Starting phenix.real_space_refine on Sun Aug 24 05:27:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u1s_41826/08_2025/8u1s_41826.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u1s_41826/08_2025/8u1s_41826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u1s_41826/08_2025/8u1s_41826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u1s_41826/08_2025/8u1s_41826.map" model { file = "/net/cci-nas-00/data/ceres_data/8u1s_41826/08_2025/8u1s_41826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u1s_41826/08_2025/8u1s_41826.cif" } resolution = 3.21 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= 0.000 sd= 0.000 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 132 5.16 5 C 11044 2.51 5 N 2966 2.21 5 O 3323 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17465 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2613 Classifications: {'peptide': 337} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 321} Chain breaks: 4 Chain: "J" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 949 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "K" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "G" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 949 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "I" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "E" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 949 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "F" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "H" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 949 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "L" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "B" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2559 Classifications: {'peptide': 331} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 315} Chain breaks: 4 Chain: "C" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2548 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 313} Chain breaks: 4 Chain: "D" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2569 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 316} Chain breaks: 4 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.40, per 1000 atoms: 0.19 Number of scatterers: 17465 At special positions: 0 Unit cell: (168.2, 168.2, 70.325, 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 132 16.00 O 3323 8.00 N 2966 7.00 C 11044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 420 " distance=2.03 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS A 229 " distance=2.01 Simple disulfide: pdb=" SG CYS A 231 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 291 " distance=2.02 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 289 " distance=1.83 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 424 " - pdb=" SG CYS A 447 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.02 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.06 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.01 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 420 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 182 " - pdb=" SG CYS B 229 " distance=2.01 Simple disulfide: pdb=" SG CYS B 231 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 291 " distance=2.02 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 289 " distance=2.02 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.02 Simple disulfide: pdb=" SG CYS B 424 " - pdb=" SG CYS B 447 " distance=2.05 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 420 " distance=2.03 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 229 " distance=2.01 Simple disulfide: pdb=" SG CYS C 231 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 277 " - pdb=" SG CYS C 291 " distance=2.02 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 289 " distance=2.02 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 337 " distance=2.04 Simple disulfide: pdb=" SG CYS C 424 " - pdb=" SG CYS C 447 " distance=2.04 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 420 " distance=2.03 Simple disulfide: pdb=" SG CYS D 122 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 182 " - pdb=" SG CYS D 229 " distance=2.12 Simple disulfide: pdb=" SG CYS D 231 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 277 " - pdb=" SG CYS D 291 " distance=2.02 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 289 " distance=2.02 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.04 Simple disulfide: pdb=" SG CYS D 424 " - pdb=" SG CYS D 447 " distance=2.05 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 A 501 " - " ASN A 284 " " NAG B 501 " - " ASN B 284 " " NAG C 501 " - " ASN C 284 " " NAG D 501 " - " ASN D 284 " Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 693.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4066 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 45 sheets defined 2.7% alpha, 40.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'J' and resid 63 through 67 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'G' and resid 61 through 67 removed outlier: 5.849A pdb=" N SER G 65 " --> pdb=" O SER G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.990A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 97 through 100B Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 386 through 390 removed outlier: 4.077A pdb=" N ASP B 390 " --> pdb=" O PRO B 387 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 98 removed outlier: 6.768A pdb=" N ILE A 445 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU A 97 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR A 443 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 122 removed outlier: 5.623A pdb=" N GLU A 117 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU A 132 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET A 174 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N SER A 158 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N PHE A 172 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 183 removed outlier: 3.529A pdb=" N SER A 178 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP A 212 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TYR A 206 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N TYR A 210 " --> pdb=" O TYR A 206 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 224 Processing sheet with id=AA5, first strand: chain 'A' and resid 222 through 224 removed outlier: 6.624A pdb=" N ARG A 257 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 268 through 269 removed outlier: 6.554A pdb=" N THR A 268 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N LEU A 316 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR A 286 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE A 281 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU A 288 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N CYS A 279 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ALA A 290 " --> pdb=" O CYS A 277 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N CYS A 277 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 356 removed outlier: 8.106A pdb=" N MET A 375 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL A 401 " --> pdb=" O MET A 375 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N MET A 377 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL A 399 " --> pdb=" O MET A 377 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU A 379 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.000A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.454A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AB4, first strand: chain 'G' and resid 11 through 12 removed outlier: 5.957A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.559A pdb=" N ALA I 84 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'E' and resid 11 through 12 removed outlier: 8.268A pdb=" N TYR E 34 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N SER E 52 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TRP E 35A" --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER E 50 " --> pdb=" O TRP E 35A" (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AC1, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.596A pdb=" N ALA F 84 " --> pdb=" O VAL F 104 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'H' and resid 11 through 12 removed outlier: 8.416A pdb=" N TYR H 34 " --> pdb=" O SER H 52 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER H 52 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TRP H 35A" --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.764A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER L 67 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 14 removed outlier: 3.585A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 93 through 98 removed outlier: 6.803A pdb=" N ILE B 445 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU B 97 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR B 443 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 116 through 123 removed outlier: 5.502A pdb=" N GLU B 117 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU B 132 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET B 174 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER B 158 " --> pdb=" O PHE B 172 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N PHE B 172 " --> pdb=" O SER B 158 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 178 through 183 removed outlier: 3.511A pdb=" N SER B 178 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TYR B 206 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR B 210 " --> pdb=" O TYR B 206 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 223 through 224 Processing sheet with id=AD2, first strand: chain 'B' and resid 223 through 224 removed outlier: 6.508A pdb=" N ARG B 257 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 268 through 269 removed outlier: 7.390A pdb=" N THR B 286 " --> pdb=" O PHE B 281 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE B 281 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU B 288 " --> pdb=" O CYS B 279 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N CYS B 279 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ALA B 290 " --> pdb=" O CYS B 277 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N CYS B 277 " --> pdb=" O ALA B 290 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 352 through 356 removed outlier: 7.002A pdb=" N MET B 377 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL B 399 " --> pdb=" O MET B 377 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU B 379 " --> pdb=" O SER B 397 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 93 through 98 removed outlier: 6.853A pdb=" N ILE C 445 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU C 97 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR C 443 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 116 through 123 removed outlier: 5.566A pdb=" N GLU C 117 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU C 132 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU C 126 " --> pdb=" O GLY C 123 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET C 174 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N SER C 158 " --> pdb=" O PHE C 172 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N PHE C 172 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 178 through 183 removed outlier: 3.898A pdb=" N SER C 178 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU C 202 " --> pdb=" O THR C 213 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR C 213 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL C 204 " --> pdb=" O THR C 211 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AD9, first strand: chain 'C' and resid 223 through 224 removed outlier: 6.644A pdb=" N ARG C 257 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ILE C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 268 through 269 removed outlier: 6.694A pdb=" N THR C 268 " --> pdb=" O ILE C 314 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N LEU C 316 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N THR C 286 " --> pdb=" O PHE C 281 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N PHE C 281 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU C 288 " --> pdb=" O CYS C 279 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS C 279 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ALA C 290 " --> pdb=" O CYS C 277 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N CYS C 277 " --> pdb=" O ALA C 290 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 352 through 356 removed outlier: 7.027A pdb=" N MET C 375 " --> pdb=" O PRO C 402 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N MET C 377 " --> pdb=" O MET C 400 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL C 381 " --> pdb=" O PHE C 396 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE C 396 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 92 through 98 removed outlier: 6.839A pdb=" N ILE D 445 " --> pdb=" O ALA D 95 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU D 97 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR D 443 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 115 through 123 removed outlier: 5.449A pdb=" N GLU D 117 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU D 132 " --> pdb=" O GLU D 117 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N HIS D 155 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N SER D 158 " --> pdb=" O PHE D 172 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N PHE D 172 " --> pdb=" O SER D 158 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LYS D 160 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N SER D 170 " --> pdb=" O LYS D 160 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 179 through 183 removed outlier: 6.167A pdb=" N TYR D 206 " --> pdb=" O TYR D 210 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR D 210 " --> pdb=" O TYR D 206 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 222 through 223 Processing sheet with id=AE7, first strand: chain 'D' and resid 222 through 223 removed outlier: 3.941A pdb=" N GLU D 250 " --> pdb=" O ASP D 242 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG D 257 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE D 261 " --> pdb=" O ARG D 257 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 268 through 269 removed outlier: 6.622A pdb=" N THR D 268 " --> pdb=" O ILE D 314 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N LEU D 316 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR D 286 " --> pdb=" O PHE D 281 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N PHE D 281 " --> pdb=" O THR D 286 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU D 288 " --> pdb=" O CYS D 279 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N CYS D 279 " --> pdb=" O GLU D 288 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA D 290 " --> pdb=" O CYS D 277 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N CYS D 277 " --> pdb=" O ALA D 290 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 352 through 354 removed outlier: 7.318A pdb=" N MET D 375 " --> pdb=" O PRO D 402 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N MET D 377 " --> pdb=" O MET D 400 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL D 381 " --> pdb=" O PHE D 396 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N PHE D 396 " --> pdb=" O VAL D 381 " (cutoff:3.500A) 604 hydrogen bonds defined for protein. 1527 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: 3.04 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3876 1.32 - 1.46: 6319 1.46 - 1.60: 7488 1.60 - 1.75: 59 1.75 - 1.89: 147 Bond restraints: 17889 Sorted by residual: bond pdb=" CB HIS D 354 " pdb=" CG HIS D 354 " ideal model delta sigma weight residual 1.497 1.369 0.128 1.40e-02 5.10e+03 8.42e+01 bond pdb=" CB HIS C 354 " pdb=" CG HIS C 354 " ideal model delta sigma weight residual 1.497 1.370 0.127 1.40e-02 5.10e+03 8.24e+01 bond pdb=" CB HIS A 354 " pdb=" CG HIS A 354 " ideal model delta sigma weight residual 1.497 1.371 0.126 1.40e-02 5.10e+03 8.11e+01 bond pdb=" CB HIS B 354 " pdb=" CG HIS B 354 " ideal model delta sigma weight residual 1.497 1.377 0.120 1.40e-02 5.10e+03 7.40e+01 bond pdb=" CB LEU C 454 " pdb=" CG LEU C 454 " ideal model delta sigma weight residual 1.530 1.676 -0.146 2.00e-02 2.50e+03 5.32e+01 ... (remaining 17884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.60: 23342 4.60 - 9.19: 831 9.19 - 13.79: 32 13.79 - 18.39: 1 18.39 - 22.99: 1 Bond angle restraints: 24207 Sorted by residual: angle pdb=" C PRO F 59 " pdb=" N SER F 60 " pdb=" CA SER F 60 " ideal model delta sigma weight residual 122.31 99.32 22.99 2.00e+00 2.50e-01 1.32e+02 angle pdb=" N TYR F 94 " pdb=" CA TYR F 94 " pdb=" CB TYR F 94 " ideal model delta sigma weight residual 110.25 125.19 -14.94 1.36e+00 5.41e-01 1.21e+02 angle pdb=" N SER K 95 " pdb=" CA SER K 95 " pdb=" C SER K 95 " ideal model delta sigma weight residual 114.56 101.67 12.89 1.27e+00 6.20e-01 1.03e+02 angle pdb=" C GLY B 335 " pdb=" N PRO B 336 " pdb=" CA PRO B 336 " ideal model delta sigma weight residual 120.21 128.12 -7.91 9.60e-01 1.09e+00 6.78e+01 angle pdb=" N LYS A 371 " pdb=" CA LYS A 371 " pdb=" C LYS A 371 " ideal model delta sigma weight residual 113.28 103.28 10.00 1.22e+00 6.72e-01 6.72e+01 ... (remaining 24202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 10297 17.92 - 35.84: 313 35.84 - 53.76: 67 53.76 - 71.67: 33 71.67 - 89.59: 13 Dihedral angle restraints: 10723 sinusoidal: 4336 harmonic: 6387 Sorted by residual: dihedral pdb=" CD ARG G 95 " pdb=" NE ARG G 95 " pdb=" CZ ARG G 95 " pdb=" NH1 ARG G 95 " ideal model delta sinusoidal sigma weight residual 0.00 81.07 -81.07 1 1.00e+01 1.00e-02 8.11e+01 dihedral pdb=" CB CYS D 182 " pdb=" SG CYS D 182 " pdb=" SG CYS D 229 " pdb=" CB CYS D 229 " ideal model delta sinusoidal sigma weight residual 93.00 39.55 53.45 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" N TYR F 94 " pdb=" C TYR F 94 " pdb=" CA TYR F 94 " pdb=" CB TYR F 94 " ideal model delta harmonic sigma weight residual 122.80 137.00 -14.20 0 2.50e+00 1.60e-01 3.23e+01 ... (remaining 10720 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1968 0.112 - 0.224: 559 0.224 - 0.335: 67 0.335 - 0.447: 15 0.447 - 0.559: 6 Chirality restraints: 2615 Sorted by residual: chirality pdb=" C1 NAG D 501 " pdb=" ND2 ASN D 284 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.80e+00 chirality pdb=" CG LEU C 454 " pdb=" CB LEU C 454 " pdb=" CD1 LEU C 454 " pdb=" CD2 LEU C 454 " both_signs ideal model delta sigma weight residual False -2.59 -3.11 0.53 2.00e-01 2.50e+01 6.89e+00 chirality pdb=" CB ILE D 114 " pdb=" CA ILE D 114 " pdb=" CG1 ILE D 114 " pdb=" CG2 ILE D 114 " both_signs ideal model delta sigma weight residual False 2.64 3.17 -0.52 2.00e-01 2.50e+01 6.82e+00 ... (remaining 2612 not shown) Planarity restraints: 3067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 501 " -0.174 2.00e-02 2.50e+03 1.44e-01 2.60e+02 pdb=" C7 NAG B 501 " 0.044 2.00e-02 2.50e+03 pdb=" C8 NAG B 501 " -0.126 2.00e-02 2.50e+03 pdb=" N2 NAG B 501 " 0.236 2.00e-02 2.50e+03 pdb=" O7 NAG B 501 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 95 " -1.108 9.50e-02 1.11e+02 4.96e-01 1.48e+02 pdb=" NE ARG G 95 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG G 95 " 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG G 95 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG G 95 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 330 " 0.029 2.00e-02 2.50e+03 6.05e-02 3.65e+01 pdb=" C ASP D 330 " -0.104 2.00e-02 2.50e+03 pdb=" O ASP D 330 " 0.041 2.00e-02 2.50e+03 pdb=" N GLY D 331 " 0.034 2.00e-02 2.50e+03 ... (remaining 3064 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 4 2.03 - 2.75: 3248 2.75 - 3.47: 22362 3.47 - 4.18: 46584 4.18 - 4.90: 78074 Nonbonded interactions: 150272 Sorted by model distance: nonbonded pdb=" OH TYR A 214 " pdb=" NH2 ARG A 252 " model vdw 1.314 3.120 nonbonded pdb=" NE ARG A 252 " pdb=" OE2 GLU A 264 " model vdw 1.548 3.120 nonbonded pdb=" CE2 TYR I 94 " pdb=" OE1 GLU C 338 " model vdw 1.749 3.340 nonbonded pdb=" OE1 GLU A 338 " pdb=" CE1 TYR L 94 " model vdw 1.955 3.340 nonbonded pdb=" OD1 ASP J 101 " pdb=" CD2 TYR J 102 " model vdw 2.081 3.340 ... (remaining 150267 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 78 through 100 or resid 115 through 150 or resid 155 throu \ gh 441 or resid 443 through 454 or resid 501)) selection = (chain 'B' and (resid 78 through 430 or resid 441 or resid 443 through 501)) selection = chain 'C' selection = (chain 'D' and (resid 78 through 100 or resid 115 through 441 or resid 443 throu \ gh 454 or resid 501)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.610 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 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 : 0.023 0.204 17933 Z= 1.220 Angle : 1.952 22.986 24299 Z= 1.282 Chirality : 0.105 0.559 2615 Planarity : 0.014 0.496 3063 Dihedral : 10.173 89.593 6537 Min Nonbonded Distance : 1.314 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.04 % Favored : 93.32 % Rotamer: Outliers : 0.79 % Allowed : 1.16 % Favored : 98.05 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: -0.28 (0.17), residues: 2185 helix: -4.85 (0.33), residues: 6 sheet: 0.59 (0.18), residues: 831 loop : -0.66 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 327 TYR 0.079 0.009 TYR A 322 PHE 0.053 0.007 PHE J 78 TRP 0.067 0.012 TRP E 103 HIS 0.016 0.003 HIS B 273 Details of bonding type rmsd covalent geometry : bond 0.02281 (17889) covalent geometry : angle 1.94799 (24207) SS BOND : bond 0.03684 ( 40) SS BOND : angle 2.35846 ( 80) hydrogen bonds : bond 0.16789 ( 591) hydrogen bonds : angle 8.89306 ( 1527) link_NAG-ASN : bond 0.05981 ( 4) link_NAG-ASN : angle 4.44602 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 678 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 HIS cc_start: 0.7413 (t70) cc_final: 0.7086 (t-170) REVERT: A 241 THR cc_start: 0.8068 (t) cc_final: 0.7705 (m) REVERT: J 32 THR cc_start: 0.7756 (p) cc_final: 0.7311 (t) REVERT: G 102 TYR cc_start: 0.7612 (m-80) cc_final: 0.7393 (m-10) REVERT: I 35 TRP cc_start: 0.6981 (m100) cc_final: 0.6672 (m100) REVERT: I 90 GLN cc_start: 0.6792 (mm-40) cc_final: 0.6549 (mm-40) REVERT: F 18 ARG cc_start: 0.7851 (ttm170) cc_final: 0.7647 (ttm170) REVERT: L 78 LEU cc_start: 0.7394 (tp) cc_final: 0.7190 (tt) REVERT: C 116 ARG cc_start: 0.7166 (mmm-85) cc_final: 0.6911 (mmm160) REVERT: C 117 GLU cc_start: 0.7760 (mp0) cc_final: 0.7379 (mp0) REVERT: D 338 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6478 (tp30) outliers start: 15 outliers final: 7 residues processed: 689 average time/residue: 0.1373 time to fit residues: 137.1099 Evaluate side-chains 422 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 414 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 338 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 216 optimal weight: 0.0270 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 0.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 235 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN E 3 GLN F 79 GLN B 235 ASN B 329 ASN C 169 ASN C 220 ASN C 230 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.177777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.153858 restraints weight = 23580.759| |-----------------------------------------------------------------------------| r_work (start): 0.4471 rms_B_bonded: 3.70 r_work: 0.4341 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 17933 Z= 0.201 Angle : 0.845 15.341 24299 Z= 0.455 Chirality : 0.051 0.307 2615 Planarity : 0.006 0.047 3063 Dihedral : 6.969 59.228 2529 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.22 % Favored : 94.14 % Rotamer: Outliers : 3.32 % Allowed : 11.01 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.69 (0.17), residues: 2185 helix: -4.87 (0.33), residues: 6 sheet: 0.36 (0.16), residues: 913 loop : -1.08 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 300 TYR 0.028 0.002 TYR K 91 PHE 0.023 0.002 PHE G 100E TRP 0.033 0.002 TRP A 408 HIS 0.008 0.002 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00436 (17889) covalent geometry : angle 0.83419 (24207) SS BOND : bond 0.00417 ( 40) SS BOND : angle 2.29602 ( 80) hydrogen bonds : bond 0.05478 ( 591) hydrogen bonds : angle 7.30289 ( 1527) link_NAG-ASN : bond 0.00489 ( 4) link_NAG-ASN : angle 2.64317 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 515 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 HIS cc_start: 0.8142 (t70) cc_final: 0.7669 (t-170) REVERT: A 194 ASP cc_start: 0.6586 (t0) cc_final: 0.6208 (t0) REVERT: A 232 ILE cc_start: 0.8137 (mt) cc_final: 0.7812 (tp) REVERT: A 241 THR cc_start: 0.7490 (t) cc_final: 0.6714 (m) REVERT: A 308 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: A 388 TRP cc_start: 0.7685 (m-10) cc_final: 0.7414 (m-10) REVERT: A 418 LYS cc_start: 0.8999 (mttm) cc_final: 0.8658 (mmtm) REVERT: J 32 THR cc_start: 0.7851 (p) cc_final: 0.7614 (t) REVERT: K 5 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8183 (p) REVERT: K 33 LEU cc_start: 0.8717 (tp) cc_final: 0.8484 (tt) REVERT: G 57 ASN cc_start: 0.7444 (OUTLIER) cc_final: 0.6816 (p0) REVERT: I 36 TYR cc_start: 0.6434 (m-80) cc_final: 0.6231 (m-10) REVERT: I 76 SER cc_start: 0.6336 (m) cc_final: 0.5956 (m) REVERT: E 82 LEU cc_start: 0.8478 (tt) cc_final: 0.8167 (tt) REVERT: E 82 ARG cc_start: 0.7532 (mtm-85) cc_final: 0.6602 (mtm-85) REVERT: E 112 SER cc_start: 0.8339 (t) cc_final: 0.7834 (p) REVERT: F 27 GLN cc_start: 0.8186 (mp10) cc_final: 0.7977 (mp10) REVERT: F 82 ASP cc_start: 0.7570 (m-30) cc_final: 0.7168 (m-30) REVERT: F 90 GLN cc_start: 0.7361 (pt0) cc_final: 0.7057 (pt0) REVERT: H 34 TYR cc_start: 0.8367 (m-80) cc_final: 0.8034 (m-80) REVERT: H 105 GLN cc_start: 0.7594 (mp10) cc_final: 0.7274 (mp10) REVERT: H 112 SER cc_start: 0.8135 (t) cc_final: 0.7753 (p) REVERT: L 94 TYR cc_start: 0.7749 (m-80) cc_final: 0.7371 (m-80) REVERT: B 83 PRO cc_start: 0.7966 (Cg_exo) cc_final: 0.7700 (Cg_endo) REVERT: B 187 GLU cc_start: 0.8333 (tp30) cc_final: 0.8010 (tp30) REVERT: B 295 ARG cc_start: 0.8340 (tpp-160) cc_final: 0.7777 (tpp-160) REVERT: B 322 TYR cc_start: 0.6651 (m-10) cc_final: 0.6188 (m-10) REVERT: B 338 GLU cc_start: 0.7357 (pt0) cc_final: 0.6830 (pp20) REVERT: B 360 LYS cc_start: 0.7314 (mtpt) cc_final: 0.7067 (ttpt) REVERT: B 405 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6484 (mt-10) REVERT: B 417 ASP cc_start: 0.8862 (t0) cc_final: 0.8487 (t0) REVERT: C 116 ARG cc_start: 0.6050 (mmm-85) cc_final: 0.5724 (mmm160) REVERT: C 117 GLU cc_start: 0.7485 (mp0) cc_final: 0.6488 (mp0) REVERT: C 295 ARG cc_start: 0.8135 (tpp-160) cc_final: 0.7927 (tpp-160) REVERT: C 340 ASP cc_start: 0.7676 (p0) cc_final: 0.7188 (p0) REVERT: C 357 MET cc_start: 0.8606 (mtm) cc_final: 0.7966 (mtm) REVERT: C 360 LYS cc_start: 0.7729 (mttt) cc_final: 0.7348 (mtmm) REVERT: D 187 GLU cc_start: 0.8638 (tp30) cc_final: 0.8358 (tp30) REVERT: D 201 LEU cc_start: 0.8416 (tp) cc_final: 0.8087 (tp) REVERT: D 215 HIS cc_start: 0.7755 (m-70) cc_final: 0.6942 (m90) REVERT: D 220 ASN cc_start: 0.7446 (m-40) cc_final: 0.6988 (m110) REVERT: D 242 ASP cc_start: 0.7170 (t0) cc_final: 0.6910 (t0) REVERT: D 338 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6238 (tm-30) REVERT: D 417 ASP cc_start: 0.8972 (t0) cc_final: 0.8627 (t0) outliers start: 63 outliers final: 32 residues processed: 549 average time/residue: 0.1439 time to fit residues: 117.4589 Evaluate side-chains 476 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 440 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 338 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 154 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 72 optimal weight: 0.0970 chunk 35 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 GLN K 79 GLN G 3 GLN G 57 ASN I 79 GLN I 90 GLN E 3 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN B 220 ASN B 230 ASN C 169 ASN ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.163084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.138999 restraints weight = 24765.894| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 3.74 r_work: 0.4125 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 17933 Z= 0.335 Angle : 0.866 8.919 24299 Z= 0.463 Chirality : 0.053 0.233 2615 Planarity : 0.006 0.056 3063 Dihedral : 6.615 58.633 2523 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.22 % Favored : 93.32 % Rotamer: Outliers : 4.69 % Allowed : 13.70 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.21 (0.17), residues: 2185 helix: -4.87 (0.33), residues: 6 sheet: -0.02 (0.17), residues: 917 loop : -1.42 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 300 TYR 0.030 0.003 TYR L 94 PHE 0.035 0.003 PHE E 100E TRP 0.024 0.003 TRP B 177 HIS 0.016 0.003 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00758 (17889) covalent geometry : angle 0.86004 (24207) SS BOND : bond 0.01001 ( 40) SS BOND : angle 1.82884 ( 80) hydrogen bonds : bond 0.05310 ( 591) hydrogen bonds : angle 7.03536 ( 1527) link_NAG-ASN : bond 0.00575 ( 4) link_NAG-ASN : angle 2.21543 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 438 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.7195 (tm-30) cc_final: 0.6542 (tm-30) REVERT: A 134 HIS cc_start: 0.8098 (t70) cc_final: 0.7606 (t-170) REVERT: A 169 ASN cc_start: 0.7937 (m-40) cc_final: 0.7547 (m110) REVERT: J 38 ARG cc_start: 0.8016 (ptm-80) cc_final: 0.7642 (ptm-80) REVERT: J 43 LYS cc_start: 0.9188 (mmtm) cc_final: 0.8954 (mmtt) REVERT: J 72 ASP cc_start: 0.7457 (t0) cc_final: 0.7239 (t0) REVERT: J 112 SER cc_start: 0.7904 (t) cc_final: 0.7374 (p) REVERT: K 48 ILE cc_start: 0.7083 (mm) cc_final: 0.6878 (mt) REVERT: G 34 TYR cc_start: 0.8515 (m-80) cc_final: 0.8126 (m-80) REVERT: I 3 GLN cc_start: 0.7607 (tt0) cc_final: 0.7034 (tp40) REVERT: E 82 LEU cc_start: 0.8341 (tt) cc_final: 0.8112 (tt) REVERT: E 82 ARG cc_start: 0.7798 (mtm-85) cc_final: 0.6883 (mtm-85) REVERT: F 82 ASP cc_start: 0.7566 (m-30) cc_final: 0.7204 (m-30) REVERT: H 34 TYR cc_start: 0.8457 (m-80) cc_final: 0.8033 (m-80) REVERT: H 43 LYS cc_start: 0.8422 (mmtt) cc_final: 0.8124 (mmtm) REVERT: H 82 LEU cc_start: 0.8275 (tt) cc_final: 0.7896 (tt) REVERT: H 100 TRP cc_start: 0.7900 (m100) cc_final: 0.7454 (m100) REVERT: B 295 ARG cc_start: 0.8416 (tpp-160) cc_final: 0.7913 (tpp-160) REVERT: B 322 TYR cc_start: 0.6532 (m-10) cc_final: 0.6182 (m-10) REVERT: B 403 MET cc_start: 0.8024 (mtp) cc_final: 0.7701 (ttm) REVERT: C 79 GLU cc_start: 0.8369 (tp30) cc_final: 0.7971 (tp30) REVERT: C 117 GLU cc_start: 0.7644 (mp0) cc_final: 0.6702 (mp0) REVERT: C 230 ASN cc_start: 0.8294 (m110) cc_final: 0.7849 (m-40) REVERT: C 295 ARG cc_start: 0.8229 (tpp-160) cc_final: 0.7998 (tpp-160) REVERT: C 327 ARG cc_start: 0.6485 (ptp90) cc_final: 0.6254 (ptt-90) REVERT: C 357 MET cc_start: 0.8632 (mtm) cc_final: 0.8410 (mtm) REVERT: D 215 HIS cc_start: 0.7885 (m-70) cc_final: 0.6994 (m90) REVERT: D 338 GLU cc_start: 0.7324 (tm-30) cc_final: 0.6625 (pp20) REVERT: D 417 ASP cc_start: 0.8996 (t0) cc_final: 0.8734 (t0) outliers start: 89 outliers final: 67 residues processed: 486 average time/residue: 0.1458 time to fit residues: 105.9624 Evaluate side-chains 466 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 399 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 332 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 160 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 150 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 182 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 GLN G 3 GLN I 90 GLN I 100 GLN E 3 GLN C 169 ASN D 220 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.165234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.141855 restraints weight = 24699.451| |-----------------------------------------------------------------------------| r_work (start): 0.4328 rms_B_bonded: 3.62 r_work: 0.4190 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17933 Z= 0.190 Angle : 0.735 9.128 24299 Z= 0.391 Chirality : 0.048 0.217 2615 Planarity : 0.005 0.055 3063 Dihedral : 6.071 57.798 2520 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.04 % Favored : 93.50 % Rotamer: Outliers : 4.79 % Allowed : 14.91 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: -1.27 (0.17), residues: 2185 helix: -4.87 (0.33), residues: 6 sheet: -0.04 (0.17), residues: 892 loop : -1.46 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 300 TYR 0.026 0.002 TYR L 94 PHE 0.018 0.002 PHE E 100E TRP 0.017 0.002 TRP K 32 HIS 0.007 0.002 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00429 (17889) covalent geometry : angle 0.72860 (24207) SS BOND : bond 0.00447 ( 40) SS BOND : angle 1.74509 ( 80) hydrogen bonds : bond 0.04508 ( 591) hydrogen bonds : angle 6.70346 ( 1527) link_NAG-ASN : bond 0.00316 ( 4) link_NAG-ASN : angle 1.78311 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 437 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7889 (tt) REVERT: A 134 HIS cc_start: 0.7863 (t70) cc_final: 0.7310 (t-170) REVERT: A 169 ASN cc_start: 0.8105 (m-40) cc_final: 0.7739 (m110) REVERT: A 296 TYR cc_start: 0.8444 (m-10) cc_final: 0.8149 (m-10) REVERT: A 429 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7251 (mtt) REVERT: J 5 GLN cc_start: 0.7351 (mp10) cc_final: 0.7141 (mp10) REVERT: J 38 ARG cc_start: 0.8121 (ptm-80) cc_final: 0.7768 (ptm-80) REVERT: J 53 TYR cc_start: 0.8175 (t80) cc_final: 0.7851 (t80) REVERT: J 72 ASP cc_start: 0.7618 (t0) cc_final: 0.7317 (t0) REVERT: K 89 GLN cc_start: 0.6742 (tt0) cc_final: 0.6171 (tt0) REVERT: G 34 TYR cc_start: 0.8621 (m-80) cc_final: 0.8333 (m-80) REVERT: I 3 GLN cc_start: 0.7904 (tt0) cc_final: 0.7470 (tp40) REVERT: I 36 TYR cc_start: 0.7029 (m-10) cc_final: 0.6703 (m-10) REVERT: E 5 GLN cc_start: 0.8103 (mp-120) cc_final: 0.7666 (mp10) REVERT: E 82 LEU cc_start: 0.8495 (tt) cc_final: 0.7631 (mp) REVERT: E 82 ARG cc_start: 0.7936 (mtm-85) cc_final: 0.7035 (mtm-85) REVERT: E 105 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8263 (mm-40) REVERT: F 82 ASP cc_start: 0.7802 (m-30) cc_final: 0.7554 (m-30) REVERT: H 34 TYR cc_start: 0.8584 (m-80) cc_final: 0.8203 (m-80) REVERT: H 82 LEU cc_start: 0.8483 (tt) cc_final: 0.8141 (tt) REVERT: L 42 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8498 (mp0) REVERT: B 96 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7959 (tt) REVERT: B 134 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.7321 (m90) REVERT: B 295 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7957 (tpp-160) REVERT: B 405 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6927 (mt-10) REVERT: C 117 GLU cc_start: 0.7754 (mp0) cc_final: 0.6773 (mp0) REVERT: C 212 ASP cc_start: 0.7372 (m-30) cc_final: 0.7162 (m-30) REVERT: C 263 LYS cc_start: 0.7314 (ttmt) cc_final: 0.7090 (tttm) REVERT: C 357 MET cc_start: 0.8563 (mtm) cc_final: 0.8112 (mtm) REVERT: D 215 HIS cc_start: 0.7842 (m-70) cc_final: 0.7035 (m90) REVERT: D 338 GLU cc_start: 0.7415 (tm-30) cc_final: 0.6813 (pp20) REVERT: D 417 ASP cc_start: 0.8982 (t0) cc_final: 0.8730 (t0) REVERT: D 418 LYS cc_start: 0.8894 (mptt) cc_final: 0.8495 (mptt) outliers start: 91 outliers final: 63 residues processed: 480 average time/residue: 0.1383 time to fit residues: 99.9534 Evaluate side-chains 457 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 389 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 98 HIS Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 319 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 121 optimal weight: 10.0000 chunk 56 optimal weight: 0.0870 chunk 53 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 chunk 212 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 193 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 3 GLN I 100 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 ASN C 219 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.167534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.143881 restraints weight = 24385.184| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 3.63 r_work: 0.4215 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17933 Z= 0.176 Angle : 0.706 8.674 24299 Z= 0.374 Chirality : 0.047 0.212 2615 Planarity : 0.005 0.081 3063 Dihedral : 5.794 56.837 2520 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.54 % Favored : 93.04 % Rotamer: Outliers : 4.95 % Allowed : 16.07 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: -1.36 (0.17), residues: 2185 helix: -4.87 (0.33), residues: 6 sheet: -0.12 (0.17), residues: 918 loop : -1.53 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 327 TYR 0.023 0.002 TYR L 94 PHE 0.019 0.002 PHE E 100E TRP 0.017 0.002 TRP F 35 HIS 0.006 0.002 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00399 (17889) covalent geometry : angle 0.70123 (24207) SS BOND : bond 0.00445 ( 40) SS BOND : angle 1.54671 ( 80) hydrogen bonds : bond 0.04204 ( 591) hydrogen bonds : angle 6.53624 ( 1527) link_NAG-ASN : bond 0.00293 ( 4) link_NAG-ASN : angle 1.61131 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 414 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7871 (tt) REVERT: A 134 HIS cc_start: 0.7777 (t70) cc_final: 0.7246 (t-170) REVERT: A 169 ASN cc_start: 0.8073 (m-40) cc_final: 0.7714 (m110) REVERT: A 296 TYR cc_start: 0.8388 (m-10) cc_final: 0.8147 (m-10) REVERT: A 308 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: A 429 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.7121 (mtt) REVERT: J 16 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8541 (mt-10) REVERT: J 38 ARG cc_start: 0.8008 (ptm-80) cc_final: 0.7665 (ptm-80) REVERT: J 53 TYR cc_start: 0.8223 (t80) cc_final: 0.7897 (t80) REVERT: J 72 ASP cc_start: 0.7684 (t0) cc_final: 0.7337 (t0) REVERT: K 89 GLN cc_start: 0.6689 (tt0) cc_final: 0.6053 (tt0) REVERT: G 34 TYR cc_start: 0.8631 (m-80) cc_final: 0.8234 (m-80) REVERT: I 3 GLN cc_start: 0.7956 (tt0) cc_final: 0.7531 (tp40) REVERT: I 36 TYR cc_start: 0.6963 (m-10) cc_final: 0.6599 (m-10) REVERT: I 49 TYR cc_start: 0.6407 (m-10) cc_final: 0.6182 (m-10) REVERT: I 69 THR cc_start: 0.7708 (m) cc_final: 0.7332 (m) REVERT: E 5 GLN cc_start: 0.8074 (mp-120) cc_final: 0.7642 (mp10) REVERT: E 16 GLU cc_start: 0.8949 (pt0) cc_final: 0.8576 (pm20) REVERT: E 38 ARG cc_start: 0.8333 (ptm160) cc_final: 0.7892 (ptm160) REVERT: E 82 LEU cc_start: 0.8437 (tt) cc_final: 0.7568 (mp) REVERT: E 82 ARG cc_start: 0.7926 (mtm-85) cc_final: 0.7030 (mtm-85) REVERT: E 100 TRP cc_start: 0.8345 (m-10) cc_final: 0.7690 (m100) REVERT: E 100 PHE cc_start: 0.4010 (OUTLIER) cc_final: 0.2914 (t80) REVERT: F 82 ASP cc_start: 0.7626 (m-30) cc_final: 0.7293 (m-30) REVERT: H 34 TYR cc_start: 0.8507 (m-80) cc_final: 0.8231 (m-80) REVERT: H 82 LEU cc_start: 0.8421 (tt) cc_final: 0.8054 (tt) REVERT: L 30 SER cc_start: 0.8772 (t) cc_final: 0.8566 (p) REVERT: L 42 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8459 (mp0) REVERT: B 96 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7986 (tt) REVERT: B 134 HIS cc_start: 0.7900 (OUTLIER) cc_final: 0.7291 (m90) REVERT: B 169 ASN cc_start: 0.7443 (m-40) cc_final: 0.6975 (m110) REVERT: B 295 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7966 (tpp-160) REVERT: B 405 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6686 (tt0) REVERT: C 79 GLU cc_start: 0.8386 (tp30) cc_final: 0.8028 (tp30) REVERT: C 117 GLU cc_start: 0.7703 (mp0) cc_final: 0.6658 (mp0) REVERT: C 212 ASP cc_start: 0.7370 (m-30) cc_final: 0.7099 (m-30) REVERT: C 357 MET cc_start: 0.8530 (mtm) cc_final: 0.8013 (mtm) REVERT: C 449 MET cc_start: 0.6986 (ptp) cc_final: 0.6391 (ptp) REVERT: D 212 ASP cc_start: 0.8928 (t70) cc_final: 0.8680 (t0) REVERT: D 215 HIS cc_start: 0.7759 (m-70) cc_final: 0.6928 (m90) REVERT: D 338 GLU cc_start: 0.7418 (tm-30) cc_final: 0.6856 (pp20) REVERT: D 417 ASP cc_start: 0.8982 (t0) cc_final: 0.8732 (t0) REVERT: D 418 LYS cc_start: 0.8840 (mptt) cc_final: 0.8509 (mptt) outliers start: 94 outliers final: 65 residues processed: 462 average time/residue: 0.1318 time to fit residues: 92.1339 Evaluate side-chains 465 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 393 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 319 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 163 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 152 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 100 GLN C 155 HIS C 169 ASN C 219 ASN D 220 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.163204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.139897 restraints weight = 24518.008| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 3.58 r_work: 0.4181 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17933 Z= 0.210 Angle : 0.722 7.932 24299 Z= 0.382 Chirality : 0.047 0.208 2615 Planarity : 0.005 0.078 3063 Dihedral : 5.700 57.394 2519 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.00 % Favored : 92.68 % Rotamer: Outliers : 5.69 % Allowed : 16.23 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: -1.49 (0.17), residues: 2185 helix: -4.87 (0.33), residues: 6 sheet: -0.27 (0.17), residues: 928 loop : -1.57 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 77 TYR 0.025 0.002 TYR L 94 PHE 0.024 0.002 PHE E 100E TRP 0.015 0.002 TRP K 32 HIS 0.008 0.002 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00476 (17889) covalent geometry : angle 0.71577 (24207) SS BOND : bond 0.00518 ( 40) SS BOND : angle 1.72264 ( 80) hydrogen bonds : bond 0.04215 ( 591) hydrogen bonds : angle 6.48578 ( 1527) link_NAG-ASN : bond 0.00267 ( 4) link_NAG-ASN : angle 1.51785 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 413 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8078 (tt) REVERT: A 134 HIS cc_start: 0.7683 (t70) cc_final: 0.7201 (t-170) REVERT: A 169 ASN cc_start: 0.8083 (m-40) cc_final: 0.7758 (m110) REVERT: A 296 TYR cc_start: 0.8390 (m-10) cc_final: 0.8181 (m-10) REVERT: A 308 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: A 343 LYS cc_start: 0.6984 (mttt) cc_final: 0.6567 (mmmt) REVERT: A 357 MET cc_start: 0.8367 (mtm) cc_final: 0.8146 (mpp) REVERT: A 429 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.6979 (mtt) REVERT: J 16 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8571 (mt-10) REVERT: J 38 ARG cc_start: 0.8122 (ptm-80) cc_final: 0.7373 (ptm-80) REVERT: J 46 GLU cc_start: 0.7269 (tt0) cc_final: 0.6529 (mp0) REVERT: J 53 TYR cc_start: 0.8399 (t80) cc_final: 0.8081 (t80) REVERT: J 72 ASP cc_start: 0.7811 (t0) cc_final: 0.7508 (t0) REVERT: J 100 PHE cc_start: 0.5919 (OUTLIER) cc_final: 0.4202 (t80) REVERT: K 65 SER cc_start: 0.8517 (t) cc_final: 0.8122 (p) REVERT: G 34 TYR cc_start: 0.8699 (m-80) cc_final: 0.8358 (m-80) REVERT: I 3 GLN cc_start: 0.8084 (tt0) cc_final: 0.7658 (tp40) REVERT: E 5 GLN cc_start: 0.8189 (mp-120) cc_final: 0.7432 (mp10) REVERT: E 16 GLU cc_start: 0.8931 (pt0) cc_final: 0.8511 (pm20) REVERT: E 23 THR cc_start: 0.8831 (m) cc_final: 0.8480 (p) REVERT: E 82 ARG cc_start: 0.8023 (mtm-85) cc_final: 0.7419 (mtm110) REVERT: E 100 PHE cc_start: 0.4422 (OUTLIER) cc_final: 0.3460 (t80) REVERT: F 82 ASP cc_start: 0.7616 (m-30) cc_final: 0.7286 (m-30) REVERT: H 82 LEU cc_start: 0.8528 (tt) cc_final: 0.8167 (tt) REVERT: L 30 SER cc_start: 0.8869 (t) cc_final: 0.8669 (p) REVERT: L 42 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8482 (mp0) REVERT: L 94 TYR cc_start: 0.7899 (m-80) cc_final: 0.7548 (m-80) REVERT: B 96 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8201 (tt) REVERT: B 134 HIS cc_start: 0.7858 (OUTLIER) cc_final: 0.7292 (m90) REVERT: B 169 ASN cc_start: 0.7539 (m-40) cc_final: 0.7100 (m110) REVERT: B 223 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.7158 (mtt-85) REVERT: B 295 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7974 (tpp-160) REVERT: B 405 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6692 (tt0) REVERT: C 117 GLU cc_start: 0.7818 (mp0) cc_final: 0.6824 (mp0) REVERT: C 187 GLU cc_start: 0.8624 (tp30) cc_final: 0.8420 (tm-30) REVERT: C 212 ASP cc_start: 0.7381 (m-30) cc_final: 0.7077 (m-30) REVERT: C 230 ASN cc_start: 0.8279 (m110) cc_final: 0.7851 (m-40) REVERT: C 238 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8391 (tt) REVERT: C 357 MET cc_start: 0.8542 (mtm) cc_final: 0.8077 (mtm) REVERT: D 338 GLU cc_start: 0.7399 (tm-30) cc_final: 0.6827 (pp20) REVERT: D 417 ASP cc_start: 0.8950 (t0) cc_final: 0.8737 (t0) REVERT: D 418 LYS cc_start: 0.8886 (mptt) cc_final: 0.8672 (mptt) outliers start: 108 outliers final: 76 residues processed: 472 average time/residue: 0.1382 time to fit residues: 99.4167 Evaluate side-chains 475 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 389 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 100 PHE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 333 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 113 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 147 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 169 ASN C 219 ASN D 220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.164316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.140992 restraints weight = 24644.557| |-----------------------------------------------------------------------------| r_work (start): 0.4327 rms_B_bonded: 3.59 r_work: 0.4198 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17933 Z= 0.181 Angle : 0.711 8.639 24299 Z= 0.374 Chirality : 0.047 0.212 2615 Planarity : 0.005 0.070 3063 Dihedral : 5.586 57.422 2519 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.86 % Favored : 92.81 % Rotamer: Outliers : 5.11 % Allowed : 17.02 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: -1.52 (0.17), residues: 2185 helix: -4.87 (0.33), residues: 6 sheet: -0.33 (0.17), residues: 921 loop : -1.56 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 77 TYR 0.024 0.002 TYR H 34 PHE 0.021 0.002 PHE E 100E TRP 0.014 0.002 TRP I 32 HIS 0.006 0.002 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00414 (17889) covalent geometry : angle 0.70498 (24207) SS BOND : bond 0.00479 ( 40) SS BOND : angle 1.68518 ( 80) hydrogen bonds : bond 0.04044 ( 591) hydrogen bonds : angle 6.42740 ( 1527) link_NAG-ASN : bond 0.00248 ( 4) link_NAG-ASN : angle 1.43860 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 413 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8068 (tt) REVERT: A 134 HIS cc_start: 0.7644 (t70) cc_final: 0.7169 (t-170) REVERT: A 169 ASN cc_start: 0.8086 (m-40) cc_final: 0.7760 (m110) REVERT: A 232 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.8063 (tp) REVERT: A 296 TYR cc_start: 0.8427 (m-10) cc_final: 0.8195 (m-10) REVERT: A 308 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: A 343 LYS cc_start: 0.7039 (mttt) cc_final: 0.6705 (mttt) REVERT: A 357 MET cc_start: 0.8388 (mtm) cc_final: 0.8123 (mpp) REVERT: A 429 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.6982 (mtt) REVERT: J 16 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8562 (mt-10) REVERT: J 38 ARG cc_start: 0.8101 (ptm-80) cc_final: 0.7427 (ptm-80) REVERT: J 46 GLU cc_start: 0.7343 (tt0) cc_final: 0.6641 (mp0) REVERT: J 53 TYR cc_start: 0.8431 (t80) cc_final: 0.8139 (t80) REVERT: J 72 ASP cc_start: 0.7903 (t0) cc_final: 0.7577 (t0) REVERT: J 100 PHE cc_start: 0.5853 (OUTLIER) cc_final: 0.4234 (t80) REVERT: K 65 SER cc_start: 0.8551 (t) cc_final: 0.8160 (p) REVERT: G 34 TYR cc_start: 0.8695 (m-80) cc_final: 0.8441 (m-80) REVERT: I 3 GLN cc_start: 0.8075 (tt0) cc_final: 0.7663 (tp40) REVERT: E 5 GLN cc_start: 0.8236 (mp-120) cc_final: 0.7496 (mp10) REVERT: E 16 GLU cc_start: 0.8936 (pt0) cc_final: 0.8508 (pm20) REVERT: E 23 THR cc_start: 0.8843 (m) cc_final: 0.8498 (p) REVERT: E 82 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7536 (mtm110) REVERT: E 100 PHE cc_start: 0.4229 (OUTLIER) cc_final: 0.3322 (t80) REVERT: F 82 ASP cc_start: 0.7629 (m-30) cc_final: 0.7302 (m-30) REVERT: H 82 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8143 (tt) REVERT: H 100 TRP cc_start: 0.8076 (m-10) cc_final: 0.7462 (m100) REVERT: L 30 SER cc_start: 0.8875 (t) cc_final: 0.8668 (p) REVERT: L 42 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8491 (mp0) REVERT: L 94 TYR cc_start: 0.7823 (m-80) cc_final: 0.7478 (m-80) REVERT: B 96 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8269 (tt) REVERT: B 134 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.7290 (m90) REVERT: B 169 ASN cc_start: 0.7542 (m-40) cc_final: 0.7126 (m110) REVERT: B 295 ARG cc_start: 0.8511 (tpp-160) cc_final: 0.7994 (tpp-160) REVERT: B 405 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6738 (tt0) REVERT: C 79 GLU cc_start: 0.8382 (tp30) cc_final: 0.8089 (tp30) REVERT: C 117 GLU cc_start: 0.7830 (mp0) cc_final: 0.6783 (mp0) REVERT: C 212 ASP cc_start: 0.7359 (m-30) cc_final: 0.7109 (m-30) REVERT: C 230 ASN cc_start: 0.8231 (m110) cc_final: 0.7801 (m-40) REVERT: C 357 MET cc_start: 0.8514 (mtm) cc_final: 0.8092 (mtm) REVERT: C 377 MET cc_start: 0.4581 (tpt) cc_final: 0.4255 (mmt) REVERT: D 212 ASP cc_start: 0.8938 (t70) cc_final: 0.8687 (t0) REVERT: D 215 HIS cc_start: 0.7755 (m-70) cc_final: 0.6917 (m90) REVERT: D 338 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7031 (pp20) REVERT: D 403 MET cc_start: 0.8975 (ttm) cc_final: 0.8441 (mpp) REVERT: D 417 ASP cc_start: 0.8937 (t0) cc_final: 0.8731 (t0) REVERT: D 418 LYS cc_start: 0.8875 (mptt) cc_final: 0.8640 (mptt) outliers start: 97 outliers final: 72 residues processed: 471 average time/residue: 0.1442 time to fit residues: 102.3356 Evaluate side-chains 468 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 387 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 100 PHE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 333 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 124 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 187 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 169 ASN C 219 ASN D 220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.165491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.142231 restraints weight = 24547.660| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 3.60 r_work: 0.4227 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17933 Z= 0.161 Angle : 0.706 8.396 24299 Z= 0.371 Chirality : 0.047 0.202 2615 Planarity : 0.005 0.063 3063 Dihedral : 5.472 57.631 2519 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.45 % Favored : 93.18 % Rotamer: Outliers : 4.90 % Allowed : 17.97 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: -1.50 (0.18), residues: 2185 helix: -4.86 (0.33), residues: 6 sheet: -0.34 (0.17), residues: 933 loop : -1.52 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 270 TYR 0.023 0.002 TYR L 94 PHE 0.022 0.002 PHE K 62 TRP 0.027 0.001 TRP G 35A HIS 0.005 0.002 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00370 (17889) covalent geometry : angle 0.70025 (24207) SS BOND : bond 0.00435 ( 40) SS BOND : angle 1.69260 ( 80) hydrogen bonds : bond 0.03945 ( 591) hydrogen bonds : angle 6.38166 ( 1527) link_NAG-ASN : bond 0.00249 ( 4) link_NAG-ASN : angle 1.38859 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 408 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8125 (tt) REVERT: A 134 HIS cc_start: 0.7588 (t70) cc_final: 0.7123 (t-170) REVERT: A 169 ASN cc_start: 0.8104 (m-40) cc_final: 0.7791 (m110) REVERT: A 232 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8087 (tp) REVERT: A 296 TYR cc_start: 0.8390 (m-10) cc_final: 0.8147 (m-10) REVERT: A 308 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: A 343 LYS cc_start: 0.7070 (mttt) cc_final: 0.6732 (mttt) REVERT: A 357 MET cc_start: 0.8427 (mtm) cc_final: 0.8158 (mpp) REVERT: A 429 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6807 (mtt) REVERT: J 38 ARG cc_start: 0.8061 (ptm-80) cc_final: 0.7189 (ptm-80) REVERT: J 46 GLU cc_start: 0.7358 (tt0) cc_final: 0.6657 (mp0) REVERT: J 53 TYR cc_start: 0.8474 (t80) cc_final: 0.8192 (t80) REVERT: J 72 ASP cc_start: 0.7919 (t0) cc_final: 0.7587 (t0) REVERT: J 100 PHE cc_start: 0.5791 (OUTLIER) cc_final: 0.4200 (t80) REVERT: K 65 SER cc_start: 0.8551 (t) cc_final: 0.8145 (p) REVERT: K 89 GLN cc_start: 0.6818 (tt0) cc_final: 0.6287 (tt0) REVERT: G 34 TYR cc_start: 0.8717 (m-80) cc_final: 0.8430 (m-80) REVERT: I 3 GLN cc_start: 0.8110 (tt0) cc_final: 0.7737 (tp40) REVERT: I 36 TYR cc_start: 0.7168 (m-10) cc_final: 0.6875 (m-10) REVERT: I 42 GLU cc_start: 0.8267 (mp0) cc_final: 0.8011 (mp0) REVERT: E 5 GLN cc_start: 0.8293 (mp-120) cc_final: 0.7550 (mp10) REVERT: E 23 THR cc_start: 0.8786 (m) cc_final: 0.8522 (p) REVERT: E 82 ARG cc_start: 0.8073 (mtm-85) cc_final: 0.7644 (mtm110) REVERT: E 100 PHE cc_start: 0.4099 (OUTLIER) cc_final: 0.3167 (t80) REVERT: F 82 ASP cc_start: 0.7595 (m-30) cc_final: 0.7265 (m-30) REVERT: H 82 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8168 (tt) REVERT: L 30 SER cc_start: 0.8922 (t) cc_final: 0.8704 (p) REVERT: L 42 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8476 (mp0) REVERT: L 94 TYR cc_start: 0.7657 (m-80) cc_final: 0.7358 (m-80) REVERT: B 134 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.7291 (m90) REVERT: B 169 ASN cc_start: 0.7512 (m-40) cc_final: 0.7134 (m110) REVERT: B 295 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8052 (tpp-160) REVERT: B 405 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6664 (tt0) REVERT: C 79 GLU cc_start: 0.8414 (tp30) cc_final: 0.8071 (tp30) REVERT: C 117 GLU cc_start: 0.7867 (mp0) cc_final: 0.6838 (mp0) REVERT: C 134 HIS cc_start: 0.7767 (OUTLIER) cc_final: 0.6879 (m90) REVERT: C 212 ASP cc_start: 0.7313 (m-30) cc_final: 0.7042 (m-30) REVERT: C 230 ASN cc_start: 0.8196 (m110) cc_final: 0.7777 (m-40) REVERT: D 212 ASP cc_start: 0.8929 (t70) cc_final: 0.8673 (t0) REVERT: D 215 HIS cc_start: 0.7715 (m-70) cc_final: 0.6920 (m90) REVERT: D 263 LYS cc_start: 0.7648 (ttmm) cc_final: 0.7294 (tttm) REVERT: D 338 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7059 (pp20) REVERT: D 403 MET cc_start: 0.8952 (ttm) cc_final: 0.8466 (mpp) REVERT: D 417 ASP cc_start: 0.8902 (t0) cc_final: 0.8680 (t0) REVERT: D 418 LYS cc_start: 0.8881 (mptt) cc_final: 0.8674 (mptt) outliers start: 93 outliers final: 70 residues processed: 463 average time/residue: 0.1414 time to fit residues: 99.4985 Evaluate side-chains 471 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 391 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 100 PHE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 333 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 171 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 153 optimal weight: 6.9990 chunk 218 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 29 optimal weight: 0.0270 chunk 173 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 5 GLN C 169 ASN C 219 ASN D 220 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.168222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.145179 restraints weight = 24375.120| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 3.55 r_work: 0.4257 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17933 Z= 0.154 Angle : 0.719 10.417 24299 Z= 0.376 Chirality : 0.046 0.199 2615 Planarity : 0.005 0.060 3063 Dihedral : 5.449 57.738 2518 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.77 % Favored : 92.86 % Rotamer: Outliers : 4.64 % Allowed : 18.65 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: -1.46 (0.18), residues: 2185 helix: None (None), residues: 0 sheet: -0.32 (0.17), residues: 933 loop : -1.51 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 270 TYR 0.022 0.002 TYR L 94 PHE 0.018 0.002 PHE E 100E TRP 0.029 0.002 TRP F 35 HIS 0.005 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00355 (17889) covalent geometry : angle 0.71142 (24207) SS BOND : bond 0.00416 ( 40) SS BOND : angle 1.90048 ( 80) hydrogen bonds : bond 0.03888 ( 591) hydrogen bonds : angle 6.34581 ( 1527) link_NAG-ASN : bond 0.00245 ( 4) link_NAG-ASN : angle 1.34947 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 404 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8135 (tt) REVERT: A 134 HIS cc_start: 0.7577 (t70) cc_final: 0.6813 (t-170) REVERT: A 169 ASN cc_start: 0.8079 (m-40) cc_final: 0.7757 (m110) REVERT: A 232 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8045 (tp) REVERT: A 296 TYR cc_start: 0.8376 (m-10) cc_final: 0.8143 (m-10) REVERT: A 343 LYS cc_start: 0.7141 (mttt) cc_final: 0.6691 (mtpt) REVERT: A 429 MET cc_start: 0.7123 (mtt) cc_final: 0.6708 (mtt) REVERT: J 38 ARG cc_start: 0.8016 (ptm-80) cc_final: 0.7140 (ptm-80) REVERT: J 46 GLU cc_start: 0.7370 (tt0) cc_final: 0.6662 (mp0) REVERT: J 53 TYR cc_start: 0.8426 (t80) cc_final: 0.8145 (t80) REVERT: J 72 ASP cc_start: 0.7902 (t0) cc_final: 0.7383 (t0) REVERT: J 100 PHE cc_start: 0.5674 (OUTLIER) cc_final: 0.4232 (t80) REVERT: J 105 GLN cc_start: 0.8764 (mp10) cc_final: 0.8542 (mp10) REVERT: K 65 SER cc_start: 0.8551 (t) cc_final: 0.8141 (p) REVERT: K 89 GLN cc_start: 0.6889 (tt0) cc_final: 0.6312 (tt0) REVERT: G 34 TYR cc_start: 0.8692 (m-80) cc_final: 0.8336 (m-80) REVERT: I 3 GLN cc_start: 0.8134 (tt0) cc_final: 0.7758 (tp40) REVERT: I 36 TYR cc_start: 0.7155 (m-10) cc_final: 0.6866 (m-10) REVERT: E 5 GLN cc_start: 0.8279 (mp-120) cc_final: 0.7473 (mp10) REVERT: E 16 GLU cc_start: 0.8814 (pt0) cc_final: 0.8399 (pm20) REVERT: E 23 THR cc_start: 0.8768 (m) cc_final: 0.8542 (p) REVERT: E 38 ARG cc_start: 0.8338 (ptm160) cc_final: 0.8007 (ptm160) REVERT: E 82 ARG cc_start: 0.8209 (mtm-85) cc_final: 0.7655 (mtm110) REVERT: E 100 PHE cc_start: 0.3861 (OUTLIER) cc_final: 0.3001 (t80) REVERT: F 82 ASP cc_start: 0.7522 (m-30) cc_final: 0.7199 (m-30) REVERT: H 82 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8105 (tt) REVERT: L 30 SER cc_start: 0.8850 (t) cc_final: 0.8632 (p) REVERT: L 42 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8457 (mp0) REVERT: L 94 TYR cc_start: 0.7543 (m-80) cc_final: 0.7265 (m-80) REVERT: B 134 HIS cc_start: 0.7727 (OUTLIER) cc_final: 0.7304 (m90) REVERT: B 169 ASN cc_start: 0.7537 (m-40) cc_final: 0.7123 (m110) REVERT: B 295 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8086 (tpp-160) REVERT: B 358 LYS cc_start: 0.9231 (ttmm) cc_final: 0.8885 (tppt) REVERT: B 405 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6577 (tt0) REVERT: C 79 GLU cc_start: 0.8427 (tp30) cc_final: 0.8081 (tp30) REVERT: C 134 HIS cc_start: 0.7724 (OUTLIER) cc_final: 0.6946 (m90) REVERT: C 212 ASP cc_start: 0.7266 (m-30) cc_final: 0.6985 (m-30) REVERT: C 418 LYS cc_start: 0.8767 (mmtm) cc_final: 0.8375 (mmtp) REVERT: D 212 ASP cc_start: 0.8922 (t70) cc_final: 0.8632 (t0) REVERT: D 215 HIS cc_start: 0.7672 (m-70) cc_final: 0.6866 (m90) REVERT: D 263 LYS cc_start: 0.7572 (ttmm) cc_final: 0.7233 (tttm) REVERT: D 338 GLU cc_start: 0.7450 (tm-30) cc_final: 0.6984 (pp20) REVERT: D 403 MET cc_start: 0.8927 (ttm) cc_final: 0.8443 (mpp) REVERT: D 417 ASP cc_start: 0.8878 (t0) cc_final: 0.8640 (t0) REVERT: D 418 LYS cc_start: 0.8871 (mptt) cc_final: 0.8623 (mptt) outliers start: 88 outliers final: 69 residues processed: 458 average time/residue: 0.1401 time to fit residues: 97.6635 Evaluate side-chains 459 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 382 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain J residue 100 PHE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 333 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 116 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN C 169 ASN C 219 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.163241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.139888 restraints weight = 24523.905| |-----------------------------------------------------------------------------| r_work (start): 0.4300 rms_B_bonded: 3.63 r_work: 0.4171 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 17933 Z= 0.233 Angle : 0.770 9.995 24299 Z= 0.405 Chirality : 0.048 0.203 2615 Planarity : 0.005 0.055 3063 Dihedral : 5.627 58.852 2517 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.37 % Favored : 92.27 % Rotamer: Outliers : 4.27 % Allowed : 19.49 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: -1.62 (0.18), residues: 2185 helix: None (None), residues: 0 sheet: -0.40 (0.17), residues: 923 loop : -1.64 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 270 TYR 0.024 0.002 TYR L 94 PHE 0.028 0.002 PHE E 100E TRP 0.032 0.002 TRP F 35 HIS 0.009 0.002 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00539 (17889) covalent geometry : angle 0.76113 (24207) SS BOND : bond 0.00519 ( 40) SS BOND : angle 2.06772 ( 80) hydrogen bonds : bond 0.04188 ( 591) hydrogen bonds : angle 6.47323 ( 1527) link_NAG-ASN : bond 0.00235 ( 4) link_NAG-ASN : angle 1.42416 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 385 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8099 (tt) REVERT: A 117 GLU cc_start: 0.7444 (tm-30) cc_final: 0.6880 (tm-30) REVERT: A 134 HIS cc_start: 0.7617 (t70) cc_final: 0.6912 (t-170) REVERT: A 169 ASN cc_start: 0.8099 (m-40) cc_final: 0.7755 (m110) REVERT: A 232 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7968 (tp) REVERT: A 343 LYS cc_start: 0.7166 (mttt) cc_final: 0.6708 (mtpt) REVERT: A 429 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6612 (mtt) REVERT: J 16 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8484 (mt-10) REVERT: J 38 ARG cc_start: 0.8025 (ptm-80) cc_final: 0.7228 (ptm-80) REVERT: J 46 GLU cc_start: 0.7539 (tt0) cc_final: 0.6720 (mp0) REVERT: J 53 TYR cc_start: 0.8445 (t80) cc_final: 0.8196 (t80) REVERT: J 100 PHE cc_start: 0.5949 (OUTLIER) cc_final: 0.4325 (t80) REVERT: J 105 GLN cc_start: 0.8731 (mp10) cc_final: 0.8491 (mp10) REVERT: K 65 SER cc_start: 0.8606 (t) cc_final: 0.8189 (p) REVERT: K 89 GLN cc_start: 0.6830 (tt0) cc_final: 0.6337 (tm-30) REVERT: K 90 GLN cc_start: 0.7275 (pt0) cc_final: 0.6995 (pt0) REVERT: G 18 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7846 (mp) REVERT: G 34 TYR cc_start: 0.8680 (m-80) cc_final: 0.8396 (m-80) REVERT: I 3 GLN cc_start: 0.8145 (tt0) cc_final: 0.7758 (tp40) REVERT: I 42 GLU cc_start: 0.8279 (mp0) cc_final: 0.8015 (mp0) REVERT: E 5 GLN cc_start: 0.8234 (mp-120) cc_final: 0.7746 (mp10) REVERT: E 16 GLU cc_start: 0.8887 (pt0) cc_final: 0.8443 (pm20) REVERT: E 38 ARG cc_start: 0.8257 (ptm160) cc_final: 0.7949 (ptm160) REVERT: E 82 ARG cc_start: 0.8208 (mtm-85) cc_final: 0.7632 (mtm110) REVERT: E 100 PHE cc_start: 0.4014 (OUTLIER) cc_final: 0.3028 (t80) REVERT: F 82 ASP cc_start: 0.7457 (m-30) cc_final: 0.7134 (m-30) REVERT: H 82 LEU cc_start: 0.8451 (tt) cc_final: 0.8013 (tt) REVERT: L 42 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8437 (mp0) REVERT: L 94 TYR cc_start: 0.7854 (m-80) cc_final: 0.7527 (m-80) REVERT: B 134 HIS cc_start: 0.7778 (OUTLIER) cc_final: 0.7322 (m90) REVERT: B 169 ASN cc_start: 0.7461 (m-40) cc_final: 0.6996 (m110) REVERT: B 295 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8128 (tpp-160) REVERT: B 358 LYS cc_start: 0.9245 (ttmm) cc_final: 0.8893 (tppt) REVERT: B 405 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6431 (tt0) REVERT: C 134 HIS cc_start: 0.7662 (OUTLIER) cc_final: 0.7149 (m90) REVERT: C 183 HIS cc_start: 0.7141 (t-90) cc_final: 0.6936 (t-90) REVERT: C 212 ASP cc_start: 0.7316 (m-30) cc_final: 0.6971 (m-30) REVERT: C 418 LYS cc_start: 0.8747 (mmtm) cc_final: 0.8391 (mmtp) REVERT: D 215 HIS cc_start: 0.7792 (m-70) cc_final: 0.6934 (m90) REVERT: D 263 LYS cc_start: 0.7533 (ttmm) cc_final: 0.7186 (tttm) REVERT: D 338 GLU cc_start: 0.7395 (tm-30) cc_final: 0.6775 (pp20) REVERT: D 377 MET cc_start: 0.5577 (OUTLIER) cc_final: 0.4985 (tpt) REVERT: D 403 MET cc_start: 0.9028 (ttm) cc_final: 0.8486 (mpp) REVERT: D 417 ASP cc_start: 0.8932 (t0) cc_final: 0.8682 (t0) REVERT: D 418 LYS cc_start: 0.8896 (mptt) cc_final: 0.8671 (mptt) outliers start: 81 outliers final: 68 residues processed: 436 average time/residue: 0.1445 time to fit residues: 95.5775 Evaluate side-chains 458 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 380 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 100 PHE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 377 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 201 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 214 optimal weight: 0.0000 chunk 8 optimal weight: 0.9990 chunk 56 optimal weight: 0.0070 chunk 193 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 183 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 overall best weight: 0.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN D 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.172354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.149055 restraints weight = 24287.018| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 3.64 r_work: 0.4271 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17933 Z= 0.133 Angle : 0.718 10.651 24299 Z= 0.374 Chirality : 0.047 0.210 2615 Planarity : 0.005 0.057 3063 Dihedral : 5.401 57.868 2517 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.90 % Favored : 93.78 % Rotamer: Outliers : 3.06 % Allowed : 20.97 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: -1.45 (0.18), residues: 2185 helix: None (None), residues: 0 sheet: -0.30 (0.17), residues: 934 loop : -1.52 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 270 TYR 0.022 0.001 TYR L 94 PHE 0.015 0.002 PHE E 100E TRP 0.034 0.002 TRP F 35 HIS 0.004 0.001 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00303 (17889) covalent geometry : angle 0.71274 (24207) SS BOND : bond 0.00344 ( 40) SS BOND : angle 1.63322 ( 80) hydrogen bonds : bond 0.03689 ( 591) hydrogen bonds : angle 6.33172 ( 1527) link_NAG-ASN : bond 0.00206 ( 4) link_NAG-ASN : angle 1.32833 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4739.64 seconds wall clock time: 82 minutes 16.42 seconds (4936.42 seconds total)