Starting phenix.real_space_refine on Sun Jun 15 11:37:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u1s_41826/06_2025/8u1s_41826.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u1s_41826/06_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_41826/06_2025/8u1s_41826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u1s_41826/06_2025/8u1s_41826.map" model { file = "/net/cci-nas-00/data/ceres_data/8u1s_41826/06_2025/8u1s_41826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u1s_41826/06_2025/8u1s_41826.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.69, per 1000 atoms: 0.61 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: 3.86 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.46 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: 5.85 Time building geometry restraints manager: 4.66 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 454 or re \ sid 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: 3.370 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: 0.010 Extract box with map and model: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.240 Process input model: 39.470 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.350 ------------------------------------------------------------------------------- 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 : 5.29 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.17), 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 TRP 0.067 0.012 TRP E 103 HIS 0.016 0.003 HIS B 273 PHE 0.053 0.007 PHE J 78 TYR 0.079 0.009 TYR A 322 ARG 0.012 0.001 ARG C 327 Details of bonding type rmsd link_NAG-ASN : bond 0.05981 ( 4) link_NAG-ASN : angle 4.44602 ( 12) hydrogen bonds : bond 0.16789 ( 591) hydrogen bonds : angle 8.89306 ( 1527) SS BOND : bond 0.03684 ( 40) SS BOND : angle 2.35846 ( 80) covalent geometry : bond 0.02281 (17889) covalent geometry : angle 1.94799 (24207) *********************** 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 : 1.824 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: symmetry clash REVERT: A 134 HIS cc_start: 0.7413 (t70) cc_final: 0.7087 (t-170) REVERT: A 241 THR cc_start: 0.8068 (t) cc_final: 0.7700 (m) REVERT: J 32 THR cc_start: 0.7756 (p) cc_final: 0.7310 (t) REVERT: G 102 TYR cc_start: 0.7612 (m-80) cc_final: 0.7392 (m-10) REVERT: I 35 TRP cc_start: 0.6981 (m100) cc_final: 0.6680 (m100) REVERT: F 18 ARG cc_start: 0.7851 (ttm170) cc_final: 0.7642 (ttm170) 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: 0.3348 time to fit residues: 330.8549 Evaluate side-chains 421 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 413 time to evaluate : 2.152 ------------------------------------------------------------------------------- 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 184 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 127 optimal weight: 0.6980 chunk 198 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 230 ASN A 235 ASN J 3 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN G 57 ASN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.172655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.148375 restraints weight = 23633.933| |-----------------------------------------------------------------------------| r_work (start): 0.4386 rms_B_bonded: 3.78 r_work: 0.4244 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 17933 Z= 0.238 Angle : 0.862 14.635 24299 Z= 0.466 Chirality : 0.051 0.266 2615 Planarity : 0.006 0.048 3063 Dihedral : 7.015 59.263 2529 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.22 % Favored : 94.14 % Rotamer: Outliers : 3.85 % Allowed : 10.85 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.17), residues: 2185 helix: -4.87 (0.33), residues: 6 sheet: 0.28 (0.16), residues: 906 loop : -1.11 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 408 HIS 0.011 0.002 HIS G 98 PHE 0.027 0.002 PHE G 100E TYR 0.031 0.002 TYR K 91 ARG 0.010 0.001 ARG D 300 Details of bonding type rmsd link_NAG-ASN : bond 0.00592 ( 4) link_NAG-ASN : angle 2.60036 ( 12) hydrogen bonds : bond 0.05606 ( 591) hydrogen bonds : angle 7.32061 ( 1527) SS BOND : bond 0.00698 ( 40) SS BOND : angle 2.27440 ( 80) covalent geometry : bond 0.00536 (17889) covalent geometry : angle 0.85134 (24207) *********************** 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 561 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 488 time to evaluate : 1.962 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: 0.8199 (t70) cc_final: 0.7709 (t-170) REVERT: A 194 ASP cc_start: 0.6707 (t0) cc_final: 0.6399 (t0) REVERT: A 308 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: A 357 MET cc_start: 0.8395 (mtm) cc_final: 0.8192 (mtm) REVERT: J 32 THR cc_start: 0.7856 (p) cc_final: 0.7615 (t) REVERT: J 72 ASP cc_start: 0.7232 (t0) cc_final: 0.6920 (t0) REVERT: K 5 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8072 (p) REVERT: K 33 LEU cc_start: 0.8704 (tp) cc_final: 0.8481 (tt) REVERT: G 46 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7085 (tm-30) REVERT: I 29 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.6804 (mt) REVERT: E 82 LEU cc_start: 0.8353 (tt) cc_final: 0.8087 (tt) REVERT: E 82 ARG cc_start: 0.7495 (mtm-85) cc_final: 0.6561 (mtm-85) REVERT: E 112 SER cc_start: 0.8350 (t) cc_final: 0.7848 (p) REVERT: F 35 TRP cc_start: 0.6362 (m100) cc_final: 0.6040 (m100) REVERT: F 82 ASP cc_start: 0.7314 (m-30) cc_final: 0.6910 (m-30) REVERT: H 13 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7823 (tmtt) REVERT: H 34 TYR cc_start: 0.8317 (m-80) cc_final: 0.7959 (m-80) REVERT: H 112 SER cc_start: 0.8065 (t) cc_final: 0.7658 (p) REVERT: B 83 PRO cc_start: 0.8001 (Cg_exo) cc_final: 0.7700 (Cg_endo) REVERT: B 178 SER cc_start: 0.8372 (t) cc_final: 0.8133 (m) REVERT: B 193 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8352 (m) REVERT: B 230 ASN cc_start: 0.8167 (m-40) cc_final: 0.7944 (m110) REVERT: B 295 ARG cc_start: 0.8316 (tpp-160) cc_final: 0.7772 (tpp-160) REVERT: B 322 TYR cc_start: 0.6651 (m-10) cc_final: 0.6182 (m-10) REVERT: B 338 GLU cc_start: 0.7321 (pt0) cc_final: 0.6803 (pp20) REVERT: B 368 THR cc_start: 0.7462 (p) cc_final: 0.7162 (t) REVERT: B 405 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6403 (mt-10) REVERT: C 79 GLU cc_start: 0.8243 (tp30) cc_final: 0.7969 (tp30) REVERT: C 116 ARG cc_start: 0.5929 (mmm-85) cc_final: 0.5580 (mmm160) REVERT: C 117 GLU cc_start: 0.7468 (mp0) cc_final: 0.6476 (mp0) REVERT: C 295 ARG cc_start: 0.8115 (tpp-160) cc_final: 0.7912 (tpp-160) REVERT: C 313 GLU cc_start: 0.7631 (tt0) cc_final: 0.7416 (tt0) REVERT: C 340 ASP cc_start: 0.7768 (p0) cc_final: 0.7260 (p0) REVERT: C 357 MET cc_start: 0.8594 (mtm) cc_final: 0.8357 (mtm) REVERT: D 187 GLU cc_start: 0.8688 (tp30) cc_final: 0.8404 (tp30) REVERT: D 215 HIS cc_start: 0.7765 (m-70) cc_final: 0.6927 (m90) REVERT: D 220 ASN cc_start: 0.7463 (m-40) cc_final: 0.6946 (m110) REVERT: D 235 ASN cc_start: 0.7984 (m-40) cc_final: 0.7783 (m-40) REVERT: D 242 ASP cc_start: 0.7281 (t0) cc_final: 0.6872 (t0) REVERT: D 417 ASP cc_start: 0.9025 (t0) cc_final: 0.8697 (t0) outliers start: 73 outliers final: 45 residues processed: 531 average time/residue: 0.3136 time to fit residues: 246.1392 Evaluate side-chains 474 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 424 time to evaluate : 1.965 ------------------------------------------------------------------------------- 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 320 ASP 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 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 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 23 THR 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 29 ILE Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 193 VAL 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 C residue 421 ASP Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 229 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 172 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 211 optimal weight: 0.0870 chunk 26 optimal weight: 0.0030 chunk 28 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.5770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 5 GLN K 79 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN I 79 GLN I 90 GLN E 3 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN C 169 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.176351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.152874 restraints weight = 23641.455| |-----------------------------------------------------------------------------| r_work (start): 0.4455 rms_B_bonded: 3.66 r_work: 0.4326 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17933 Z= 0.155 Angle : 0.734 7.208 24299 Z= 0.393 Chirality : 0.048 0.223 2615 Planarity : 0.005 0.041 3063 Dihedral : 6.217 56.509 2520 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.40 % Favored : 94.14 % Rotamer: Outliers : 3.27 % Allowed : 14.17 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.17), residues: 2185 helix: -4.87 (0.33), residues: 6 sheet: 0.28 (0.17), residues: 894 loop : -1.22 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 177 HIS 0.009 0.002 HIS A 354 PHE 0.023 0.002 PHE E 100E TYR 0.023 0.002 TYR L 94 ARG 0.012 0.001 ARG F 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 4) link_NAG-ASN : angle 2.03564 ( 12) hydrogen bonds : bond 0.04636 ( 591) hydrogen bonds : angle 6.79595 ( 1527) SS BOND : bond 0.00404 ( 40) SS BOND : angle 1.43810 ( 80) covalent geometry : bond 0.00342 (17889) covalent geometry : angle 0.72910 (24207) *********************** 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 541 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 479 time to evaluate : 1.830 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: A 116 ARG cc_start: 0.6196 (mmm160) cc_final: 0.5877 (mmm160) REVERT: A 117 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6501 (tm-30) REVERT: A 134 HIS cc_start: 0.8043 (t70) cc_final: 0.7554 (t-170) REVERT: A 169 ASN cc_start: 0.8017 (m-40) cc_final: 0.7589 (m110) REVERT: A 187 GLU cc_start: 0.8251 (tp30) cc_final: 0.8040 (tp30) REVERT: A 194 ASP cc_start: 0.6630 (t0) cc_final: 0.6359 (t0) REVERT: A 296 TYR cc_start: 0.8549 (m-10) cc_final: 0.8147 (m-10) REVERT: A 340 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8302 (t0) REVERT: A 388 TRP cc_start: 0.7715 (m-10) cc_final: 0.7478 (m-10) REVERT: J 32 THR cc_start: 0.7970 (p) cc_final: 0.7679 (t) REVERT: J 38 ARG cc_start: 0.8028 (ptm-80) cc_final: 0.7803 (ptm-80) REVERT: J 72 ASP cc_start: 0.7349 (t0) cc_final: 0.6961 (t0) REVERT: J 112 SER cc_start: 0.8009 (t) cc_final: 0.7533 (p) REVERT: K 5 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8267 (p) REVERT: K 33 LEU cc_start: 0.8829 (tp) cc_final: 0.8557 (tt) REVERT: G 46 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7194 (tm-30) REVERT: G 57 ASN cc_start: 0.7467 (OUTLIER) cc_final: 0.6939 (p0) REVERT: I 3 GLN cc_start: 0.7791 (tt0) cc_final: 0.7330 (tp40) REVERT: I 36 TYR cc_start: 0.6746 (m-10) cc_final: 0.6282 (m-10) REVERT: I 42 GLU cc_start: 0.7750 (mp0) cc_final: 0.7413 (mp0) REVERT: E 16 GLU cc_start: 0.8999 (pt0) cc_final: 0.8661 (pm20) REVERT: E 46 GLU cc_start: 0.6657 (mp0) cc_final: 0.6406 (mp0) REVERT: E 82 LEU cc_start: 0.8429 (tt) cc_final: 0.8172 (tt) REVERT: E 82 ARG cc_start: 0.7704 (mtm-85) cc_final: 0.6807 (mtm-85) REVERT: E 112 SER cc_start: 0.8307 (t) cc_final: 0.7775 (p) REVERT: F 82 ASP cc_start: 0.7536 (m-30) cc_final: 0.7156 (m-30) REVERT: H 13 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7595 (tmtt) REVERT: H 16 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8025 (mt-10) REVERT: H 34 TYR cc_start: 0.8458 (m-80) cc_final: 0.8108 (m-80) REVERT: H 43 LYS cc_start: 0.8522 (mmtt) cc_final: 0.8207 (mmtm) REVERT: H 105 GLN cc_start: 0.8022 (mp10) cc_final: 0.7692 (mp10) REVERT: H 112 SER cc_start: 0.8246 (t) cc_final: 0.7804 (p) REVERT: L 30 SER cc_start: 0.8777 (t) cc_final: 0.8531 (p) REVERT: B 193 VAL cc_start: 0.8586 (t) cc_final: 0.8379 (m) REVERT: B 295 ARG cc_start: 0.8412 (tpp-160) cc_final: 0.7891 (tpp-160) REVERT: B 322 TYR cc_start: 0.6739 (m-10) cc_final: 0.6531 (m-10) REVERT: B 368 THR cc_start: 0.7434 (p) cc_final: 0.7212 (t) REVERT: B 369 MET cc_start: 0.8282 (mmm) cc_final: 0.8069 (mmm) REVERT: B 405 GLU cc_start: 0.7068 (mt-10) cc_final: 0.6635 (mt-10) REVERT: C 117 GLU cc_start: 0.7519 (mp0) cc_final: 0.6530 (mp0) REVERT: C 132 LEU cc_start: 0.8264 (mp) cc_final: 0.8032 (mp) REVERT: C 220 ASN cc_start: 0.7359 (t0) cc_final: 0.7106 (t0) REVERT: C 295 ARG cc_start: 0.8211 (tpp-160) cc_final: 0.7997 (tpp-160) REVERT: C 313 GLU cc_start: 0.7665 (tt0) cc_final: 0.7411 (tt0) REVERT: C 340 ASP cc_start: 0.7867 (p0) cc_final: 0.7438 (p0) REVERT: C 357 MET cc_start: 0.8426 (mtm) cc_final: 0.7935 (mtm) REVERT: C 403 MET cc_start: 0.8128 (ppp) cc_final: 0.7469 (mpp) REVERT: C 405 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6771 (tm-30) REVERT: C 424 CYS cc_start: 0.6839 (m) cc_final: 0.6316 (m) REVERT: C 429 MET cc_start: 0.7056 (mtt) cc_final: 0.6584 (mtt) REVERT: D 187 GLU cc_start: 0.8613 (tp30) cc_final: 0.8371 (tp30) REVERT: D 215 HIS cc_start: 0.7714 (m-70) cc_final: 0.6923 (m90) REVERT: D 220 ASN cc_start: 0.7315 (m-40) cc_final: 0.6885 (m110) REVERT: D 242 ASP cc_start: 0.7170 (t0) cc_final: 0.6905 (t0) REVERT: D 417 ASP cc_start: 0.8911 (t0) cc_final: 0.8670 (t0) outliers start: 62 outliers final: 43 residues processed: 510 average time/residue: 0.2974 time to fit residues: 226.4728 Evaluate side-chains 461 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 414 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 334 THR Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 418 LYS 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 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 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 I residue 37 GLN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 22 CYS 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 13 LYS 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 69 THR 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 220 ASN Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 334 THR 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 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 229 CYS Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 85 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 chunk 128 optimal weight: 0.7980 chunk 215 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 118 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN G 5 GLN I 100 GLN E 3 GLN C 169 ASN C 219 ASN D 230 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.170951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.147896 restraints weight = 24128.336| |-----------------------------------------------------------------------------| r_work (start): 0.4391 rms_B_bonded: 3.55 r_work: 0.4255 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.4105 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= 0.177 Angle : 0.701 8.323 24299 Z= 0.374 Chirality : 0.047 0.216 2615 Planarity : 0.005 0.063 3063 Dihedral : 5.876 55.412 2520 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.86 % Favored : 93.68 % Rotamer: Outliers : 4.27 % Allowed : 14.96 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.17), residues: 2185 helix: -4.87 (0.33), residues: 6 sheet: 0.19 (0.17), residues: 908 loop : -1.26 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 32 HIS 0.007 0.002 HIS D 173 PHE 0.018 0.002 PHE E 100E TYR 0.021 0.002 TYR L 94 ARG 0.009 0.001 ARG E 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 4) link_NAG-ASN : angle 1.69678 ( 12) hydrogen bonds : bond 0.04345 ( 591) hydrogen bonds : angle 6.53336 ( 1527) SS BOND : bond 0.00604 ( 40) SS BOND : angle 1.52416 ( 80) covalent geometry : bond 0.00401 (17889) covalent geometry : angle 0.69561 (24207) *********************** 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: 81 poor density : 447 time to evaluate : 1.993 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 116 ARG cc_start: 0.6483 (mmm160) cc_final: 0.6246 (mmm160) REVERT: A 117 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7022 (tm-30) REVERT: A 134 HIS cc_start: 0.7937 (t70) cc_final: 0.7380 (t-170) REVERT: A 169 ASN cc_start: 0.8067 (m-40) cc_final: 0.7668 (m110) REVERT: A 194 ASP cc_start: 0.6775 (t0) cc_final: 0.6573 (t0) REVERT: A 296 TYR cc_start: 0.8580 (m-10) cc_final: 0.8185 (m-10) REVERT: A 377 MET cc_start: 0.4821 (tpt) cc_final: 0.4314 (mmt) REVERT: J 32 THR cc_start: 0.8121 (p) cc_final: 0.7803 (t) REVERT: J 38 ARG cc_start: 0.8081 (ptm-80) cc_final: 0.7846 (ptm-80) REVERT: J 72 ASP cc_start: 0.7419 (t0) cc_final: 0.7059 (t0) REVERT: J 112 SER cc_start: 0.8043 (t) cc_final: 0.7530 (p) REVERT: K 5 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8355 (p) REVERT: K 17 ASP cc_start: 0.8572 (m-30) cc_final: 0.8198 (p0) REVERT: G 34 TYR cc_start: 0.8582 (m-80) cc_final: 0.8168 (m-80) REVERT: I 3 GLN cc_start: 0.8041 (tt0) cc_final: 0.7647 (tp40) REVERT: E 16 GLU cc_start: 0.8954 (pt0) cc_final: 0.8547 (pm20) REVERT: E 46 GLU cc_start: 0.6857 (mp0) cc_final: 0.6502 (mp0) REVERT: E 82 LEU cc_start: 0.8553 (tt) cc_final: 0.8306 (tt) REVERT: E 82 ARG cc_start: 0.7858 (mtm-85) cc_final: 0.6985 (mtm-85) REVERT: E 105 GLN cc_start: 0.8460 (mm-40) cc_final: 0.8217 (mm-40) REVERT: E 112 SER cc_start: 0.8355 (t) cc_final: 0.7795 (p) REVERT: F 82 ASP cc_start: 0.7567 (m-30) cc_final: 0.7227 (m-30) REVERT: H 13 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7705 (tmtt) REVERT: H 16 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8079 (mt-10) REVERT: H 34 TYR cc_start: 0.8547 (m-80) cc_final: 0.8127 (m-80) REVERT: H 112 SER cc_start: 0.8352 (t) cc_final: 0.7884 (p) REVERT: L 30 SER cc_start: 0.8871 (t) cc_final: 0.8629 (p) REVERT: L 42 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8542 (mp0) REVERT: B 134 HIS cc_start: 0.7940 (OUTLIER) cc_final: 0.7256 (m90) REVERT: B 193 VAL cc_start: 0.8621 (t) cc_final: 0.8415 (m) REVERT: B 295 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7901 (tpp-160) REVERT: B 405 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6811 (mt-10) REVERT: C 79 GLU cc_start: 0.8310 (tp30) cc_final: 0.8101 (tp30) REVERT: C 117 GLU cc_start: 0.7675 (mp0) cc_final: 0.6697 (mp0) REVERT: C 132 LEU cc_start: 0.8373 (mp) cc_final: 0.8166 (mp) REVERT: C 220 ASN cc_start: 0.7341 (t0) cc_final: 0.7072 (t0) REVERT: C 295 ARG cc_start: 0.8185 (tpp-160) cc_final: 0.7962 (tpp-160) REVERT: C 313 GLU cc_start: 0.7787 (tt0) cc_final: 0.7555 (tt0) REVERT: C 327 ARG cc_start: 0.6558 (ptp90) cc_final: 0.6258 (ptt-90) REVERT: C 405 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6922 (tm-30) REVERT: D 187 GLU cc_start: 0.8569 (tp30) cc_final: 0.8362 (tp30) REVERT: D 215 HIS cc_start: 0.7737 (m-70) cc_final: 0.7018 (m90) REVERT: D 417 ASP cc_start: 0.8893 (t0) cc_final: 0.8635 (t0) outliers start: 81 outliers final: 58 residues processed: 483 average time/residue: 0.3114 time to fit residues: 223.0658 Evaluate side-chains 472 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 410 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 334 THR Chi-restraints excluded: chain A residue 421 ASP 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 K residue 5 THR Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 53 ASN 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 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 82 LEU Chi-restraints excluded: chain G residue 83 THR 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 23 THR 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 13 LYS 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 B residue 134 HIS Chi-restraints excluded: chain B residue 166 THR 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 295 ARG Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 360 LYS 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 222 LEU 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 303 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 208 optimal weight: 0.7980 chunk 202 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 187 optimal weight: 0.9980 chunk 154 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN K 53 ASN G 3 GLN I 100 GLN C 169 ASN C 219 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 = 0.4607 r_free = 0.4607 target = 0.166970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.143481 restraints weight = 24627.469| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 3.64 r_work: 0.4209 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 17933 Z= 0.235 Angle : 0.747 8.223 24299 Z= 0.396 Chirality : 0.048 0.219 2615 Planarity : 0.005 0.048 3063 Dihedral : 5.792 57.304 2519 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.68 % Favored : 92.91 % Rotamer: Outliers : 5.06 % Allowed : 15.49 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.18), residues: 2185 helix: -4.87 (0.33), residues: 6 sheet: -0.01 (0.17), residues: 915 loop : -1.40 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 388 HIS 0.006 0.002 HIS A 354 PHE 0.023 0.002 PHE E 100E TYR 0.025 0.002 TYR L 94 ARG 0.009 0.001 ARG D 300 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 4) link_NAG-ASN : angle 1.63235 ( 12) hydrogen bonds : bond 0.04375 ( 591) hydrogen bonds : angle 6.50930 ( 1527) SS BOND : bond 0.00613 ( 40) SS BOND : angle 1.69373 ( 80) covalent geometry : bond 0.00539 (17889) covalent geometry : angle 0.74118 (24207) *********************** 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 524 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 428 time to evaluate : 1.954 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: 0.8038 (OUTLIER) cc_final: 0.7827 (tt) REVERT: A 117 GLU cc_start: 0.7408 (tm-30) cc_final: 0.6860 (tm-30) REVERT: A 134 HIS cc_start: 0.7828 (t70) cc_final: 0.7252 (t-170) REVERT: A 169 ASN cc_start: 0.8068 (m-40) cc_final: 0.7683 (m110) REVERT: A 296 TYR cc_start: 0.8454 (m-10) cc_final: 0.8151 (m-10) REVERT: A 429 MET cc_start: 0.7588 (mtp) cc_final: 0.7217 (mtt) REVERT: J 16 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8524 (mt-10) REVERT: J 38 ARG cc_start: 0.8065 (ptm-80) cc_final: 0.7611 (ptm-80) REVERT: J 43 LYS cc_start: 0.9016 (mmtt) cc_final: 0.8790 (mmtt) REVERT: J 72 ASP cc_start: 0.7452 (t0) cc_final: 0.7215 (t0) REVERT: K 61 ARG cc_start: 0.6880 (ptp-170) cc_final: 0.6562 (ptt180) REVERT: G 34 TYR cc_start: 0.8603 (m-80) cc_final: 0.8208 (m-80) REVERT: G 46 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7209 (tm-30) REVERT: I 3 GLN cc_start: 0.7976 (tt0) cc_final: 0.7608 (tp40) REVERT: I 36 TYR cc_start: 0.7054 (m-10) cc_final: 0.6814 (m-10) REVERT: I 42 GLU cc_start: 0.7942 (mp0) cc_final: 0.7604 (mp0) REVERT: E 46 GLU cc_start: 0.6599 (mp0) cc_final: 0.6222 (mp0) REVERT: E 82 LEU cc_start: 0.8481 (tt) cc_final: 0.7626 (mp) REVERT: E 82 ARG cc_start: 0.7887 (mtm-85) cc_final: 0.6961 (mtm-85) REVERT: E 100 TRP cc_start: 0.8332 (m-10) cc_final: 0.7728 (m100) REVERT: E 100 PHE cc_start: 0.3863 (OUTLIER) cc_final: 0.3020 (t80) REVERT: E 105 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8226 (mm-40) REVERT: F 82 ASP cc_start: 0.7466 (m-30) cc_final: 0.7187 (m-30) REVERT: H 13 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7770 (tmtt) REVERT: H 16 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8060 (mt-10) REVERT: H 34 TYR cc_start: 0.8542 (m-80) cc_final: 0.8173 (m-80) REVERT: L 30 SER cc_start: 0.8799 (t) cc_final: 0.8573 (p) REVERT: L 42 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8484 (mp0) REVERT: B 134 HIS cc_start: 0.7922 (OUTLIER) cc_final: 0.7237 (m90) REVERT: B 295 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7987 (tpp-160) REVERT: B 403 MET cc_start: 0.8023 (mtp) cc_final: 0.7753 (ttm) REVERT: C 117 GLU cc_start: 0.7656 (mp0) cc_final: 0.6637 (mp0) REVERT: C 220 ASN cc_start: 0.7491 (t0) cc_final: 0.7249 (t0) REVERT: C 313 GLU cc_start: 0.7877 (tt0) cc_final: 0.7506 (tt0) REVERT: C 327 ARG cc_start: 0.6572 (ptp90) cc_final: 0.6341 (ptt-90) REVERT: D 187 GLU cc_start: 0.8672 (tp30) cc_final: 0.8389 (tp30) REVERT: D 215 HIS cc_start: 0.7730 (m-70) cc_final: 0.6978 (m90) REVERT: D 417 ASP cc_start: 0.9006 (t0) cc_final: 0.8737 (t0) REVERT: D 418 LYS cc_start: 0.8875 (mptt) cc_final: 0.8527 (mptt) outliers start: 96 outliers final: 62 residues processed: 477 average time/residue: 0.3564 time to fit residues: 255.0728 Evaluate side-chains 464 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 397 time to evaluate : 3.188 ------------------------------------------------------------------------------- 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 241 THR 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 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 47 LEU 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 57 ASN Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 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 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 23 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 15 VAL 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 13 LYS 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 46 LEU 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 215 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 360 LYS 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 222 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 201 LEU 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 Chi-restraints excluded: chain D residue 332 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 111 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 chunk 179 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 175 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4589 r_free = 0.4589 target = 0.165301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.141945 restraints weight = 24312.172| |-----------------------------------------------------------------------------| r_work (start): 0.4324 rms_B_bonded: 3.61 r_work: 0.4189 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 17933 Z= 0.221 Angle : 0.731 8.512 24299 Z= 0.388 Chirality : 0.047 0.213 2615 Planarity : 0.005 0.046 3063 Dihedral : 5.717 58.040 2519 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.91 % Favored : 92.77 % Rotamer: Outliers : 4.79 % Allowed : 16.60 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.17), residues: 2185 helix: -4.86 (0.33), residues: 6 sheet: -0.15 (0.17), residues: 922 loop : -1.53 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 32 HIS 0.006 0.002 HIS J 98 PHE 0.021 0.002 PHE C 413 TYR 0.025 0.002 TYR L 94 ARG 0.008 0.001 ARG D 300 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 4) link_NAG-ASN : angle 1.57093 ( 12) hydrogen bonds : bond 0.04235 ( 591) hydrogen bonds : angle 6.44006 ( 1527) SS BOND : bond 0.00557 ( 40) SS BOND : angle 1.77070 ( 80) covalent geometry : bond 0.00506 (17889) covalent geometry : angle 0.72482 (24207) *********************** 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 520 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 429 time to evaluate : 2.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7882 (tt) REVERT: A 116 ARG cc_start: 0.6348 (mmm160) cc_final: 0.6126 (mmm160) REVERT: A 117 GLU cc_start: 0.7424 (tm-30) cc_final: 0.6889 (tm-30) REVERT: A 134 HIS cc_start: 0.7775 (t70) cc_final: 0.7236 (t-170) REVERT: A 169 ASN cc_start: 0.8065 (m-40) cc_final: 0.7695 (m110) REVERT: A 296 TYR cc_start: 0.8365 (m-10) cc_final: 0.8159 (m-10) REVERT: A 418 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8768 (mmtm) REVERT: J 16 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8536 (mt-10) REVERT: J 38 ARG cc_start: 0.8082 (ptm-80) cc_final: 0.6946 (ptm-80) REVERT: J 46 GLU cc_start: 0.7252 (tt0) cc_final: 0.6510 (mp0) REVERT: J 53 TYR cc_start: 0.8270 (t80) cc_final: 0.7923 (t80) REVERT: J 72 ASP cc_start: 0.7793 (t0) cc_final: 0.7454 (t0) REVERT: K 65 SER cc_start: 0.8530 (t) cc_final: 0.8105 (p) REVERT: G 34 TYR cc_start: 0.8616 (m-80) cc_final: 0.8332 (m-80) REVERT: G 75 LYS cc_start: 0.8735 (mtpp) cc_final: 0.8232 (mttt) REVERT: I 3 GLN cc_start: 0.8041 (tt0) cc_final: 0.7651 (tp40) REVERT: E 5 GLN cc_start: 0.7924 (mp-120) cc_final: 0.7212 (mp10) REVERT: E 16 GLU cc_start: 0.8922 (pt0) cc_final: 0.8420 (pm20) REVERT: E 46 GLU cc_start: 0.6637 (mp0) cc_final: 0.6226 (mp0) REVERT: E 82 LEU cc_start: 0.8460 (tt) cc_final: 0.8237 (tt) REVERT: E 82 ARG cc_start: 0.7974 (mtm-85) cc_final: 0.7079 (mtm-85) REVERT: E 100 PHE cc_start: 0.4092 (OUTLIER) cc_final: 0.3106 (t80) REVERT: F 82 ASP cc_start: 0.7436 (m-30) cc_final: 0.7150 (m-30) REVERT: H 13 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7755 (tmtt) REVERT: H 16 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8114 (mt-10) REVERT: H 34 TYR cc_start: 0.8549 (m-80) cc_final: 0.8254 (m-80) REVERT: L 30 SER cc_start: 0.8816 (t) cc_final: 0.8604 (p) REVERT: L 42 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8473 (mp0) REVERT: B 134 HIS cc_start: 0.7913 (OUTLIER) cc_final: 0.7270 (m90) REVERT: B 169 ASN cc_start: 0.7485 (m-40) cc_final: 0.7019 (m110) REVERT: B 295 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8039 (tpp-160) REVERT: B 405 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6820 (mt-10) REVERT: C 79 GLU cc_start: 0.8323 (tp30) cc_final: 0.8094 (tp30) REVERT: C 117 GLU cc_start: 0.7696 (mp0) cc_final: 0.6661 (mp0) REVERT: C 220 ASN cc_start: 0.7557 (t0) cc_final: 0.7336 (t0) REVERT: C 230 ASN cc_start: 0.8264 (m110) cc_final: 0.7813 (m-40) REVERT: C 313 GLU cc_start: 0.7886 (tt0) cc_final: 0.7528 (tt0) REVERT: C 377 MET cc_start: 0.4674 (tpt) cc_final: 0.4378 (tpt) REVERT: C 429 MET cc_start: 0.6920 (mtt) cc_final: 0.6599 (mtt) REVERT: D 187 GLU cc_start: 0.8697 (tp30) cc_final: 0.8383 (tp30) REVERT: D 215 HIS cc_start: 0.7767 (m-70) cc_final: 0.6955 (m90) REVERT: D 417 ASP cc_start: 0.9009 (t0) cc_final: 0.8761 (t0) REVERT: D 418 LYS cc_start: 0.8873 (mptt) cc_final: 0.8594 (mptt) outliers start: 91 outliers final: 74 residues processed: 476 average time/residue: 0.3388 time to fit residues: 241.5870 Evaluate side-chains 469 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 389 time to evaluate : 2.151 ------------------------------------------------------------------------------- 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 241 THR 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 418 LYS 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 30 SER Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 47 LEU 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 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 82 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 23 THR 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 13 LYS 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 46 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 93 ILE 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 360 LYS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 134 HIS 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 193 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 201 LEU 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 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 96 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 59 optimal weight: 0.0470 chunk 65 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 144 optimal weight: 0.5980 overall best weight: 1.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 105 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 = 0.4605 r_free = 0.4605 target = 0.166338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.143262 restraints weight = 24311.278| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 3.58 r_work: 0.4223 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.4791 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= 0.174 Angle : 0.711 9.089 24299 Z= 0.374 Chirality : 0.047 0.208 2615 Planarity : 0.005 0.087 3063 Dihedral : 5.571 58.117 2519 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.82 % Favored : 92.86 % Rotamer: Outliers : 4.74 % Allowed : 17.33 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.18), residues: 2185 helix: -4.86 (0.33), residues: 6 sheet: -0.21 (0.17), residues: 920 loop : -1.52 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 32 HIS 0.009 0.002 HIS D 173 PHE 0.018 0.002 PHE E 100E TYR 0.025 0.002 TYR L 94 ARG 0.008 0.001 ARG C 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 4) link_NAG-ASN : angle 1.48701 ( 12) hydrogen bonds : bond 0.03990 ( 591) hydrogen bonds : angle 6.33999 ( 1527) SS BOND : bond 0.00464 ( 40) SS BOND : angle 1.76687 ( 80) covalent geometry : bond 0.00397 (17889) covalent geometry : angle 0.70386 (24207) *********************** 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 504 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 414 time to evaluate : 1.837 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: 0.8249 (OUTLIER) cc_final: 0.8023 (tt) REVERT: A 134 HIS cc_start: 0.7679 (t70) cc_final: 0.7185 (t-170) REVERT: A 169 ASN cc_start: 0.8103 (m-40) cc_final: 0.7752 (m110) REVERT: A 357 MET cc_start: 0.8293 (mtm) cc_final: 0.8061 (mpp) REVERT: A 418 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8744 (mmtm) REVERT: A 429 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7334 (mtt) REVERT: J 16 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8594 (mt-10) REVERT: J 38 ARG cc_start: 0.8106 (ptm-80) cc_final: 0.7026 (ptm-80) REVERT: J 46 GLU cc_start: 0.7278 (tt0) cc_final: 0.6534 (mp0) REVERT: J 53 TYR cc_start: 0.8374 (t80) cc_final: 0.8056 (t80) REVERT: J 72 ASP cc_start: 0.7840 (t0) cc_final: 0.7556 (t0) REVERT: J 100 PHE cc_start: 0.5902 (OUTLIER) cc_final: 0.3971 (t80) REVERT: K 61 ARG cc_start: 0.6860 (ptp-170) cc_final: 0.6563 (ptt180) REVERT: K 65 SER cc_start: 0.8558 (t) cc_final: 0.8121 (p) REVERT: K 90 GLN cc_start: 0.7387 (pt0) cc_final: 0.6658 (pt0) REVERT: G 34 TYR cc_start: 0.8710 (m-80) cc_final: 0.8339 (m-80) REVERT: G 75 LYS cc_start: 0.8759 (mtpp) cc_final: 0.8326 (mttt) REVERT: I 3 GLN cc_start: 0.8054 (tt0) cc_final: 0.7692 (tp40) REVERT: I 36 TYR cc_start: 0.7159 (m-10) cc_final: 0.6939 (m-10) REVERT: E 5 GLN cc_start: 0.7933 (mp-120) cc_final: 0.7483 (mp10) REVERT: E 16 GLU cc_start: 0.8894 (pt0) cc_final: 0.8418 (pm20) REVERT: E 45 LEU cc_start: 0.7734 (mt) cc_final: 0.7279 (mt) REVERT: E 46 GLU cc_start: 0.6709 (mp0) cc_final: 0.6280 (mp0) REVERT: E 82 LEU cc_start: 0.8564 (tt) cc_final: 0.8275 (tt) REVERT: E 82 ARG cc_start: 0.8027 (mtm-85) cc_final: 0.7443 (mtm110) REVERT: E 100 PHE cc_start: 0.3910 (OUTLIER) cc_final: 0.2918 (t80) REVERT: F 82 ASP cc_start: 0.7444 (m-30) cc_final: 0.7165 (m-30) REVERT: H 13 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7756 (tmtt) REVERT: H 16 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8172 (mt-10) REVERT: H 34 TYR cc_start: 0.8612 (m-80) cc_final: 0.8409 (m-80) REVERT: L 30 SER cc_start: 0.8929 (t) cc_final: 0.8692 (p) REVERT: L 42 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8477 (mp0) REVERT: L 94 TYR cc_start: 0.7744 (m-80) cc_final: 0.7442 (m-80) REVERT: B 134 HIS cc_start: 0.7878 (OUTLIER) cc_final: 0.7279 (m90) REVERT: B 169 ASN cc_start: 0.7578 (m-40) cc_final: 0.7171 (m110) REVERT: B 295 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7956 (tpp-160) REVERT: B 405 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6853 (mt-10) REVERT: C 117 GLU cc_start: 0.7774 (mp0) cc_final: 0.6742 (mp0) REVERT: C 220 ASN cc_start: 0.7463 (t0) cc_final: 0.7243 (t0) REVERT: C 230 ASN cc_start: 0.8227 (m110) cc_final: 0.7796 (m-40) REVERT: C 313 GLU cc_start: 0.7916 (tt0) cc_final: 0.7559 (tt0) REVERT: D 187 GLU cc_start: 0.8604 (tp30) cc_final: 0.8345 (tp30) REVERT: D 215 HIS cc_start: 0.7738 (m-70) cc_final: 0.6942 (m90) REVERT: D 403 MET cc_start: 0.8951 (ttm) cc_final: 0.8356 (mpp) REVERT: D 417 ASP cc_start: 0.8966 (t0) cc_final: 0.8744 (t0) REVERT: D 418 LYS cc_start: 0.8917 (mptt) cc_final: 0.8628 (mptt) outliers start: 90 outliers final: 69 residues processed: 466 average time/residue: 0.3208 time to fit residues: 223.8376 Evaluate side-chains 476 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 399 time to evaluate : 2.005 ------------------------------------------------------------------------------- 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 202 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 286 THR 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 418 LYS 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 30 SER Chi-restraints excluded: chain K residue 47 LEU 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 55 GLU 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 82 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 23 THR 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 13 LYS 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 69 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 166 THR 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 360 LYS Chi-restraints excluded: chain C residue 134 HIS 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 193 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 201 LEU 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 333 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 73 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 128 optimal weight: 0.5980 chunk 203 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 190 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN 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 = 0.4619 r_free = 0.4619 target = 0.167630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.144468 restraints weight = 24415.696| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 3.60 r_work: 0.4239 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.4958 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= 0.159 Angle : 0.705 8.760 24299 Z= 0.370 Chirality : 0.047 0.202 2615 Planarity : 0.005 0.086 3063 Dihedral : 5.471 58.166 2519 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.77 % Favored : 92.91 % Rotamer: Outliers : 4.48 % Allowed : 18.49 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.18), residues: 2185 helix: -4.86 (0.33), residues: 6 sheet: -0.23 (0.17), residues: 929 loop : -1.49 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 35 HIS 0.008 0.002 HIS D 173 PHE 0.015 0.002 PHE E 100E TYR 0.024 0.002 TYR L 94 ARG 0.017 0.001 ARG C 252 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 4) link_NAG-ASN : angle 1.39004 ( 12) hydrogen bonds : bond 0.03897 ( 591) hydrogen bonds : angle 6.26487 ( 1527) SS BOND : bond 0.00423 ( 40) SS BOND : angle 1.67752 ( 80) covalent geometry : bond 0.00366 (17889) covalent geometry : angle 0.69947 (24207) *********************** 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 504 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 419 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8080 (tt) REVERT: A 134 HIS cc_start: 0.7626 (t70) cc_final: 0.7116 (t-170) REVERT: A 169 ASN cc_start: 0.8084 (m-40) cc_final: 0.7740 (m110) REVERT: A 357 MET cc_start: 0.8339 (mtm) cc_final: 0.8107 (mpp) REVERT: A 429 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.7100 (mtt) REVERT: J 16 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8592 (mt-10) REVERT: J 38 ARG cc_start: 0.8052 (ptm-80) cc_final: 0.7017 (ptm-80) REVERT: J 46 GLU cc_start: 0.7307 (tt0) cc_final: 0.6558 (mp0) REVERT: J 53 TYR cc_start: 0.8385 (t80) cc_final: 0.8078 (t80) REVERT: J 72 ASP cc_start: 0.7806 (t0) cc_final: 0.7541 (t0) REVERT: K 61 ARG cc_start: 0.6887 (ptp-170) cc_final: 0.6606 (ptt180) REVERT: K 65 SER cc_start: 0.8569 (t) cc_final: 0.8145 (p) REVERT: G 34 TYR cc_start: 0.8713 (m-80) cc_final: 0.8406 (m-80) REVERT: G 75 LYS cc_start: 0.8761 (mtpp) cc_final: 0.8360 (mttt) REVERT: I 3 GLN cc_start: 0.8050 (tt0) cc_final: 0.7705 (tp40) REVERT: I 36 TYR cc_start: 0.7202 (m-10) cc_final: 0.6965 (m-10) REVERT: E 5 GLN cc_start: 0.7994 (mp-120) cc_final: 0.7598 (mp10) REVERT: E 45 LEU cc_start: 0.7712 (mt) cc_final: 0.7299 (mt) REVERT: E 46 GLU cc_start: 0.6681 (mp0) cc_final: 0.6269 (mp0) REVERT: E 82 LEU cc_start: 0.8555 (tt) cc_final: 0.8228 (tt) REVERT: E 82 ARG cc_start: 0.8031 (mtm-85) cc_final: 0.7544 (mtm110) REVERT: E 100 PHE cc_start: 0.3734 (OUTLIER) cc_final: 0.2850 (t80) REVERT: F 82 ASP cc_start: 0.7359 (m-30) cc_final: 0.7041 (m-30) REVERT: H 13 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7746 (tmtt) REVERT: H 16 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8148 (mt-10) REVERT: L 30 SER cc_start: 0.8894 (t) cc_final: 0.8654 (p) REVERT: L 42 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8443 (mp0) REVERT: B 134 HIS cc_start: 0.7834 (OUTLIER) cc_final: 0.7288 (m90) REVERT: B 169 ASN cc_start: 0.7590 (m-40) cc_final: 0.7161 (m110) REVERT: B 295 ARG cc_start: 0.8507 (tpp-160) cc_final: 0.7987 (tpp-160) REVERT: B 405 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6798 (mt-10) REVERT: C 79 GLU cc_start: 0.8330 (tp30) cc_final: 0.7948 (tp30) REVERT: C 117 GLU cc_start: 0.7782 (mp0) cc_final: 0.6762 (mp0) REVERT: C 163 LYS cc_start: 0.8405 (mtpt) cc_final: 0.8148 (mtpp) REVERT: C 220 ASN cc_start: 0.7422 (t0) cc_final: 0.7193 (t0) REVERT: C 313 GLU cc_start: 0.7892 (tt0) cc_final: 0.7535 (tt0) REVERT: C 377 MET cc_start: 0.4485 (tpt) cc_final: 0.4179 (mmt) REVERT: D 187 GLU cc_start: 0.8613 (tp30) cc_final: 0.8383 (tp30) REVERT: D 215 HIS cc_start: 0.7722 (m-70) cc_final: 0.6922 (m90) REVERT: D 403 MET cc_start: 0.8938 (ttm) cc_final: 0.8385 (mpp) REVERT: D 417 ASP cc_start: 0.8932 (t0) cc_final: 0.8703 (t0) REVERT: D 418 LYS cc_start: 0.8895 (mptt) cc_final: 0.8607 (mptt) outliers start: 85 outliers final: 68 residues processed: 466 average time/residue: 0.3055 time to fit residues: 215.5908 Evaluate side-chains 473 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 400 time to evaluate : 2.002 ------------------------------------------------------------------------------- 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 202 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 421 ASP 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 47 LEU Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 55 GLU 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 82 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 92 CYS 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 23 THR 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 13 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain L residue 46 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 166 THR Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 220 ASN 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 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 180 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 271 VAL 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 Chi-restraints excluded: chain D residue 352 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 20 optimal weight: 6.9990 chunk 196 optimal weight: 8.9990 chunk 88 optimal weight: 0.2980 chunk 164 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 105 GLN L 37 GLN 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 = 0.4642 r_free = 0.4642 target = 0.169683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.146380 restraints weight = 24180.676| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 3.57 r_work: 0.4280 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17933 Z= 0.138 Angle : 0.698 8.662 24299 Z= 0.365 Chirality : 0.046 0.199 2615 Planarity : 0.005 0.086 3063 Dihedral : 5.309 57.437 2518 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.54 % Favored : 93.14 % Rotamer: Outliers : 3.79 % Allowed : 19.65 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.18), residues: 2185 helix: None (None), residues: 0 sheet: -0.19 (0.17), residues: 918 loop : -1.47 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 35 HIS 0.007 0.001 HIS D 173 PHE 0.021 0.002 PHE K 98 TYR 0.024 0.002 TYR H 34 ARG 0.014 0.001 ARG C 252 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 4) link_NAG-ASN : angle 1.34093 ( 12) hydrogen bonds : bond 0.03782 ( 591) hydrogen bonds : angle 6.22210 ( 1527) SS BOND : bond 0.00368 ( 40) SS BOND : angle 1.63300 ( 80) covalent geometry : bond 0.00313 (17889) covalent geometry : angle 0.69279 (24207) *********************** 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 478 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 406 time to evaluate : 1.820 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 134 HIS cc_start: 0.7599 (t70) cc_final: 0.6781 (t-170) REVERT: A 169 ASN cc_start: 0.8070 (m-40) cc_final: 0.7748 (m110) REVERT: A 295 ARG cc_start: 0.8313 (tpp-160) cc_final: 0.8076 (tpp-160) REVERT: A 357 MET cc_start: 0.8324 (mtm) cc_final: 0.8078 (mpp) REVERT: A 377 MET cc_start: 0.5047 (tpt) cc_final: 0.4433 (mmt) REVERT: A 429 MET cc_start: 0.7334 (mtt) cc_final: 0.6910 (mtt) REVERT: J 38 ARG cc_start: 0.7975 (ptm-80) cc_final: 0.7643 (ptm-80) REVERT: J 53 TYR cc_start: 0.8405 (t80) cc_final: 0.8071 (t80) REVERT: J 72 ASP cc_start: 0.7826 (t0) cc_final: 0.7552 (t0) REVERT: J 100 PHE cc_start: 0.5633 (OUTLIER) cc_final: 0.3990 (t80) REVERT: K 17 ASP cc_start: 0.8650 (m-30) cc_final: 0.8312 (p0) REVERT: K 27 GLN cc_start: 0.8388 (mp10) cc_final: 0.8055 (mp10) REVERT: K 61 ARG cc_start: 0.6805 (ptp-170) cc_final: 0.6580 (ptt180) REVERT: K 65 SER cc_start: 0.8566 (t) cc_final: 0.8148 (p) REVERT: G 34 TYR cc_start: 0.8672 (m-80) cc_final: 0.8453 (m-80) REVERT: G 75 LYS cc_start: 0.8777 (mtpp) cc_final: 0.8446 (mttt) REVERT: I 3 GLN cc_start: 0.8009 (tt0) cc_final: 0.7698 (tp40) REVERT: I 42 GLU cc_start: 0.8472 (mp0) cc_final: 0.7964 (mp0) REVERT: E 5 GLN cc_start: 0.7975 (mp-120) cc_final: 0.7505 (mp10) REVERT: E 16 GLU cc_start: 0.8846 (pt0) cc_final: 0.8437 (pm20) REVERT: E 46 GLU cc_start: 0.6452 (mp0) cc_final: 0.6102 (mp0) REVERT: E 82 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7583 (mtm110) REVERT: E 100 PHE cc_start: 0.3565 (OUTLIER) cc_final: 0.2781 (t80) REVERT: F 82 ASP cc_start: 0.7269 (m-30) cc_final: 0.6951 (m-30) REVERT: H 13 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7714 (tmtt) REVERT: H 16 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8190 (mt-10) REVERT: L 30 SER cc_start: 0.8895 (t) cc_final: 0.8648 (p) REVERT: L 42 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8387 (mp0) REVERT: B 134 HIS cc_start: 0.7728 (OUTLIER) cc_final: 0.7254 (m90) REVERT: B 169 ASN cc_start: 0.7502 (m-40) cc_final: 0.7101 (m110) REVERT: B 295 ARG cc_start: 0.8520 (tpp-160) cc_final: 0.8040 (tpp-160) REVERT: B 338 GLU cc_start: 0.7686 (pt0) cc_final: 0.7256 (pt0) REVERT: B 405 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6717 (mt-10) REVERT: C 79 GLU cc_start: 0.8342 (tp30) cc_final: 0.7922 (tp30) REVERT: C 117 GLU cc_start: 0.7748 (mp0) cc_final: 0.6739 (mp0) REVERT: C 220 ASN cc_start: 0.7363 (t0) cc_final: 0.7137 (t0) REVERT: C 313 GLU cc_start: 0.7825 (tt0) cc_final: 0.7464 (tt0) REVERT: C 418 LYS cc_start: 0.8797 (mmtm) cc_final: 0.8372 (mmtp) REVERT: D 215 HIS cc_start: 0.7660 (m-70) cc_final: 0.6883 (m90) REVERT: D 403 MET cc_start: 0.8950 (ttm) cc_final: 0.8690 (mmt) REVERT: D 417 ASP cc_start: 0.8922 (t0) cc_final: 0.8674 (t0) REVERT: D 418 LYS cc_start: 0.8864 (mptt) cc_final: 0.8584 (mptt) outliers start: 72 outliers final: 56 residues processed: 448 average time/residue: 0.3265 time to fit residues: 222.9222 Evaluate side-chains 450 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 390 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 421 ASP 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 30 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 75 ILE 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 82 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 37 GLN 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 13 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain L residue 69 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 166 THR 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 334 THR Chi-restraints excluded: chain B residue 360 LYS 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 222 LEU Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 283 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 229 CYS Chi-restraints excluded: chain D residue 271 VAL 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 333 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 67 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 115 optimal weight: 0.1980 chunk 121 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 192 optimal weight: 8.9990 chunk 167 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 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 = 0.4596 r_free = 0.4596 target = 0.165770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.142253 restraints weight = 24521.921| |-----------------------------------------------------------------------------| r_work (start): 0.4346 rms_B_bonded: 3.64 r_work: 0.4223 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17933 Z= 0.202 Angle : 0.747 11.300 24299 Z= 0.391 Chirality : 0.048 0.200 2615 Planarity : 0.005 0.087 3063 Dihedral : 5.467 57.609 2517 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.14 % Favored : 92.59 % Rotamer: Outliers : 3.48 % Allowed : 20.02 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.18), residues: 2185 helix: None (None), residues: 0 sheet: -0.37 (0.17), residues: 934 loop : -1.56 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 35A HIS 0.008 0.002 HIS D 173 PHE 0.024 0.002 PHE K 98 TYR 0.024 0.002 TYR L 94 ARG 0.013 0.001 ARG C 252 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 4) link_NAG-ASN : angle 1.31569 ( 12) hydrogen bonds : bond 0.04084 ( 591) hydrogen bonds : angle 6.27763 ( 1527) SS BOND : bond 0.00561 ( 40) SS BOND : angle 1.91368 ( 80) covalent geometry : bond 0.00469 (17889) covalent geometry : angle 0.74007 (24207) ********************** 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 463 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 397 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.6308 (mmm160) cc_final: 0.6082 (mmm160) REVERT: A 117 GLU cc_start: 0.7406 (tm-30) cc_final: 0.6910 (tm-30) REVERT: A 134 HIS cc_start: 0.7610 (t70) cc_final: 0.6827 (t-170) REVERT: A 169 ASN cc_start: 0.8097 (m-40) cc_final: 0.7755 (m110) REVERT: A 187 GLU cc_start: 0.8106 (tp30) cc_final: 0.7850 (tm-30) REVERT: A 239 MET cc_start: 0.7555 (tmm) cc_final: 0.7177 (tmm) REVERT: A 295 ARG cc_start: 0.8277 (tpp-160) cc_final: 0.8038 (tpp-160) REVERT: A 343 LYS cc_start: 0.7028 (mttt) cc_final: 0.6686 (mttt) REVERT: A 357 MET cc_start: 0.8412 (mtm) cc_final: 0.8117 (mpp) REVERT: A 429 MET cc_start: 0.7382 (mtt) cc_final: 0.6838 (mtt) REVERT: J 53 TYR cc_start: 0.8384 (t80) cc_final: 0.8069 (t80) REVERT: J 72 ASP cc_start: 0.7876 (t0) cc_final: 0.7625 (t0) REVERT: J 100 PHE cc_start: 0.5820 (OUTLIER) cc_final: 0.4116 (t80) REVERT: J 105 GLN cc_start: 0.8695 (mp10) cc_final: 0.8469 (mp10) REVERT: K 4 MET cc_start: 0.7238 (mmm) cc_final: 0.7017 (mtp) REVERT: K 17 ASP cc_start: 0.8729 (m-30) cc_final: 0.8441 (p0) REVERT: K 65 SER cc_start: 0.8591 (t) cc_final: 0.8169 (p) REVERT: G 34 TYR cc_start: 0.8703 (m-80) cc_final: 0.8379 (m-80) REVERT: G 75 LYS cc_start: 0.8795 (mtpp) cc_final: 0.8451 (mttt) REVERT: I 3 GLN cc_start: 0.8053 (tt0) cc_final: 0.7725 (tp40) REVERT: E 5 GLN cc_start: 0.8018 (mp-120) cc_final: 0.7505 (mp10) REVERT: E 16 GLU cc_start: 0.8872 (pt0) cc_final: 0.8456 (pm20) REVERT: E 45 LEU cc_start: 0.7528 (mt) cc_final: 0.7163 (mp) REVERT: E 46 GLU cc_start: 0.6507 (mp0) cc_final: 0.6145 (mp0) REVERT: E 82 ARG cc_start: 0.8168 (mtm-85) cc_final: 0.7574 (mtm110) REVERT: E 100 PHE cc_start: 0.3874 (OUTLIER) cc_final: 0.2834 (t80) REVERT: F 82 ASP cc_start: 0.7270 (m-30) cc_final: 0.6949 (m-30) REVERT: H 13 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7713 (tmtt) REVERT: H 16 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8214 (mt-10) REVERT: L 30 SER cc_start: 0.8886 (t) cc_final: 0.8629 (p) REVERT: L 42 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8423 (mp0) REVERT: L 94 TYR cc_start: 0.7651 (m-80) cc_final: 0.7356 (m-80) REVERT: B 134 HIS cc_start: 0.7742 (OUTLIER) cc_final: 0.7285 (m90) REVERT: B 169 ASN cc_start: 0.7473 (m-40) cc_final: 0.7035 (m110) REVERT: B 295 ARG cc_start: 0.8603 (tpp-160) cc_final: 0.8119 (tpp-160) REVERT: B 405 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6722 (mt-10) REVERT: C 79 GLU cc_start: 0.8361 (tp30) cc_final: 0.7932 (tp30) REVERT: C 117 GLU cc_start: 0.7824 (mp0) cc_final: 0.6828 (mp0) REVERT: C 134 HIS cc_start: 0.7721 (OUTLIER) cc_final: 0.6965 (m90) REVERT: C 220 ASN cc_start: 0.7528 (t0) cc_final: 0.7312 (t0) REVERT: C 230 ASN cc_start: 0.8229 (m110) cc_final: 0.7785 (m-40) REVERT: C 295 ARG cc_start: 0.8175 (tpp-160) cc_final: 0.7731 (tpp-160) REVERT: C 313 GLU cc_start: 0.7858 (tt0) cc_final: 0.7512 (tt0) REVERT: C 418 LYS cc_start: 0.8799 (mmtm) cc_final: 0.8393 (mmtp) REVERT: D 215 HIS cc_start: 0.7708 (m-70) cc_final: 0.6898 (m90) REVERT: D 263 LYS cc_start: 0.7591 (ttmm) cc_final: 0.7264 (tttm) REVERT: D 403 MET cc_start: 0.8984 (ttm) cc_final: 0.8689 (mmt) REVERT: D 417 ASP cc_start: 0.8980 (t0) cc_final: 0.8739 (t0) REVERT: D 418 LYS cc_start: 0.8882 (mptt) cc_final: 0.8624 (mptt) outliers start: 66 outliers final: 55 residues processed: 437 average time/residue: 0.2976 time to fit residues: 194.7750 Evaluate side-chains 447 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 387 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 421 ASP 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 30 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 69 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 37 GLN Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 23 THR 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 13 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain L residue 69 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 215 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 283 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 74 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.170175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.146683 restraints weight = 24217.992| |-----------------------------------------------------------------------------| r_work (start): 0.4399 rms_B_bonded: 3.64 r_work: 0.4278 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17933 Z= 0.143 Angle : 0.708 10.020 24299 Z= 0.369 Chirality : 0.047 0.193 2615 Planarity : 0.005 0.088 3063 Dihedral : 5.345 57.164 2517 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.54 % Favored : 93.18 % Rotamer: Outliers : 3.42 % Allowed : 20.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.18), residues: 2185 helix: None (None), residues: 0 sheet: -0.33 (0.17), residues: 940 loop : -1.53 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP G 35A HIS 0.007 0.001 HIS D 173 PHE 0.018 0.002 PHE K 98 TYR 0.024 0.002 TYR L 94 ARG 0.010 0.001 ARG C 252 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 4) link_NAG-ASN : angle 1.28125 ( 12) hydrogen bonds : bond 0.03785 ( 591) hydrogen bonds : angle 6.20389 ( 1527) SS BOND : bond 0.00388 ( 40) SS BOND : angle 1.69455 ( 80) covalent geometry : bond 0.00331 (17889) covalent geometry : angle 0.70227 (24207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10547.23 seconds wall clock time: 183 minutes 9.92 seconds (10989.92 seconds total)