) cc_final: 0.6922 (mmtt) REVERT: A 2690 ARG cc_start: 0.8367 (ptm160) cc_final: 0.8061 (tmm-80) REVERT: A 2813 MET cc_start: 0.9170 (ttp) cc_final: 0.8925 (ttt) REVERT: B 218 MET cc_start: 0.8477 (tpt) cc_final: 0.8129 (tpp) REVERT: B 698 MET cc_start: 0.9209 (tpp) cc_final: 0.8925 (tpp) REVERT: B 749 MET cc_start: 0.7740 (ttp) cc_final: 0.7405 (ttp) REVERT: B 1040 ASN cc_start: 0.7129 (p0) cc_final: 0.6796 (p0) REVERT: B 1156 MET cc_start: 0.8841 (tpt) cc_final: 0.8536 (tpt) REVERT: B 1376 MET cc_start: 0.8364 (mmm) cc_final: 0.8027 (mpp) REVERT: B 1704 MET cc_start: 0.8615 (ppp) cc_final: 0.8361 (ppp) REVERT: B 1716 THR cc_start: 0.7067 (m) cc_final: 0.6778 (p) REVERT: B 2014 LEU cc_start: 0.8706 (tt) cc_final: 0.8460 (tp) REVERT: B 2317 ASP cc_start: 0.9125 (t0) cc_final: 0.8916 (t0) REVERT: B 2485 ILE cc_start: 0.9258 (mt) cc_final: 0.8944 (mp) REVERT: B 2553 MET cc_start: 0.8604 (mtp) cc_final: 0.8289 (mpp) REVERT: B 2716 GLN cc_start: 0.8624 (tt0) cc_final: 0.8226 (mp10) REVERT: C 237 MET cc_start: 0.7993 (tpp) cc_final: 0.7792 (tpt) REVERT: C 541 MET cc_start: 0.8514 (mmt) cc_final: 0.8295 (mmt) REVERT: C 597 LEU cc_start: 0.9580 (tp) cc_final: 0.9344 (tp) REVERT: C 698 MET cc_start: 0.9216 (tpp) cc_final: 0.8983 (tpp) REVERT: C 1147 MET cc_start: 0.9467 (tpp) cc_final: 0.9080 (mmt) REVERT: C 1161 MET cc_start: 0.8584 (ttp) cc_final: 0.8244 (tmm) REVERT: C 1716 THR cc_start: 0.7083 (m) cc_final: 0.6859 (p) REVERT: C 2013 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8932 (tp) REVERT: C 2314 MET cc_start: 0.8857 (mtm) cc_final: 0.8519 (mtt) REVERT: C 2470 VAL cc_start: 0.9521 (m) cc_final: 0.9126 (p) REVERT: C 2481 LEU cc_start: 0.9415 (tp) cc_final: 0.9118 (tt) REVERT: C 2485 ILE cc_start: 0.8977 (mt) cc_final: 0.8624 (mt) REVERT: C 2508 ASP cc_start: 0.8674 (t0) cc_final: 0.8417 (t0) REVERT: C 2513 ILE cc_start: 0.9538 (mp) cc_final: 0.9306 (tp) REVERT: C 2553 MET cc_start: 0.8425 (mtp) cc_final: 0.8027 (mpp) REVERT: C 2690 ARG cc_start: 0.7303 (ptm-80) cc_final: 0.6878 (ptm-80) REVERT: C 2741 MET cc_start: 0.7280 (tpp) cc_final: 0.7012 (mmp) REVERT: C 2769 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8588 (mm-30) outliers start: 41 outliers final: 22 residues processed: 457 average time/residue: 0.2341 time to fit residues: 189.7544 Evaluate side-chains 421 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 397 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1433 SER Chi-restraints excluded: chain A residue 1713 ASN Chi-restraints excluded: chain A residue 2019 ILE Chi-restraints excluded: chain A residue 2087 LEU Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 1670 TRP Chi-restraints excluded: chain B residue 2760 SER Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 518 TRP Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 1193 ILE Chi-restraints excluded: chain C residue 1433 SER Chi-restraints excluded: chain C residue 1977 PHE Chi-restraints excluded: chain C residue 2013 LEU Chi-restraints excluded: chain C residue 2019 ILE Chi-restraints excluded: chain C residue 2601 VAL Chi-restraints excluded: chain C residue 2685 THR Chi-restraints excluded: chain C residue 2767 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 311 optimal weight: 2.9990 chunk 280 optimal weight: 0.2980 chunk 244 optimal weight: 0.4980 chunk 101 optimal weight: 9.9990 chunk 339 optimal weight: 0.6980 chunk 514 optimal weight: 7.9990 chunk 243 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 47 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2310 GLN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2607 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.075587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.058545 restraints weight = 211061.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.060221 restraints weight = 97250.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.061231 restraints weight = 60922.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.061965 restraints weight = 46292.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.062326 restraints weight = 39067.128| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 46140 Z= 0.115 Angle : 0.569 15.140 62625 Z= 0.282 Chirality : 0.040 0.243 7110 Planarity : 0.004 0.063 7569 Dihedral : 4.110 25.949 5910 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.27 % Allowed : 11.99 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.12), residues: 5358 helix: 1.59 (0.09), residues: 3507 sheet: -0.95 (0.32), residues: 216 loop : -2.91 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C2690 TYR 0.020 0.001 TYR B 501 PHE 0.031 0.001 PHE C1372 TRP 0.012 0.001 TRP A 986 HIS 0.005 0.001 HIS C1559 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (46125) covalent geometry : angle 0.56803 / 0.28 (62583) SS BOND : bond 0.00045 / 0.02 ( 3) SS BOND : angle 0.12654 / 0.07 ( 6) hydrogen bonds : bond 0.03605 / 2.35 ( 2721) hydrogen bonds : angle 3.71174 / 2.66 ( 8052) link_NAG-ASN : bond 0.00159 / 0.11 ( 12) link_NAG-ASN : angle 1.18361 / 0.71 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 426 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 MET cc_start: 0.8144 (tpp) cc_final: 0.7823 (tpt) REVERT: A 518 TRP cc_start: 0.7209 (OUTLIER) cc_final: 0.6612 (t60) REVERT: A 554 LEU cc_start: 0.9738 (OUTLIER) cc_final: 0.9436 (pp) REVERT: A 1147 MET cc_start: 0.9326 (tpp) cc_final: 0.9046 (mmp) REVERT: A 1271 MET cc_start: 0.8179 (ptm) cc_final: 0.7881 (ptp) REVERT: A 1704 MET cc_start: 0.8831 (ttm) cc_final: 0.8526 (tmm) REVERT: A 2421 MET cc_start: 0.8676 (mmp) cc_final: 0.8457 (mmp) REVERT: A 2470 VAL cc_start: 0.9525 (m) cc_final: 0.9319 (p) REVERT: A 2610 MET cc_start: 0.4965 (mmm) cc_final: 0.4709 (mmm) REVERT: A 2656 ILE cc_start: 0.8728 (mm) cc_final: 0.8331 (mp) REVERT: A 2690 ARG cc_start: 0.8337 (ptm160) cc_final: 0.8018 (tmm-80) REVERT: A 2702 VAL cc_start: 0.7378 (OUTLIER) cc_final: 0.7140 (p) REVERT: A 2753 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.8604 (tmmm) REVERT: A 2813 MET cc_start: 0.9190 (ttp) cc_final: 0.8939 (ttt) REVERT: B 698 MET cc_start: 0.9219 (tpp) cc_final: 0.8926 (tpp) REVERT: B 749 MET cc_start: 0.7708 (ttp) cc_final: 0.7461 (ttp) REVERT: B 1040 ASN cc_start: 0.6852 (p0) cc_final: 0.6528 (p0) REVERT: B 1156 MET cc_start: 0.8914 (tpt) cc_final: 0.8642 (tpt) REVERT: B 1376 MET cc_start: 0.8358 (mmm) cc_final: 0.8015 (mpp) REVERT: B 1704 MET cc_start: 0.8648 (ppp) cc_final: 0.8416 (ppp) REVERT: B 1716 THR cc_start: 0.6978 (m) cc_final: 0.6679 (p) REVERT: B 1984 MET cc_start: 0.9065 (mtm) cc_final: 0.8652 (mmt) REVERT: B 2014 LEU cc_start: 0.8670 (tt) cc_final: 0.8392 (tp) REVERT: B 2317 ASP cc_start: 0.9143 (t0) cc_final: 0.8922 (t0) REVERT: B 2485 ILE cc_start: 0.9237 (mt) cc_final: 0.8918 (mp) REVERT: B 2553 MET cc_start: 0.8631 (mtp) cc_final: 0.8252 (mpp) REVERT: B 2716 GLN cc_start: 0.8611 (tt0) cc_final: 0.8239 (mp10) REVERT: C 541 MET cc_start: 0.8500 (mmt) cc_final: 0.8284 (mmt) REVERT: C 597 LEU cc_start: 0.9566 (tp) cc_final: 0.9338 (tp) REVERT: C 676 MET cc_start: 0.8109 (mmm) cc_final: 0.7839 (mmt) REVERT: C 698 MET cc_start: 0.9210 (tpp) cc_final: 0.8980 (tpp) REVERT: C 1147 MET cc_start: 0.9452 (tpp) cc_final: 0.9045 (mmt) REVERT: C 1161 MET cc_start: 0.8526 (ttp) cc_final: 0.8174 (tmm) REVERT: C 1562 MET cc_start: 0.9153 (ttm) cc_final: 0.8797 (ptp) REVERT: C 1704 MET cc_start: 0.8896 (ptm) cc_final: 0.8537 (ppp) REVERT: C 2013 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8913 (tp) REVERT: C 2314 MET cc_start: 0.8850 (mtm) cc_final: 0.8495 (mtt) REVERT: C 2344 MET cc_start: 0.8887 (mmm) cc_final: 0.8638 (tpt) REVERT: C 2470 VAL cc_start: 0.9522 (m) cc_final: 0.9142 (p) REVERT: C 2485 ILE cc_start: 0.8947 (mt) cc_final: 0.8632 (mt) REVERT: C 2508 ASP cc_start: 0.8632 (t0) cc_final: 0.8387 (t0) REVERT: C 2513 ILE cc_start: 0.9536 (mp) cc_final: 0.9304 (tp) REVERT: C 2553 MET cc_start: 0.8458 (mtp) cc_final: 0.8061 (mpp) REVERT: C 2638 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8689 (tpp) REVERT: C 2716 GLN cc_start: 0.8787 (tt0) cc_final: 0.8344 (mp10) REVERT: C 2741 MET cc_start: 0.7240 (tpp) cc_final: 0.6944 (mmp) REVERT: C 2769 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8586 (mm-30) outliers start: 62 outliers final: 28 residues processed: 464 average time/residue: 0.2278 time to fit residues: 187.2644 Evaluate side-chains 435 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 401 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1433 SER Chi-restraints excluded: chain A residue 1670 TRP Chi-restraints excluded: chain A residue 1713 ASN Chi-restraints excluded: chain A residue 2087 LEU Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2702 VAL Chi-restraints excluded: chain A residue 2753 LYS Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 1271 MET Chi-restraints excluded: chain B residue 1320 THR Chi-restraints excluded: chain B residue 1670 TRP Chi-restraints excluded: chain B residue 2601 VAL Chi-restraints excluded: chain B residue 2760 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 518 TRP Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 1193 ILE Chi-restraints excluded: chain C residue 1433 SER Chi-restraints excluded: chain C residue 1977 PHE Chi-restraints excluded: chain C residue 2013 LEU Chi-restraints excluded: chain C residue 2019 ILE Chi-restraints excluded: chain C residue 2304 LEU Chi-restraints excluded: chain C residue 2601 VAL Chi-restraints excluded: chain C residue 2638 MET Chi-restraints excluded: chain C residue 2685 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 196 optimal weight: 1.9990 chunk 456 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 170 optimal weight: 7.9990 chunk 502 optimal weight: 5.9990 chunk 449 optimal weight: 1.9990 chunk 286 optimal weight: 0.0870 chunk 360 optimal weight: 1.9990 chunk 390 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 332 optimal weight: 8.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 ASN ** C 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.075545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.058511 restraints weight = 205066.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.060170 restraints weight = 96532.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.061224 restraints weight = 60877.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.061822 restraints weight = 46175.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.062327 restraints weight = 39214.318| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 46140 Z= 0.117 Angle : 0.567 12.802 62625 Z= 0.281 Chirality : 0.040 0.345 7110 Planarity : 0.004 0.062 7569 Dihedral : 4.046 25.516 5910 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.17 % Allowed : 13.02 % 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: 0.41 (0.12), residues: 5358 helix: 1.65 (0.09), residues: 3528 sheet: -0.88 (0.32), residues: 216 loop : -2.85 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B2608 TYR 0.021 0.001 TYR B 501 PHE 0.031 0.001 PHE A2625 TRP 0.016 0.001 TRP B 561 HIS 0.004 0.001 HIS B1559 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (46125) covalent geometry : angle 0.56676 / 0.28 (62583) SS BOND : bond 0.00025 / 0.01 ( 3) SS BOND : angle 0.14547 / 0.08 ( 6) hydrogen bonds : bond 0.03563 / 2.32 ( 2721) hydrogen bonds : angle 3.70009 / 2.64 ( 8052) link_NAG-ASN : bond 0.00160 / 0.11 ( 12) link_NAG-ASN : angle 1.14817 / 0.69 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 420 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 MET cc_start: 0.8068 (tpp) cc_final: 0.7714 (tpt) REVERT: A 518 TRP cc_start: 0.7192 (OUTLIER) cc_final: 0.6596 (t60) REVERT: A 554 LEU cc_start: 0.9747 (OUTLIER) cc_final: 0.9410 (pp) REVERT: A 1147 MET cc_start: 0.9342 (tpp) cc_final: 0.9062 (mmp) REVERT: A 1271 MET cc_start: 0.8183 (ptm) cc_final: 0.7887 (ptp) REVERT: A 1562 MET cc_start: 0.9130 (ttm) cc_final: 0.8509 (ptp) REVERT: A 1704 MET cc_start: 0.8838 (ttm) cc_final: 0.8526 (tmm) REVERT: A 2587 MET cc_start: 0.9366 (ttm) cc_final: 0.8973 (tpp) REVERT: A 2610 MET cc_start: 0.4832 (mmm) cc_final: 0.4568 (mmm) REVERT: A 2690 ARG cc_start: 0.8274 (ptm160) cc_final: 0.7947 (tmm-80) REVERT: A 2702 VAL cc_start: 0.7312 (OUTLIER) cc_final: 0.7089 (p) REVERT: A 2753 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.8603 (tmmm) REVERT: A 2813 MET cc_start: 0.9202 (ttp) cc_final: 0.8928 (ttt) REVERT: B 698 MET cc_start: 0.9221 (tpp) cc_final: 0.8918 (tpp) REVERT: B 749 MET cc_start: 0.7817 (ttp) cc_final: 0.7563 (ttp) REVERT: B 1040 ASN cc_start: 0.6679 (p0) cc_final: 0.6444 (p0) REVERT: B 1156 MET cc_start: 0.8927 (tpt) cc_final: 0.8659 (tpt) REVERT: B 1704 MET cc_start: 0.8686 (ppp) cc_final: 0.8436 (ppp) REVERT: B 1716 THR cc_start: 0.7081 (m) cc_final: 0.6796 (p) REVERT: B 1984 MET cc_start: 0.9070 (mtm) cc_final: 0.8655 (mmt) REVERT: B 2014 LEU cc_start: 0.8633 (tt) cc_final: 0.8352 (tp) REVERT: B 2317 ASP cc_start: 0.9138 (t0) cc_final: 0.8846 (t0) REVERT: B 2485 ILE cc_start: 0.9245 (mt) cc_final: 0.8962 (mp) REVERT: B 2553 MET cc_start: 0.8691 (mtp) cc_final: 0.8331 (mpp) REVERT: B 2604 TRP cc_start: 0.8415 (p90) cc_final: 0.7404 (p90) REVERT: B 2716 GLN cc_start: 0.8610 (tt0) cc_final: 0.8225 (mp10) REVERT: C 597 LEU cc_start: 0.9568 (tp) cc_final: 0.9347 (tp) REVERT: C 676 MET cc_start: 0.8159 (mmm) cc_final: 0.7876 (mmt) REVERT: C 698 MET cc_start: 0.9212 (tpp) cc_final: 0.8982 (tpp) REVERT: C 1147 MET cc_start: 0.9428 (tpp) cc_final: 0.9016 (mmt) REVERT: C 1161 MET cc_start: 0.8528 (ttp) cc_final: 0.8182 (tmm) REVERT: C 1562 MET cc_start: 0.9147 (ttm) cc_final: 0.8937 (ptp) REVERT: C 1704 MET cc_start: 0.8920 (ptm) cc_final: 0.8539 (ppp) REVERT: C 2314 MET cc_start: 0.8853 (mtm) cc_final: 0.8496 (mtt) REVERT: C 2344 MET cc_start: 0.8917 (mmm) cc_final: 0.8684 (tpt) REVERT: C 2470 VAL cc_start: 0.9524 (m) cc_final: 0.9152 (p) REVERT: C 2485 ILE cc_start: 0.8990 (mt) cc_final: 0.8739 (mp) REVERT: C 2508 ASP cc_start: 0.8638 (t0) cc_final: 0.8393 (t0) REVERT: C 2513 ILE cc_start: 0.9532 (mp) cc_final: 0.9318 (tp) REVERT: C 2553 MET cc_start: 0.8553 (mtp) cc_final: 0.8152 (mpp) REVERT: C 2638 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8706 (tpp) REVERT: C 2716 GLN cc_start: 0.8796 (tt0) cc_final: 0.8350 (mp10) REVERT: C 2741 MET cc_start: 0.7290 (tpp) cc_final: 0.6987 (mmp) REVERT: C 2769 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8582 (mm-30) outliers start: 57 outliers final: 31 residues processed: 454 average time/residue: 0.2342 time to fit residues: 188.3073 Evaluate side-chains 438 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 402 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1433 SER Chi-restraints excluded: chain A residue 1670 TRP Chi-restraints excluded: chain A residue 1713 ASN Chi-restraints excluded: chain A residue 2087 LEU Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2702 VAL Chi-restraints excluded: chain A residue 2753 LYS Chi-restraints excluded: chain A residue 2760 SER Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 1271 MET Chi-restraints excluded: chain B residue 1320 THR Chi-restraints excluded: chain B residue 1373 VAL Chi-restraints excluded: chain B residue 1670 TRP Chi-restraints excluded: chain B residue 2303 PHE Chi-restraints excluded: chain B residue 2601 VAL Chi-restraints excluded: chain B residue 2760 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 518 TRP Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 1193 ILE Chi-restraints excluded: chain C residue 1433 SER Chi-restraints excluded: chain C residue 1977 PHE Chi-restraints excluded: chain C residue 2304 LEU Chi-restraints excluded: chain C residue 2601 VAL Chi-restraints excluded: chain C residue 2638 MET Chi-restraints excluded: chain C residue 2685 THR Chi-restraints excluded: chain C residue 2767 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 359 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 324 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 278 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 126 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1154 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2607 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.075419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.058189 restraints weight = 234784.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.060336 restraints weight = 103984.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.061809 restraints weight = 56954.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.061964 restraints weight = 39569.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.062026 restraints weight = 38348.949| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 46140 Z= 0.123 Angle : 0.566 12.522 62625 Z= 0.281 Chirality : 0.040 0.251 7110 Planarity : 0.004 0.062 7569 Dihedral : 4.020 25.377 5910 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.23 % Allowed : 13.47 % Favored : 85.30 % 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: 0.50 (0.12), residues: 5358 helix: 1.69 (0.09), residues: 3540 sheet: -0.77 (0.33), residues: 216 loop : -2.79 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B2608 TYR 0.019 0.001 TYR B 501 PHE 0.030 0.001 PHE A1977 TRP 0.040 0.001 TRP C2604 HIS 0.005 0.001 HIS B1559 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (46125) covalent geometry : angle 0.56602 / 0.28 (62583) SS BOND : bond 0.00008 / 0.00 ( 3) SS BOND : angle 0.15482 / 0.09 ( 6) hydrogen bonds : bond 0.03544 / 2.32 ( 2721) hydrogen bonds : angle 3.70375 / 2.65 ( 8052) link_NAG-ASN : bond 0.00156 / 0.10 ( 12) link_NAG-ASN : angle 1.11873 / 0.67 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 417 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9058 (mm) REVERT: A 518 TRP cc_start: 0.7184 (OUTLIER) cc_final: 0.6583 (t60) REVERT: A 554 LEU cc_start: 0.9755 (OUTLIER) cc_final: 0.9437 (pp) REVERT: A 1147 MET cc_start: 0.9334 (tpp) cc_final: 0.9055 (mmp) REVERT: A 1235 ILE cc_start: 0.8737 (tp) cc_final: 0.8523 (mm) REVERT: A 1271 MET cc_start: 0.8203 (ptm) cc_final: 0.7928 (ptp) REVERT: A 1562 MET cc_start: 0.9144 (ttm) cc_final: 0.8499 (ptp) REVERT: A 1678 ASP cc_start: 0.8654 (m-30) cc_final: 0.8398 (m-30) REVERT: A 1704 MET cc_start: 0.8877 (ttm) cc_final: 0.8554 (tmm) REVERT: A 2587 MET cc_start: 0.9361 (ttm) cc_final: 0.8950 (tpp) REVERT: A 2610 MET cc_start: 0.4824 (mmm) cc_final: 0.4560 (mmm) REVERT: A 2690 ARG cc_start: 0.8267 (ptm160) cc_final: 0.7936 (tmm-80) REVERT: A 2702 VAL cc_start: 0.7227 (OUTLIER) cc_final: 0.7012 (p) REVERT: A 2753 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.8607 (tmmm) REVERT: A 2813 MET cc_start: 0.9206 (ttp) cc_final: 0.8931 (ttt) REVERT: B 698 MET cc_start: 0.9231 (tpp) cc_final: 0.8914 (tpp) REVERT: B 1156 MET cc_start: 0.8924 (tpt) cc_final: 0.8665 (tpt) REVERT: B 1562 MET cc_start: 0.9051 (ttm) cc_final: 0.8626 (ptp) REVERT: B 1704 MET cc_start: 0.8755 (ppp) cc_final: 0.8493 (ppp) REVERT: B 1716 THR cc_start: 0.6889 (m) cc_final: 0.6568 (p) REVERT: B 1984 MET cc_start: 0.9082 (mtm) cc_final: 0.8660 (mmt) REVERT: B 2014 LEU cc_start: 0.8626 (tt) cc_final: 0.8349 (tp) REVERT: B 2317 ASP cc_start: 0.9126 (t0) cc_final: 0.8832 (t0) REVERT: B 2485 ILE cc_start: 0.9228 (mt) cc_final: 0.8951 (mp) REVERT: B 2553 MET cc_start: 0.8699 (mtp) cc_final: 0.8331 (mpp) REVERT: B 2604 TRP cc_start: 0.8423 (p90) cc_final: 0.7404 (p90) REVERT: B 2716 GLN cc_start: 0.8638 (tt0) cc_final: 0.8227 (mp10) REVERT: C 40 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9235 (mm) REVERT: C 502 ILE cc_start: 0.9193 (mm) cc_final: 0.8950 (tt) REVERT: C 597 LEU cc_start: 0.9564 (tp) cc_final: 0.9342 (tp) REVERT: C 676 MET cc_start: 0.8180 (mmm) cc_final: 0.7913 (mmt) REVERT: C 698 MET cc_start: 0.9215 (tpp) cc_final: 0.8959 (tpp) REVERT: C 1147 MET cc_start: 0.9371 (tpp) cc_final: 0.8971 (mmt) REVERT: C 1161 MET cc_start: 0.8522 (ttp) cc_final: 0.8184 (tmm) REVERT: C 1562 MET cc_start: 0.9170 (ttm) cc_final: 0.8943 (ptp) REVERT: C 1704 MET cc_start: 0.8971 (ptm) cc_final: 0.8588 (ppp) REVERT: C 2314 MET cc_start: 0.8853 (mtm) cc_final: 0.8485 (mtt) REVERT: C 2344 MET cc_start: 0.8930 (mmm) cc_final: 0.8686 (tpt) REVERT: C 2470 VAL cc_start: 0.9522 (m) cc_final: 0.9160 (p) REVERT: C 2485 ILE cc_start: 0.8974 (mt) cc_final: 0.8703 (mp) REVERT: C 2508 ASP cc_start: 0.8684 (t0) cc_final: 0.8348 (t0) REVERT: C 2513 ILE cc_start: 0.9536 (mp) cc_final: 0.9322 (tp) REVERT: C 2524 MET cc_start: 0.9147 (tpp) cc_final: 0.8902 (tpp) REVERT: C 2527 GLN cc_start: 0.8339 (mt0) cc_final: 0.7988 (mt0) REVERT: C 2553 MET cc_start: 0.8564 (mtp) cc_final: 0.8157 (mpp) REVERT: C 2638 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8749 (tpp) REVERT: C 2741 MET cc_start: 0.7150 (tpp) cc_final: 0.6843 (mmp) REVERT: C 2769 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8582 (mm-30) outliers start: 60 outliers final: 41 residues processed: 454 average time/residue: 0.2186 time to fit residues: 176.4876 Evaluate side-chains 453 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 405 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1433 SER Chi-restraints excluded: chain A residue 1670 TRP Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1713 ASN Chi-restraints excluded: chain A residue 2087 LEU Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain A residue 2702 VAL Chi-restraints excluded: chain A residue 2753 LYS Chi-restraints excluded: chain A residue 2760 SER Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1271 MET Chi-restraints excluded: chain B residue 1303 LEU Chi-restraints excluded: chain B residue 1320 THR Chi-restraints excluded: chain B residue 1373 VAL Chi-restraints excluded: chain B residue 1670 TRP Chi-restraints excluded: chain B residue 1671 VAL Chi-restraints excluded: chain B residue 1713 ASN Chi-restraints excluded: chain B residue 2303 PHE Chi-restraints excluded: chain B residue 2601 VAL Chi-restraints excluded: chain B residue 2760 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 518 TRP Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 1156 MET Chi-restraints excluded: chain C residue 1193 ILE Chi-restraints excluded: chain C residue 1433 SER Chi-restraints excluded: chain C residue 1671 VAL Chi-restraints excluded: chain C residue 1977 PHE Chi-restraints excluded: chain C residue 2303 PHE Chi-restraints excluded: chain C residue 2304 LEU Chi-restraints excluded: chain C residue 2601 VAL Chi-restraints excluded: chain C residue 2638 MET Chi-restraints excluded: chain C residue 2685 THR Chi-restraints excluded: chain C residue 2767 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 449 optimal weight: 0.9980 chunk 342 optimal weight: 5.9990 chunk 367 optimal weight: 9.9990 chunk 488 optimal weight: 6.9990 chunk 479 optimal weight: 3.9990 chunk 515 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 328 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 417 optimal weight: 0.8980 chunk 398 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1442 GLN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 ASN ** C 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.074636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.057399 restraints weight = 223292.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.059026 restraints weight = 102543.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.060110 restraints weight = 64258.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.060837 restraints weight = 48433.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.061141 restraints weight = 40646.416| |-----------------------------------------------------------------------------| r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 46140 Z= 0.148 Angle : 0.584 11.672 62625 Z= 0.291 Chirality : 0.040 0.246 7110 Planarity : 0.004 0.062 7569 Dihedral : 4.057 25.833 5910 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.33 % Allowed : 13.92 % Favored : 84.75 % 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: 0.55 (0.12), residues: 5358 helix: 1.70 (0.09), residues: 3558 sheet: -0.79 (0.32), residues: 216 loop : -2.72 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2608 TYR 0.024 0.001 TYR A 34 PHE 0.030 0.001 PHE A1977 TRP 0.033 0.001 TRP C2604 HIS 0.005 0.001 HIS B1559 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (46125) covalent geometry : angle 0.58396 / 0.29 (62583) SS BOND : bond 0.00034 / 0.02 ( 3) SS BOND : angle 0.23213 / 0.14 ( 6) hydrogen bonds : bond 0.03701 / 2.42 ( 2721) hydrogen bonds : angle 3.77721 / 2.70 ( 8052) link_NAG-ASN : bond 0.00179 / 0.12 ( 12) link_NAG-ASN : angle 1.13551 / 0.68 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 409 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9128 (mm) REVERT: A 237 MET cc_start: 0.7654 (tpp) cc_final: 0.7323 (tpt) REVERT: A 518 TRP cc_start: 0.7233 (OUTLIER) cc_final: 0.6634 (t60) REVERT: A 554 LEU cc_start: 0.9766 (OUTLIER) cc_final: 0.9464 (pp) REVERT: A 1147 MET cc_start: 0.9332 (tpp) cc_final: 0.9059 (mmp) REVERT: A 1271 MET cc_start: 0.8210 (ptm) cc_final: 0.7911 (ptp) REVERT: A 1562 MET cc_start: 0.9183 (ttm) cc_final: 0.8425 (ptp) REVERT: A 1678 ASP cc_start: 0.8661 (m-30) cc_final: 0.8404 (m-30) REVERT: A 1704 MET cc_start: 0.8864 (ttm) cc_final: 0.8579 (tmm) REVERT: A 2546 PHE cc_start: 0.7252 (m-80) cc_final: 0.7045 (m-80) REVERT: A 2610 MET cc_start: 0.4623 (mmm) cc_final: 0.4396 (mmm) REVERT: A 2690 ARG cc_start: 0.8264 (ptm160) cc_final: 0.7936 (tmm-80) REVERT: A 2702 VAL cc_start: 0.7319 (OUTLIER) cc_final: 0.7090 (p) REVERT: A 2753 LYS cc_start: 0.9382 (OUTLIER) cc_final: 0.8634 (tmmm) REVERT: A 2813 MET cc_start: 0.9219 (ttp) cc_final: 0.8951 (ttt) REVERT: B 532 MET cc_start: 0.8343 (ptm) cc_final: 0.8140 (ptp) REVERT: B 1156 MET cc_start: 0.8892 (tpt) cc_final: 0.8661 (tpt) REVERT: B 1704 MET cc_start: 0.8745 (ppp) cc_final: 0.8475 (ppp) REVERT: B 1716 THR cc_start: 0.6408 (m) cc_final: 0.6131 (p) REVERT: B 2014 LEU cc_start: 0.8724 (tt) cc_final: 0.8473 (tp) REVERT: B 2317 ASP cc_start: 0.9158 (t0) cc_final: 0.8849 (t0) REVERT: B 2485 ILE cc_start: 0.9261 (mt) cc_final: 0.8970 (mp) REVERT: B 2553 MET cc_start: 0.8728 (mtp) cc_final: 0.8347 (mpp) REVERT: B 2716 GLN cc_start: 0.8669 (tt0) cc_final: 0.8210 (mp10) REVERT: C 40 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9292 (mm) REVERT: C 497 MET cc_start: 0.8098 (mmm) cc_final: 0.7866 (ptt) REVERT: C 502 ILE cc_start: 0.9203 (mm) cc_final: 0.8960 (tt) REVERT: C 597 LEU cc_start: 0.9557 (tp) cc_final: 0.9346 (tp) REVERT: C 676 MET cc_start: 0.8214 (mmm) cc_final: 0.7911 (mmt) REVERT: C 698 MET cc_start: 0.9271 (tpp) cc_final: 0.9007 (tpp) REVERT: C 1161 MET cc_start: 0.8542 (ttp) cc_final: 0.8226 (tmm) REVERT: C 1271 MET cc_start: 0.8559 (ptm) cc_final: 0.8346 (ptt) REVERT: C 1704 MET cc_start: 0.8915 (ptm) cc_final: 0.8522 (ppp) REVERT: C 2314 MET cc_start: 0.8889 (mtm) cc_final: 0.8531 (mtt) REVERT: C 2344 MET cc_start: 0.8909 (mmm) cc_final: 0.8649 (tpt) REVERT: C 2470 VAL cc_start: 0.9546 (m) cc_final: 0.9181 (p) REVERT: C 2508 ASP cc_start: 0.8709 (t0) cc_final: 0.8403 (t0) REVERT: C 2513 ILE cc_start: 0.9558 (mp) cc_final: 0.9343 (tp) REVERT: C 2524 MET cc_start: 0.9211 (tpp) cc_final: 0.8998 (tpp) REVERT: C 2527 GLN cc_start: 0.8354 (mt0) cc_final: 0.8012 (mt0) REVERT: C 2553 MET cc_start: 0.8578 (mtp) cc_final: 0.8158 (mpp) REVERT: C 2638 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8724 (tpp) REVERT: C 2741 MET cc_start: 0.7259 (tpp) cc_final: 0.6921 (mmp) REVERT: C 2769 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8577 (mm-30) outliers start: 65 outliers final: 44 residues processed: 449 average time/residue: 0.1928 time to fit residues: 154.3095 Evaluate side-chains 447 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 396 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1433 SER Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1713 ASN Chi-restraints excluded: chain A residue 2019 ILE Chi-restraints excluded: chain A residue 2087 LEU Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2702 VAL Chi-restraints excluded: chain A residue 2753 LYS Chi-restraints excluded: chain A residue 2760 SER Chi-restraints excluded: chain A residue 2784 ILE Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1271 MET Chi-restraints excluded: chain B residue 1303 LEU Chi-restraints excluded: chain B residue 1320 THR Chi-restraints excluded: chain B residue 1373 VAL Chi-restraints excluded: chain B residue 1670 TRP Chi-restraints excluded: chain B residue 1671 VAL Chi-restraints excluded: chain B residue 1713 ASN Chi-restraints excluded: chain B residue 2400 VAL Chi-restraints excluded: chain B residue 2601 VAL Chi-restraints excluded: chain B residue 2760 SER Chi-restraints excluded: chain B residue 2784 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 518 TRP Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 1156 MET Chi-restraints excluded: chain C residue 1193 ILE Chi-restraints excluded: chain C residue 1433 SER Chi-restraints excluded: chain C residue 1671 VAL Chi-restraints excluded: chain C residue 1724 TYR Chi-restraints excluded: chain C residue 1977 PHE Chi-restraints excluded: chain C residue 2019 ILE Chi-restraints excluded: chain C residue 2304 LEU Chi-restraints excluded: chain C residue 2601 VAL Chi-restraints excluded: chain C residue 2638 MET Chi-restraints excluded: chain C residue 2685 THR Chi-restraints excluded: chain C residue 2767 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 228 optimal weight: 0.9990 chunk 203 optimal weight: 0.0670 chunk 483 optimal weight: 0.9980 chunk 346 optimal weight: 8.9990 chunk 167 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 271 optimal weight: 0.6980 chunk 202 optimal weight: 0.7980 chunk 238 optimal weight: 0.9980 chunk 185 optimal weight: 0.7980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.075982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.058919 restraints weight = 199202.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.060540 restraints weight = 95416.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.061382 restraints weight = 60770.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.062214 restraints weight = 47794.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.062614 restraints weight = 40063.525| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 46140 Z= 0.111 Angle : 0.577 12.475 62625 Z= 0.283 Chirality : 0.040 0.244 7110 Planarity : 0.004 0.063 7569 Dihedral : 3.995 27.387 5910 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.15 % Allowed : 14.21 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.12), residues: 5358 helix: 1.78 (0.09), residues: 3540 sheet: -0.76 (0.32), residues: 216 loop : -2.66 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2462 TYR 0.027 0.001 TYR A 34 PHE 0.028 0.001 PHE A1977 TRP 0.029 0.001 TRP C2604 HIS 0.005 0.001 HIS B1559 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (46125) covalent geometry : angle 0.57617 / 0.28 (62583) SS BOND : bond 0.00028 / 0.02 ( 3) SS BOND : angle 0.16434 / 0.09 ( 6) hydrogen bonds : bond 0.03468 / 2.27 ( 2721) hydrogen bonds : angle 3.67103 / 2.62 ( 8052) link_NAG-ASN : bond 0.00179 / 0.12 ( 12) link_NAG-ASN : angle 1.04995 / 0.62 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 433 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9059 (mm) REVERT: A 237 MET cc_start: 0.7513 (tpp) cc_final: 0.7190 (tpt) REVERT: A 518 TRP cc_start: 0.7110 (OUTLIER) cc_final: 0.6604 (t60) REVERT: A 554 LEU cc_start: 0.9739 (OUTLIER) cc_final: 0.9385 (pp) REVERT: A 980 TYR cc_start: 0.8565 (t80) cc_final: 0.8302 (t80) REVERT: A 1147 MET cc_start: 0.9330 (tpp) cc_final: 0.9065 (mmp) REVERT: A 1235 ILE cc_start: 0.8789 (tp) cc_final: 0.8565 (mm) REVERT: A 1271 MET cc_start: 0.8203 (ptm) cc_final: 0.7953 (ptp) REVERT: A 1678 ASP cc_start: 0.8648 (m-30) cc_final: 0.8386 (m-30) REVERT: A 1704 MET cc_start: 0.8831 (ttm) cc_final: 0.8525 (tmm) REVERT: A 2587 MET cc_start: 0.9325 (ttm) cc_final: 0.8993 (tpp) REVERT: A 2610 MET cc_start: 0.4579 (mmm) cc_final: 0.4316 (tpt) REVERT: A 2655 LYS cc_start: 0.7024 (mmtm) cc_final: 0.6753 (tppt) REVERT: A 2690 ARG cc_start: 0.8236 (ptm160) cc_final: 0.7922 (tmm-80) REVERT: A 2702 VAL cc_start: 0.7479 (OUTLIER) cc_final: 0.7274 (p) REVERT: A 2753 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.8614 (tmmm) REVERT: A 2813 MET cc_start: 0.9198 (ttp) cc_final: 0.8910 (ttt) REVERT: B 1704 MET cc_start: 0.8740 (ppp) cc_final: 0.8463 (ppp) REVERT: B 1716 THR cc_start: 0.6408 (m) cc_final: 0.6160 (p) REVERT: B 1984 MET cc_start: 0.9073 (mtm) cc_final: 0.8659 (mmt) REVERT: B 2014 LEU cc_start: 0.8483 (tt) cc_final: 0.8200 (tp) REVERT: B 2317 ASP cc_start: 0.9168 (t0) cc_final: 0.8868 (t0) REVERT: B 2485 ILE cc_start: 0.9248 (mt) cc_final: 0.8953 (mp) REVERT: B 2508 ASP cc_start: 0.8704 (t0) cc_final: 0.8310 (m-30) REVERT: B 2553 MET cc_start: 0.8716 (mtp) cc_final: 0.8349 (mpp) REVERT: B 2604 TRP cc_start: 0.8375 (p90) cc_final: 0.7460 (p90) REVERT: B 2716 GLN cc_start: 0.8653 (tt0) cc_final: 0.8237 (mp10) REVERT: C 502 ILE cc_start: 0.9167 (mm) cc_final: 0.8906 (tt) REVERT: C 597 LEU cc_start: 0.9545 (tp) cc_final: 0.9324 (tp) REVERT: C 676 MET cc_start: 0.8289 (mmm) cc_final: 0.8024 (mmt) REVERT: C 698 MET cc_start: 0.9247 (tpp) cc_final: 0.8986 (tpp) REVERT: C 1147 MET cc_start: 0.9327 (mmm) cc_final: 0.8790 (mmt) REVERT: C 1161 MET cc_start: 0.8526 (ttp) cc_final: 0.8194 (tmm) REVERT: C 1704 MET cc_start: 0.8896 (ptm) cc_final: 0.8497 (ppp) REVERT: C 2314 MET cc_start: 0.8887 (mtm) cc_final: 0.8621 (mtt) REVERT: C 2344 MET cc_start: 0.8871 (mmm) cc_final: 0.8585 (tpt) REVERT: C 2470 VAL cc_start: 0.9527 (m) cc_final: 0.9286 (p) REVERT: C 2508 ASP cc_start: 0.8686 (t0) cc_final: 0.8405 (t0) REVERT: C 2524 MET cc_start: 0.9159 (tpp) cc_final: 0.8883 (tpp) REVERT: C 2527 GLN cc_start: 0.8300 (mt0) cc_final: 0.7951 (mt0) REVERT: C 2553 MET cc_start: 0.8584 (mtp) cc_final: 0.8182 (mpp) REVERT: C 2638 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8735 (tpp) REVERT: C 2716 GLN cc_start: 0.8861 (tt0) cc_final: 0.8396 (mp10) REVERT: C 2741 MET cc_start: 0.7269 (tpp) cc_final: 0.6960 (mmp) REVERT: C 2769 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8550 (mm-30) outliers start: 56 outliers final: 40 residues processed: 471 average time/residue: 0.2063 time to fit residues: 172.3957 Evaluate side-chains 460 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 414 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1433 SER Chi-restraints excluded: chain A residue 1670 TRP Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1713 ASN Chi-restraints excluded: chain A residue 2087 LEU Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 2702 VAL Chi-restraints excluded: chain A residue 2753 LYS Chi-restraints excluded: chain A residue 2760 SER Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 1271 MET Chi-restraints excluded: chain B residue 1303 LEU Chi-restraints excluded: chain B residue 1670 TRP Chi-restraints excluded: chain B residue 1671 VAL Chi-restraints excluded: chain B residue 1713 ASN Chi-restraints excluded: chain B residue 2303 PHE Chi-restraints excluded: chain B residue 2400 VAL Chi-restraints excluded: chain B residue 2601 VAL Chi-restraints excluded: chain B residue 2760 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 518 TRP Chi-restraints excluded: chain C residue 1156 MET Chi-restraints excluded: chain C residue 1193 ILE Chi-restraints excluded: chain C residue 1433 SER Chi-restraints excluded: chain C residue 1671 VAL Chi-restraints excluded: chain C residue 1724 TYR Chi-restraints excluded: chain C residue 1977 PHE Chi-restraints excluded: chain C residue 2303 PHE Chi-restraints excluded: chain C residue 2304 LEU Chi-restraints excluded: chain C residue 2400 VAL Chi-restraints excluded: chain C residue 2601 VAL Chi-restraints excluded: chain C residue 2638 MET Chi-restraints excluded: chain C residue 2685 THR Chi-restraints excluded: chain C residue 2767 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 442 optimal weight: 0.9980 chunk 374 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 454 optimal weight: 1.9990 chunk 501 optimal weight: 0.9990 chunk 435 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 319 optimal weight: 3.9990 chunk 369 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 485 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.075755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.058432 restraints weight = 216581.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.060121 restraints weight = 101525.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.061154 restraints weight = 63456.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.061920 restraints weight = 48310.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.062407 restraints weight = 40471.763| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 46140 Z= 0.120 Angle : 0.588 15.116 62625 Z= 0.287 Chirality : 0.040 0.335 7110 Planarity : 0.004 0.062 7569 Dihedral : 3.966 26.042 5910 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.27 % Allowed : 14.39 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.66 (0.12), residues: 5358 helix: 1.77 (0.09), residues: 3543 sheet: -0.77 (0.32), residues: 216 loop : -2.61 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2608 TYR 0.028 0.001 TYR B 34 PHE 0.029 0.001 PHE A1977 TRP 0.027 0.001 TRP C2604 HIS 0.005 0.001 HIS C1559 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (46125) covalent geometry : angle 0.58715 / 0.29 (62583) SS BOND : bond 0.00016 / 0.01 ( 3) SS BOND : angle 0.17247 / 0.10 ( 6) hydrogen bonds : bond 0.03509 / 2.29 ( 2721) hydrogen bonds : angle 3.68357 / 2.62 ( 8052) link_NAG-ASN : bond 0.00167 / 0.11 ( 12) link_NAG-ASN : angle 1.07544 / 0.64 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 423 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9061 (mm) REVERT: A 237 MET cc_start: 0.7513 (tpp) cc_final: 0.7183 (tpt) REVERT: A 518 TRP cc_start: 0.7105 (OUTLIER) cc_final: 0.6606 (t60) REVERT: A 554 LEU cc_start: 0.9741 (OUTLIER) cc_final: 0.9394 (pp) REVERT: A 980 TYR cc_start: 0.8573 (t80) cc_final: 0.8308 (t80) REVERT: A 1147 MET cc_start: 0.9323 (tpp) cc_final: 0.9048 (mmp) REVERT: A 1271 MET cc_start: 0.8199 (ptm) cc_final: 0.7958 (ptp) REVERT: A 1562 MET cc_start: 0.8142 (ttp) cc_final: 0.7902 (ptm) REVERT: A 1704 MET cc_start: 0.8833 (ttm) cc_final: 0.8521 (tmm) REVERT: A 2587 MET cc_start: 0.9316 (ttm) cc_final: 0.8977 (tpp) REVERT: A 2610 MET cc_start: 0.4806 (mmm) cc_final: 0.4570 (tpt) REVERT: A 2655 LYS cc_start: 0.6909 (mmtm) cc_final: 0.6666 (tppt) REVERT: A 2690 ARG cc_start: 0.8159 (ptm160) cc_final: 0.7883 (tmm-80) REVERT: A 2753 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.8613 (tmmm) REVERT: A 2813 MET cc_start: 0.9224 (ttp) cc_final: 0.8920 (ttt) REVERT: B 43 LEU cc_start: 0.8511 (tt) cc_final: 0.8259 (tt) REVERT: B 532 MET cc_start: 0.8552 (ptp) cc_final: 0.8143 (ptm) REVERT: B 980 TYR cc_start: 0.8516 (t80) cc_final: 0.8125 (t80) REVERT: B 1080 MET cc_start: 0.8380 (ttm) cc_final: 0.8047 (ttm) REVERT: B 1704 MET cc_start: 0.8747 (ppp) cc_final: 0.8467 (ppp) REVERT: B 1716 THR cc_start: 0.6353 (m) cc_final: 0.6107 (p) REVERT: B 1984 MET cc_start: 0.9071 (mtm) cc_final: 0.8660 (mmt) REVERT: B 2014 LEU cc_start: 0.8529 (tt) cc_final: 0.8241 (tp) REVERT: B 2317 ASP cc_start: 0.9176 (t0) cc_final: 0.8873 (t0) REVERT: B 2485 ILE cc_start: 0.9254 (mt) cc_final: 0.8956 (mp) REVERT: B 2553 MET cc_start: 0.8726 (mtp) cc_final: 0.8356 (mpp) REVERT: B 2604 TRP cc_start: 0.8390 (p90) cc_final: 0.7469 (p90) REVERT: B 2716 GLN cc_start: 0.8656 (tt0) cc_final: 0.8240 (mp10) REVERT: C 39 LEU cc_start: 0.8916 (tt) cc_final: 0.8347 (tp) REVERT: C 597 LEU cc_start: 0.9535 (tp) cc_final: 0.9313 (tp) REVERT: C 676 MET cc_start: 0.8299 (mmm) cc_final: 0.8035 (mmt) REVERT: C 698 MET cc_start: 0.9249 (tpp) cc_final: 0.8996 (tpp) REVERT: C 1147 MET cc_start: 0.9297 (mmm) cc_final: 0.8755 (mmt) REVERT: C 1161 MET cc_start: 0.8523 (ttp) cc_final: 0.8202 (tmm) REVERT: C 1704 MET cc_start: 0.8953 (ptm) cc_final: 0.8642 (tmm) REVERT: C 2314 MET cc_start: 0.8882 (mtm) cc_final: 0.8512 (mtt) REVERT: C 2344 MET cc_start: 0.8773 (mmm) cc_final: 0.8525 (tpt) REVERT: C 2470 VAL cc_start: 0.9538 (m) cc_final: 0.9201 (p) REVERT: C 2508 ASP cc_start: 0.8692 (t0) cc_final: 0.8421 (t0) REVERT: C 2524 MET cc_start: 0.9173 (tpp) cc_final: 0.8956 (tpp) REVERT: C 2527 GLN cc_start: 0.8283 (mt0) cc_final: 0.7948 (mt0) REVERT: C 2553 MET cc_start: 0.8525 (mtp) cc_final: 0.8125 (mpp) REVERT: C 2577 TRP cc_start: 0.9495 (OUTLIER) cc_final: 0.8772 (t60) REVERT: C 2638 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8732 (tpp) REVERT: C 2716 GLN cc_start: 0.8857 (tt0) cc_final: 0.8396 (mp10) REVERT: C 2741 MET cc_start: 0.7226 (tpp) cc_final: 0.6984 (mmp) REVERT: C 2769 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8562 (mm-30) outliers start: 62 outliers final: 44 residues processed: 465 average time/residue: 0.1917 time to fit residues: 157.6841 Evaluate side-chains 466 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 416 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1433 SER Chi-restraints excluded: chain A residue 1670 TRP Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1713 ASN Chi-restraints excluded: chain A residue 2087 LEU Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2533 VAL Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 2753 LYS Chi-restraints excluded: chain A residue 2760 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1271 MET Chi-restraints excluded: chain B residue 1303 LEU Chi-restraints excluded: chain B residue 1373 VAL Chi-restraints excluded: chain B residue 1670 TRP Chi-restraints excluded: chain B residue 1671 VAL Chi-restraints excluded: chain B residue 1713 ASN Chi-restraints excluded: chain B residue 2303 PHE Chi-restraints excluded: chain B residue 2400 VAL Chi-restraints excluded: chain B residue 2601 VAL Chi-restraints excluded: chain B residue 2760 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 518 TRP Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 1156 MET Chi-restraints excluded: chain C residue 1193 ILE Chi-restraints excluded: chain C residue 1433 SER Chi-restraints excluded: chain C residue 1671 VAL Chi-restraints excluded: chain C residue 1724 TYR Chi-restraints excluded: chain C residue 1977 PHE Chi-restraints excluded: chain C residue 2303 PHE Chi-restraints excluded: chain C residue 2304 LEU Chi-restraints excluded: chain C residue 2400 VAL Chi-restraints excluded: chain C residue 2577 TRP Chi-restraints excluded: chain C residue 2638 MET Chi-restraints excluded: chain C residue 2685 THR Chi-restraints excluded: chain C residue 2767 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 182 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 348 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 529 optimal weight: 0.0980 chunk 390 optimal weight: 0.9980 chunk 301 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 442 optimal weight: 0.0020 chunk 501 optimal weight: 8.9990 chunk 216 optimal weight: 0.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 HIS ** C 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.076479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.059511 restraints weight = 187856.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.061095 restraints weight = 92379.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.062079 restraints weight = 59632.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.062786 restraints weight = 46137.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.063135 restraints weight = 39224.277| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 46140 Z= 0.108 Angle : 0.588 13.207 62625 Z= 0.286 Chirality : 0.040 0.375 7110 Planarity : 0.004 0.063 7569 Dihedral : 3.923 27.486 5910 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.03 % Allowed : 14.76 % Favored : 84.21 % 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: 0.73 (0.12), residues: 5358 helix: 1.81 (0.09), residues: 3546 sheet: -0.73 (0.32), residues: 216 loop : -2.54 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2462 TYR 0.033 0.001 TYR B 34 PHE 0.029 0.001 PHE A1977 TRP 0.027 0.001 TRP C2604 HIS 0.004 0.001 HIS B2004 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (46125) covalent geometry : angle 0.58776 / 0.29 (62583) SS BOND : bond 0.00045 / 0.02 ( 3) SS BOND : angle 0.15178 / 0.08 ( 6) hydrogen bonds : bond 0.03389 / 2.22 ( 2721) hydrogen bonds : angle 3.63557 / 2.59 ( 8052) link_NAG-ASN : bond 0.00188 / 0.12 ( 12) link_NAG-ASN : angle 1.01644 / 0.60 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 443 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9055 (mm) REVERT: A 237 MET cc_start: 0.7410 (tpp) cc_final: 0.7110 (tpt) REVERT: A 554 LEU cc_start: 0.9735 (OUTLIER) cc_final: 0.9371 (pp) REVERT: A 716 MET cc_start: 0.9213 (tpp) cc_final: 0.8750 (mmp) REVERT: A 980 TYR cc_start: 0.8490 (t80) cc_final: 0.8267 (t80) REVERT: A 1147 MET cc_start: 0.9315 (tpp) cc_final: 0.9046 (mmp) REVERT: A 1562 MET cc_start: 0.7189 (ttp) cc_final: 0.6888 (ptm) REVERT: A 1678 ASP cc_start: 0.8997 (m-30) cc_final: 0.8639 (m-30) REVERT: A 1704 MET cc_start: 0.8825 (ttm) cc_final: 0.8506 (tmm) REVERT: A 1969 LYS cc_start: 0.8994 (ttpt) cc_final: 0.8775 (ttmm) REVERT: A 2587 MET cc_start: 0.9298 (ttm) cc_final: 0.8975 (tpp) REVERT: A 2589 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8440 (mm-40) REVERT: A 2610 MET cc_start: 0.4743 (mmm) cc_final: 0.4507 (tpt) REVERT: A 2690 ARG cc_start: 0.8129 (ptm160) cc_final: 0.7848 (tmm-80) REVERT: A 2753 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.8614 (tmmm) REVERT: A 2813 MET cc_start: 0.9202 (ttp) cc_final: 0.8877 (ttt) REVERT: B 980 TYR cc_start: 0.8513 (t80) cc_final: 0.8161 (t80) REVERT: B 1704 MET cc_start: 0.8735 (ppp) cc_final: 0.8450 (ppp) REVERT: B 1716 THR cc_start: 0.6555 (m) cc_final: 0.6303 (p) REVERT: B 1984 MET cc_start: 0.9057 (mtm) cc_final: 0.8650 (mmt) REVERT: B 2014 LEU cc_start: 0.8431 (tt) cc_final: 0.8161 (tp) REVERT: B 2317 ASP cc_start: 0.9157 (t0) cc_final: 0.8861 (t0) REVERT: B 2485 ILE cc_start: 0.9249 (mt) cc_final: 0.8974 (mt) REVERT: B 2508 ASP cc_start: 0.8670 (t0) cc_final: 0.8273 (m-30) REVERT: B 2553 MET cc_start: 0.8721 (mtp) cc_final: 0.8418 (mpp) REVERT: B 2589 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8685 (mm110) REVERT: B 2604 TRP cc_start: 0.8333 (p90) cc_final: 0.7430 (p90) REVERT: B 2610 MET cc_start: 0.4914 (mmm) cc_final: 0.4598 (tpt) REVERT: B 2716 GLN cc_start: 0.8643 (tt0) cc_final: 0.8250 (mp10) REVERT: C 597 LEU cc_start: 0.9523 (tp) cc_final: 0.9304 (tp) REVERT: C 676 MET cc_start: 0.8293 (mmm) cc_final: 0.8034 (mmt) REVERT: C 698 MET cc_start: 0.9239 (tpp) cc_final: 0.8992 (tpp) REVERT: C 1161 MET cc_start: 0.8509 (ttp) cc_final: 0.8177 (tmm) REVERT: C 1704 MET cc_start: 0.8942 (ptm) cc_final: 0.8627 (tmm) REVERT: C 2314 MET cc_start: 0.8881 (mtm) cc_final: 0.8621 (mtt) REVERT: C 2344 MET cc_start: 0.8729 (mmm) cc_final: 0.8481 (tpt) REVERT: C 2470 VAL cc_start: 0.9517 (m) cc_final: 0.9286 (p) REVERT: C 2487 TRP cc_start: 0.8296 (t60) cc_final: 0.7886 (t60) REVERT: C 2508 ASP cc_start: 0.8663 (t0) cc_final: 0.8387 (t0) REVERT: C 2524 MET cc_start: 0.9182 (tpp) cc_final: 0.8980 (tpp) REVERT: C 2527 GLN cc_start: 0.8277 (mt0) cc_final: 0.7925 (mt0) REVERT: C 2553 MET cc_start: 0.8528 (mtp) cc_final: 0.8132 (mpp) REVERT: C 2577 TRP cc_start: 0.9456 (OUTLIER) cc_final: 0.8804 (t60) REVERT: C 2716 GLN cc_start: 0.8828 (tt0) cc_final: 0.8365 (mp10) REVERT: C 2741 MET cc_start: 0.7300 (tpp) cc_final: 0.7009 (mmp) REVERT: C 2769 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8554 (mm-30) outliers start: 50 outliers final: 36 residues processed: 475 average time/residue: 0.1842 time to fit residues: 155.3079 Evaluate side-chains 467 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 427 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1433 SER Chi-restraints excluded: chain A residue 1670 TRP Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1713 ASN Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 2753 LYS Chi-restraints excluded: chain A residue 2760 SER Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1670 TRP Chi-restraints excluded: chain B residue 1671 VAL Chi-restraints excluded: chain B residue 1713 ASN Chi-restraints excluded: chain B residue 2303 PHE Chi-restraints excluded: chain B residue 2400 VAL Chi-restraints excluded: chain B residue 2601 VAL Chi-restraints excluded: chain B residue 2760 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 518 TRP Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 1193 ILE Chi-restraints excluded: chain C residue 1433 SER Chi-restraints excluded: chain C residue 1671 VAL Chi-restraints excluded: chain C residue 1724 TYR Chi-restraints excluded: chain C residue 1977 PHE Chi-restraints excluded: chain C residue 2303 PHE Chi-restraints excluded: chain C residue 2304 LEU Chi-restraints excluded: chain C residue 2400 VAL Chi-restraints excluded: chain C residue 2577 TRP Chi-restraints excluded: chain C residue 2685 THR Chi-restraints excluded: chain C residue 2767 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 306 optimal weight: 0.5980 chunk 190 optimal weight: 10.0000 chunk 523 optimal weight: 0.1980 chunk 436 optimal weight: 0.6980 chunk 192 optimal weight: 0.8980 chunk 477 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 454 optimal weight: 0.7980 chunk 330 optimal weight: 0.4980 chunk 165 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.076926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.059580 restraints weight = 221312.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.061273 restraints weight = 101808.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.062400 restraints weight = 63909.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.062957 restraints weight = 47823.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.063439 restraints weight = 41409.332| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 46140 Z= 0.107 Angle : 0.595 13.021 62625 Z= 0.286 Chirality : 0.040 0.355 7110 Planarity : 0.004 0.062 7569 Dihedral : 3.879 31.669 5910 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.90 % Allowed : 15.23 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.78 (0.12), residues: 5358 helix: 1.86 (0.09), residues: 3534 sheet: -0.71 (0.32), residues: 216 loop : -2.52 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2462 TYR 0.032 0.001 TYR B 34 PHE 0.029 0.001 PHE A1977 TRP 0.026 0.001 TRP C2604 HIS 0.004 0.001 HIS B1559 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (46125) covalent geometry : angle 0.59440 / 0.29 (62583) SS BOND : bond 0.00045 / 0.02 ( 3) SS BOND : angle 0.11131 / 0.06 ( 6) hydrogen bonds : bond 0.03329 / 2.17 ( 2721) hydrogen bonds : angle 3.60870 / 2.56 ( 8052) link_NAG-ASN : bond 0.00186 / 0.12 ( 12) link_NAG-ASN : angle 1.03845 / 0.61 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8402.45 seconds wall clock time: 145 minutes 25.10 seconds (8725.10 seconds total)