Starting phenix.real_space_refine on Mon May 19 18:26:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u1q_41824/05_2025/8u1q_41824.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u1q_41824/05_2025/8u1q_41824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u1q_41824/05_2025/8u1q_41824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u1q_41824/05_2025/8u1q_41824.map" model { file = "/net/cci-nas-00/data/ceres_data/8u1q_41824/05_2025/8u1q_41824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u1q_41824/05_2025/8u1q_41824.cif" } resolution = 3.36 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= 0.059 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 136 5.16 5 C 11972 2.51 5 N 3228 2.21 5 O 3680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19016 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2994 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 18, 'TRANS': 368} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Restraints were copied for chains: J, L, O, C, G, M, I, H, N, F, K, P Time building chain proxies: 8.31, per 1000 atoms: 0.44 Number of scatterers: 19016 At special positions: 0 Unit cell: (185.15, 185.15, 69, 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 136 16.00 O 3680 8.00 N 3228 7.00 C 11972 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 420 " distance=2.06 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=1.41 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=2.02 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 C 87 " - pdb=" SG CYS C 420 " distance=2.06 Simple disulfide: pdb=" SG CYS G 87 " - pdb=" SG CYS G 420 " distance=2.06 Simple disulfide: pdb=" SG CYS M 87 " - pdb=" SG CYS M 420 " distance=2.06 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS G 122 " - pdb=" SG CYS G 127 " distance=2.03 Simple disulfide: pdb=" SG CYS M 122 " - pdb=" SG CYS M 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 229 " distance=1.41 Simple disulfide: pdb=" SG CYS G 182 " - pdb=" SG CYS G 229 " distance=1.41 Simple disulfide: pdb=" SG CYS M 182 " - pdb=" SG CYS M 229 " distance=1.41 Simple disulfide: pdb=" SG CYS C 231 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS G 231 " - pdb=" SG CYS G 236 " distance=2.03 Simple disulfide: pdb=" SG CYS M 231 " - pdb=" SG CYS M 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 277 " - pdb=" SG CYS C 291 " distance=2.02 Simple disulfide: pdb=" SG CYS G 277 " - pdb=" SG CYS G 291 " distance=2.02 Simple disulfide: pdb=" SG CYS M 277 " - pdb=" SG CYS M 291 " distance=2.02 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 289 " distance=2.02 Simple disulfide: pdb=" SG CYS G 279 " - pdb=" SG CYS G 289 " distance=2.02 Simple disulfide: pdb=" SG CYS M 279 " - pdb=" SG CYS M 289 " distance=2.02 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 337 " distance=2.03 Simple disulfide: pdb=" SG CYS G 318 " - pdb=" SG CYS G 337 " distance=2.03 Simple disulfide: pdb=" SG CYS M 318 " - pdb=" SG CYS M 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 424 " - pdb=" SG CYS C 447 " distance=2.04 Simple disulfide: pdb=" SG CYS G 424 " - pdb=" SG CYS G 447 " distance=2.04 Simple disulfide: pdb=" SG CYS M 424 " - pdb=" SG CYS M 447 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG F 1 " - " NAG F 2 " " NAG K 1 " - " NAG K 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG B 1 " - " ASN A 284 " " NAG F 1 " - " ASN C 284 " " NAG K 1 " - " ASN G 284 " " NAG P 1 " - " ASN M 284 " Time building additional restraints: 4.47 Conformation dependent library (CDL) restraints added in 2.4 seconds 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4392 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 44 sheets defined 2.3% alpha, 42.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 99 through 103 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 99 through 103 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'G' and resid 99 through 103 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'M' and resid 99 through 103 Processing helix chain 'N' and resid 61 through 64 Processing helix chain 'N' and resid 83 through 87 Processing sheet with id=1, first strand: chain 'A' and resid 92 through 97 removed outlier: 6.807A pdb=" N ILE A 445 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU A 97 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR A 443 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 440 " --> pdb=" O HIS A 431 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU A 428 " --> pdb=" O TYR A 409 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TYR A 409 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 113 through 122 removed outlier: 4.901A pdb=" N LEU A 113 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA A 136 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ILE A 115 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N HIS A 134 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLU A 117 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU A 132 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET A 174 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N SER A 158 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N PHE A 172 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 178 through 183 removed outlier: 3.723A pdb=" N SER A 178 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU A 202 " --> pdb=" O THR A 213 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR A 213 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 204 " --> pdb=" O THR A 211 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 222 through 224 Processing sheet with id=5, first strand: chain 'A' and resid 222 through 224 removed outlier: 4.060A pdb=" N GLU A 250 " --> pdb=" O ASP A 242 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG A 257 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 268 through 269 removed outlier: 6.738A pdb=" N THR A 268 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N LEU A 316 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR A 286 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE A 281 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU A 288 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N CYS A 279 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA A 290 " --> pdb=" O CYS A 277 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N CYS A 277 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 352 through 356 removed outlier: 7.183A pdb=" N MET A 375 " --> pdb=" O PRO A 402 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N MET A 377 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL A 381 " --> pdb=" O PHE A 396 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N PHE A 396 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=9, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.842A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N SER H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP H 35A" --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.519A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 11.234A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 10.862A pdb=" N ILE L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N SER L 65 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.347A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'C' and resid 92 through 97 removed outlier: 6.807A pdb=" N ILE C 445 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU C 97 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR C 443 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 440 " --> pdb=" O HIS C 431 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU C 428 " --> pdb=" O TYR C 409 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TYR C 409 " --> pdb=" O GLU C 428 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'C' and resid 113 through 122 removed outlier: 4.901A pdb=" N LEU C 113 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA C 136 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ILE C 115 " --> pdb=" O HIS C 134 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N HIS C 134 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLU C 117 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU C 132 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET C 174 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N SER C 158 " --> pdb=" O PHE C 172 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N PHE C 172 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'C' and resid 178 through 183 removed outlier: 3.723A pdb=" N SER C 178 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU C 202 " --> pdb=" O THR C 213 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR C 213 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL C 204 " --> pdb=" O THR C 211 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 222 through 224 Processing sheet with id=16, first strand: chain 'C' and resid 222 through 224 removed outlier: 4.060A pdb=" N GLU C 250 " --> pdb=" O ASP C 242 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG C 257 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'C' and resid 268 through 269 removed outlier: 6.738A pdb=" N THR C 268 " --> pdb=" O ILE C 314 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N LEU C 316 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR C 286 " --> pdb=" O PHE C 281 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE C 281 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU C 288 " --> pdb=" O CYS C 279 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N CYS C 279 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA C 290 " --> pdb=" O CYS C 277 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N CYS C 277 " --> pdb=" O ALA C 290 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'C' and resid 352 through 356 removed outlier: 7.183A pdb=" N MET C 375 " --> pdb=" O PRO C 402 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N MET C 377 " --> pdb=" O MET C 400 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL C 381 " --> pdb=" O PHE C 396 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N PHE C 396 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=20, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.842A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N SER D 50 " --> pdb=" O TRP D 35A" (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP D 35A" --> pdb=" O SER D 50 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'E' and resid 4 through 7 removed outlier: 4.519A pdb=" N THR E 69 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N GLN E 27 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 11.234A pdb=" N SER E 67 " --> pdb=" O GLN E 27 " (cutoff:3.500A) removed outlier: 10.862A pdb=" N ILE E 29 " --> pdb=" O SER E 65 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N SER E 65 " --> pdb=" O ILE E 29 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.347A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'G' and resid 92 through 97 removed outlier: 6.807A pdb=" N ILE G 445 " --> pdb=" O ALA G 95 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU G 97 " --> pdb=" O THR G 443 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR G 443 " --> pdb=" O LEU G 97 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER G 440 " --> pdb=" O HIS G 431 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU G 428 " --> pdb=" O TYR G 409 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TYR G 409 " --> pdb=" O GLU G 428 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'G' and resid 113 through 122 removed outlier: 4.901A pdb=" N LEU G 113 " --> pdb=" O ALA G 136 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA G 136 " --> pdb=" O LEU G 113 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ILE G 115 " --> pdb=" O HIS G 134 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N HIS G 134 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLU G 117 " --> pdb=" O LEU G 132 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU G 132 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET G 174 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N SER G 158 " --> pdb=" O PHE G 172 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N PHE G 172 " --> pdb=" O SER G 158 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'G' and resid 178 through 183 removed outlier: 3.723A pdb=" N SER G 178 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU G 202 " --> pdb=" O THR G 213 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR G 213 " --> pdb=" O LEU G 202 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL G 204 " --> pdb=" O THR G 211 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'G' and resid 222 through 224 Processing sheet with id=27, first strand: chain 'G' and resid 222 through 224 removed outlier: 4.060A pdb=" N GLU G 250 " --> pdb=" O ASP G 242 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG G 257 " --> pdb=" O ILE G 261 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE G 261 " --> pdb=" O ARG G 257 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'G' and resid 268 through 269 removed outlier: 6.738A pdb=" N THR G 268 " --> pdb=" O ILE G 314 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N LEU G 316 " --> pdb=" O THR G 268 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR G 286 " --> pdb=" O PHE G 281 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE G 281 " --> pdb=" O THR G 286 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU G 288 " --> pdb=" O CYS G 279 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N CYS G 279 " --> pdb=" O GLU G 288 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA G 290 " --> pdb=" O CYS G 277 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N CYS G 277 " --> pdb=" O ALA G 290 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'G' and resid 352 through 356 removed outlier: 7.183A pdb=" N MET G 375 " --> pdb=" O PRO G 402 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N MET G 377 " --> pdb=" O MET G 400 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL G 381 " --> pdb=" O PHE G 396 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N PHE G 396 " --> pdb=" O VAL G 381 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=31, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.842A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N SER I 50 " --> pdb=" O TRP I 35A" (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP I 35A" --> pdb=" O SER I 50 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'J' and resid 4 through 7 removed outlier: 4.519A pdb=" N THR J 69 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N GLN J 27 " --> pdb=" O SER J 67 " (cutoff:3.500A) removed outlier: 11.234A pdb=" N SER J 67 " --> pdb=" O GLN J 27 " (cutoff:3.500A) removed outlier: 10.862A pdb=" N ILE J 29 " --> pdb=" O SER J 65 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N SER J 65 " --> pdb=" O ILE J 29 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.347A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'M' and resid 92 through 97 removed outlier: 6.807A pdb=" N ILE M 445 " --> pdb=" O ALA M 95 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU M 97 " --> pdb=" O THR M 443 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR M 443 " --> pdb=" O LEU M 97 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER M 440 " --> pdb=" O HIS M 431 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU M 428 " --> pdb=" O TYR M 409 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TYR M 409 " --> pdb=" O GLU M 428 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'M' and resid 113 through 122 removed outlier: 4.901A pdb=" N LEU M 113 " --> pdb=" O ALA M 136 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA M 136 " --> pdb=" O LEU M 113 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ILE M 115 " --> pdb=" O HIS M 134 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N HIS M 134 " --> pdb=" O ILE M 115 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLU M 117 " --> pdb=" O LEU M 132 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU M 132 " --> pdb=" O GLU M 117 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET M 174 " --> pdb=" O LEU M 156 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N SER M 158 " --> pdb=" O PHE M 172 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N PHE M 172 " --> pdb=" O SER M 158 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'M' and resid 178 through 183 removed outlier: 3.723A pdb=" N SER M 178 " --> pdb=" O VAL M 193 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU M 202 " --> pdb=" O THR M 213 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR M 213 " --> pdb=" O LEU M 202 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL M 204 " --> pdb=" O THR M 211 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'M' and resid 222 through 224 Processing sheet with id=38, first strand: chain 'M' and resid 222 through 224 removed outlier: 4.060A pdb=" N GLU M 250 " --> pdb=" O ASP M 242 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG M 257 " --> pdb=" O ILE M 261 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE M 261 " --> pdb=" O ARG M 257 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'M' and resid 268 through 269 removed outlier: 6.738A pdb=" N THR M 268 " --> pdb=" O ILE M 314 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N LEU M 316 " --> pdb=" O THR M 268 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR M 286 " --> pdb=" O PHE M 281 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE M 281 " --> pdb=" O THR M 286 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU M 288 " --> pdb=" O CYS M 279 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N CYS M 279 " --> pdb=" O GLU M 288 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA M 290 " --> pdb=" O CYS M 277 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N CYS M 277 " --> pdb=" O ALA M 290 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'M' and resid 352 through 356 removed outlier: 7.183A pdb=" N MET M 375 " --> pdb=" O PRO M 402 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N MET M 377 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL M 381 " --> pdb=" O PHE M 396 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N PHE M 396 " --> pdb=" O VAL M 381 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=42, first strand: chain 'N' and resid 57 through 59 removed outlier: 6.842A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N SER N 50 " --> pdb=" O TRP N 35A" (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP N 35A" --> pdb=" O SER N 50 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'O' and resid 4 through 7 removed outlier: 4.519A pdb=" N THR O 69 " --> pdb=" O ALA O 25 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N GLN O 27 " --> pdb=" O SER O 67 " (cutoff:3.500A) removed outlier: 11.234A pdb=" N SER O 67 " --> pdb=" O GLN O 27 " (cutoff:3.500A) removed outlier: 10.862A pdb=" N ILE O 29 " --> pdb=" O SER O 65 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N SER O 65 " --> pdb=" O ILE O 29 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.347A pdb=" N LEU O 11 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1500 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.29 Time building geometry restraints manager: 5.25 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: 3780 1.32 - 1.45: 6292 1.45 - 1.59: 9192 1.59 - 1.73: 40 1.73 - 1.86: 180 Bond restraints: 19484 Sorted by residual: bond pdb=" CB HIS C 354 " pdb=" CG HIS C 354 " ideal model delta sigma weight residual 1.497 1.378 0.119 1.40e-02 5.10e+03 7.18e+01 bond pdb=" CB HIS A 354 " pdb=" CG HIS A 354 " ideal model delta sigma weight residual 1.497 1.378 0.119 1.40e-02 5.10e+03 7.18e+01 bond pdb=" CB HIS G 354 " pdb=" CG HIS G 354 " ideal model delta sigma weight residual 1.497 1.378 0.119 1.40e-02 5.10e+03 7.18e+01 bond pdb=" CB HIS M 354 " pdb=" CG HIS M 354 " ideal model delta sigma weight residual 1.497 1.378 0.119 1.40e-02 5.10e+03 7.18e+01 bond pdb=" NE ARG C 327 " pdb=" CZ ARG C 327 " ideal model delta sigma weight residual 1.326 1.389 -0.063 1.10e-02 8.26e+03 3.31e+01 ... (remaining 19479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 20708 2.06 - 4.13: 4360 4.13 - 6.19: 1028 6.19 - 8.26: 232 8.26 - 10.32: 60 Bond angle restraints: 26388 Sorted by residual: angle pdb=" C GLY G 335 " pdb=" N PRO G 336 " pdb=" CA PRO G 336 " ideal model delta sigma weight residual 119.92 128.47 -8.55 1.07e+00 8.73e-01 6.39e+01 angle pdb=" C GLY C 335 " pdb=" N PRO C 336 " pdb=" CA PRO C 336 " ideal model delta sigma weight residual 119.92 128.47 -8.55 1.07e+00 8.73e-01 6.39e+01 angle pdb=" C GLY M 335 " pdb=" N PRO M 336 " pdb=" CA PRO M 336 " ideal model delta sigma weight residual 119.92 128.47 -8.55 1.07e+00 8.73e-01 6.39e+01 angle pdb=" C GLY A 335 " pdb=" N PRO A 336 " pdb=" CA PRO A 336 " ideal model delta sigma weight residual 119.92 128.47 -8.55 1.07e+00 8.73e-01 6.39e+01 angle pdb=" C LYS H 13 " pdb=" N PRO H 14 " pdb=" CA PRO H 14 " ideal model delta sigma weight residual 120.03 127.91 -7.88 9.90e-01 1.02e+00 6.34e+01 ... (remaining 26383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 11112 15.96 - 31.92: 372 31.92 - 47.88: 80 47.88 - 63.84: 60 63.84 - 79.80: 32 Dihedral angle restraints: 11656 sinusoidal: 4692 harmonic: 6964 Sorted by residual: dihedral pdb=" CB CYS A 182 " pdb=" SG CYS A 182 " pdb=" SG CYS A 229 " pdb=" CB CYS A 229 " ideal model delta sinusoidal sigma weight residual -86.00 -17.42 -68.58 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS G 182 " pdb=" SG CYS G 182 " pdb=" SG CYS G 229 " pdb=" CB CYS G 229 " ideal model delta sinusoidal sigma weight residual -86.00 -17.42 -68.58 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS M 182 " pdb=" SG CYS M 182 " pdb=" SG CYS M 229 " pdb=" CB CYS M 229 " ideal model delta sinusoidal sigma weight residual -86.00 -17.42 -68.58 1 1.00e+01 1.00e-02 6.09e+01 ... (remaining 11653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1968 0.099 - 0.198: 676 0.198 - 0.298: 164 0.298 - 0.397: 20 0.397 - 0.496: 12 Chirality restraints: 2840 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.36e+01 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.36e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.36e+01 ... (remaining 2837 not shown) Planarity restraints: 3360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 52 " -0.072 2.00e-02 2.50e+03 3.85e-02 2.97e+01 pdb=" CG TYR D 52 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR D 52 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR D 52 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR D 52 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR D 52 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR D 52 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR D 52 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 52 " 0.072 2.00e-02 2.50e+03 3.85e-02 2.97e+01 pdb=" CG TYR H 52 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR H 52 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR H 52 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR H 52 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR H 52 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR H 52 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR H 52 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 52 " 0.072 2.00e-02 2.50e+03 3.85e-02 2.97e+01 pdb=" CG TYR N 52 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR N 52 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR N 52 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR N 52 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR N 52 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR N 52 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR N 52 " 0.059 2.00e-02 2.50e+03 ... (remaining 3357 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 296 2.60 - 3.17: 15556 3.17 - 3.75: 29008 3.75 - 4.32: 44396 4.32 - 4.90: 71520 Nonbonded interactions: 160776 Sorted by model distance: nonbonded pdb=" SG CYS N 22 " pdb=" SG CYS N 92 " model vdw 2.021 3.760 nonbonded pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " model vdw 2.021 3.760 nonbonded pdb=" SG CYS I 22 " pdb=" SG CYS I 92 " model vdw 2.021 3.760 nonbonded pdb=" SG CYS D 22 " pdb=" SG CYS D 92 " model vdw 2.021 3.760 nonbonded pdb=" SG CYS E 23 " pdb=" SG CYS E 88 " model vdw 2.043 3.760 ... (remaining 160771 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: 0.15 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'H' selection = chain 'N' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'K' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 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: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 39.530 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 0.624 19524 Z= 1.210 Angle : 2.085 63.784 26476 Z= 1.322 Chirality : 0.108 0.496 2840 Planarity : 0.010 0.088 3356 Dihedral : 10.357 79.802 7168 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.83 % Allowed : 4.13 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 3.70 % 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: -0.75 (0.16), residues: 2424 helix: -4.87 (0.12), residues: 24 sheet: 0.18 (0.16), residues: 972 loop : -0.91 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.010 TRP C 456 HIS 0.017 0.003 HIS C 273 PHE 0.030 0.006 PHE E 98 TYR 0.072 0.009 TYR I 52 ARG 0.012 0.002 ARG A 260 Details of bonding type rmsd link_NAG-ASN : bond 0.10366 ( 4) link_NAG-ASN : angle 3.71335 ( 12) link_BETA1-4 : bond 0.06911 ( 4) link_BETA1-4 : angle 4.24575 ( 12) hydrogen bonds : bond 0.17002 ( 588) hydrogen bonds : angle 9.18637 ( 1500) SS BOND : bond 0.22104 ( 32) SS BOND : angle 16.20646 ( 64) covalent geometry : bond 0.02125 (19484) covalent geometry : angle 1.92610 (26388) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 2.118 Fit side-chains REVERT: L 78 LEU cc_start: 0.7766 (tt) cc_final: 0.7563 (tt) REVERT: C 116 ARG cc_start: 0.8039 (mtp180) cc_final: 0.7839 (mmm160) REVERT: E 78 LEU cc_start: 0.7765 (tt) cc_final: 0.7564 (tt) REVERT: G 116 ARG cc_start: 0.8043 (mtp180) cc_final: 0.7841 (mmm160) REVERT: M 116 ARG cc_start: 0.8041 (mtp180) cc_final: 0.7841 (mmm160) outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 0.3098 time to fit residues: 233.0495 Evaluate side-chains 299 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 184 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 214 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN H 77 GLN C 294 ASN C 439 HIS D 77 GLN G 294 ASN G 439 HIS I 77 GLN M 294 ASN M 439 HIS N 77 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.156399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.134643 restraints weight = 25332.515| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.79 r_work: 0.3684 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19524 Z= 0.181 Angle : 0.800 20.136 26476 Z= 0.417 Chirality : 0.050 0.163 2840 Planarity : 0.005 0.051 3356 Dihedral : 6.639 62.656 2844 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.40 % Favored : 94.10 % Rotamer: Outliers : 2.34 % Allowed : 7.46 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.17 % 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: -1.12 (0.16), residues: 2424 helix: None (None), residues: 0 sheet: 0.22 (0.17), residues: 936 loop : -1.45 (0.14), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 103 HIS 0.015 0.002 HIS C 101 PHE 0.030 0.002 PHE O 83 TYR 0.025 0.002 TYR N 34 ARG 0.007 0.001 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 4) link_NAG-ASN : angle 3.99350 ( 12) link_BETA1-4 : bond 0.00645 ( 4) link_BETA1-4 : angle 2.95360 ( 12) hydrogen bonds : bond 0.05216 ( 588) hydrogen bonds : angle 7.38908 ( 1500) SS BOND : bond 0.00302 ( 32) SS BOND : angle 1.16402 ( 64) covalent geometry : bond 0.00408 (19484) covalent geometry : angle 0.79239 (26388) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 363 time to evaluate : 1.977 Fit side-chains REVERT: A 242 ASP cc_start: 0.6938 (t0) cc_final: 0.6664 (t0) REVERT: A 435 LYS cc_start: 0.7159 (mmtt) cc_final: 0.6912 (mmtm) REVERT: L 78 LEU cc_start: 0.7576 (tt) cc_final: 0.7198 (tt) REVERT: L 86 TYR cc_start: 0.7194 (m-80) cc_final: 0.6569 (m-80) REVERT: C 116 ARG cc_start: 0.8117 (mtp180) cc_final: 0.7909 (mtp180) REVERT: C 242 ASP cc_start: 0.6929 (t0) cc_final: 0.6655 (t0) REVERT: C 435 LYS cc_start: 0.7144 (mmtt) cc_final: 0.6918 (mmtm) REVERT: E 78 LEU cc_start: 0.7586 (tt) cc_final: 0.7205 (tt) REVERT: E 86 TYR cc_start: 0.7200 (m-80) cc_final: 0.6572 (m-80) REVERT: G 242 ASP cc_start: 0.6932 (t0) cc_final: 0.6657 (t0) REVERT: G 435 LYS cc_start: 0.7143 (mmtt) cc_final: 0.6922 (mmtm) REVERT: J 86 TYR cc_start: 0.7198 (m-80) cc_final: 0.6572 (m-80) REVERT: M 116 ARG cc_start: 0.8121 (mtp180) cc_final: 0.7911 (mtp180) REVERT: M 242 ASP cc_start: 0.6937 (t0) cc_final: 0.6664 (t0) REVERT: M 435 LYS cc_start: 0.7151 (mmtt) cc_final: 0.6928 (mmtm) REVERT: O 86 TYR cc_start: 0.7201 (m-80) cc_final: 0.6574 (m-80) outliers start: 48 outliers final: 21 residues processed: 387 average time/residue: 0.2947 time to fit residues: 175.6927 Evaluate side-chains 330 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 309 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain M residue 278 THR Chi-restraints excluded: chain M residue 342 ASP Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 215 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 93 optimal weight: 0.0170 chunk 202 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 195 optimal weight: 0.8980 chunk 205 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 100AASN L 6 GLN L 79 GLN D 39 GLN D 100AASN E 6 GLN E 79 GLN G 294 ASN I 39 GLN I 100AASN J 6 GLN M 294 ASN N 39 GLN N 100AASN O 6 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.153261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.131498 restraints weight = 25240.110| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.81 r_work: 0.3616 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19524 Z= 0.195 Angle : 0.785 31.581 26476 Z= 0.377 Chirality : 0.048 0.167 2840 Planarity : 0.005 0.064 3356 Dihedral : 6.255 60.907 2844 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.64 % Favored : 93.03 % Rotamer: Outliers : 2.53 % Allowed : 9.41 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -1.70 (0.15), residues: 2424 helix: None (None), residues: 0 sheet: -0.29 (0.16), residues: 944 loop : -1.77 (0.14), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 438 HIS 0.007 0.002 HIS C 101 PHE 0.024 0.002 PHE H 78 TYR 0.022 0.002 TYR D 53 ARG 0.005 0.001 ARG J 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00728 ( 4) link_NAG-ASN : angle 2.87848 ( 12) link_BETA1-4 : bond 0.00926 ( 4) link_BETA1-4 : angle 2.17256 ( 12) hydrogen bonds : bond 0.04716 ( 588) hydrogen bonds : angle 6.84495 ( 1500) SS BOND : bond 0.00245 ( 32) SS BOND : angle 0.73912 ( 64) covalent geometry : bond 0.00461 (19484) covalent geometry : angle 0.78201 (26388) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 346 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 ASP cc_start: 0.7081 (t0) cc_final: 0.6857 (t0) REVERT: A 308 GLU cc_start: 0.8533 (tm-30) cc_final: 0.7870 (tm-30) REVERT: A 428 GLU cc_start: 0.7563 (tt0) cc_final: 0.7310 (tt0) REVERT: H 75 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8058 (mtmt) REVERT: L 86 TYR cc_start: 0.7272 (m-80) cc_final: 0.6514 (m-80) REVERT: L 103 LYS cc_start: 0.8128 (ptmt) cc_final: 0.7920 (ptmt) REVERT: C 116 ARG cc_start: 0.8292 (mtp180) cc_final: 0.7977 (mtp180) REVERT: C 242 ASP cc_start: 0.7068 (t0) cc_final: 0.6849 (t0) REVERT: C 308 GLU cc_start: 0.8519 (tm-30) cc_final: 0.7861 (tm-30) REVERT: D 75 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8054 (mtmt) REVERT: E 86 TYR cc_start: 0.7286 (m-80) cc_final: 0.6522 (m-80) REVERT: E 103 LYS cc_start: 0.8134 (ptmt) cc_final: 0.7921 (ptmt) REVERT: G 242 ASP cc_start: 0.7083 (t0) cc_final: 0.6862 (t0) REVERT: G 308 GLU cc_start: 0.8519 (tm-30) cc_final: 0.7860 (tm-30) REVERT: I 75 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8053 (mtmt) REVERT: J 86 TYR cc_start: 0.7277 (m-80) cc_final: 0.6515 (m-80) REVERT: M 116 ARG cc_start: 0.8294 (mtp180) cc_final: 0.7976 (mtp180) REVERT: M 242 ASP cc_start: 0.7072 (t0) cc_final: 0.6849 (t0) REVERT: M 308 GLU cc_start: 0.8544 (tm-30) cc_final: 0.7884 (tm-30) REVERT: N 75 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8050 (mtmt) REVERT: O 86 TYR cc_start: 0.7285 (m-80) cc_final: 0.6522 (m-80) outliers start: 52 outliers final: 31 residues processed: 380 average time/residue: 0.3035 time to fit residues: 175.3296 Evaluate side-chains 346 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 311 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain G residue 229 CYS Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 429 MET Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 278 THR Chi-restraints excluded: chain M residue 342 ASP Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain M residue 429 MET Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 75 LYS Chi-restraints excluded: chain N residue 83 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 213 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 232 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN H 100AASN C 230 ASN D 100AASN G 230 ASN ** G 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 100AASN M 230 ASN N 100AASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.145600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.123296 restraints weight = 26004.398| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.82 r_work: 0.3554 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 19524 Z= 0.265 Angle : 0.806 30.545 26476 Z= 0.390 Chirality : 0.050 0.200 2840 Planarity : 0.005 0.076 3356 Dihedral : 6.426 62.003 2844 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.27 % Favored : 93.40 % Rotamer: Outliers : 3.22 % Allowed : 10.96 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -1.99 (0.15), residues: 2424 helix: -3.42 (0.71), residues: 24 sheet: -0.29 (0.16), residues: 916 loop : -2.06 (0.14), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 438 HIS 0.009 0.002 HIS G 101 PHE 0.025 0.002 PHE E 83 TYR 0.023 0.002 TYR A 143 ARG 0.006 0.001 ARG J 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 4) link_NAG-ASN : angle 2.86648 ( 12) link_BETA1-4 : bond 0.00538 ( 4) link_BETA1-4 : angle 1.62222 ( 12) hydrogen bonds : bond 0.04560 ( 588) hydrogen bonds : angle 6.86893 ( 1500) SS BOND : bond 0.00333 ( 32) SS BOND : angle 0.85520 ( 64) covalent geometry : bond 0.00634 (19484) covalent geometry : angle 0.80271 (26388) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 328 time to evaluate : 2.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7469 (tp30) REVERT: A 308 GLU cc_start: 0.8574 (tm-30) cc_final: 0.7872 (tm-30) REVERT: A 428 GLU cc_start: 0.7714 (tt0) cc_final: 0.7422 (tt0) REVERT: H 5 GLN cc_start: 0.7188 (pt0) cc_final: 0.6986 (pt0) REVERT: L 86 TYR cc_start: 0.7313 (m-80) cc_final: 0.6496 (m-80) REVERT: C 116 ARG cc_start: 0.8382 (mtp180) cc_final: 0.8011 (mtp180) REVERT: C 208 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7475 (tp30) REVERT: C 308 GLU cc_start: 0.8566 (tm-30) cc_final: 0.7867 (tm-30) REVERT: E 86 TYR cc_start: 0.7324 (m-80) cc_final: 0.6501 (m-80) REVERT: G 208 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7478 (tp30) REVERT: G 308 GLU cc_start: 0.8566 (tm-30) cc_final: 0.7863 (tm-30) REVERT: I 5 GLN cc_start: 0.7196 (pt0) cc_final: 0.6993 (pt0) REVERT: J 14 SER cc_start: 0.7505 (t) cc_final: 0.7124 (p) REVERT: J 86 TYR cc_start: 0.7314 (m-80) cc_final: 0.6495 (m-80) REVERT: M 116 ARG cc_start: 0.8385 (mtp180) cc_final: 0.8012 (mtp180) REVERT: M 208 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7479 (tp30) REVERT: M 308 GLU cc_start: 0.8574 (tm-30) cc_final: 0.7874 (tm-30) REVERT: N 5 GLN cc_start: 0.7191 (pt0) cc_final: 0.6991 (pt0) REVERT: O 14 SER cc_start: 0.7510 (t) cc_final: 0.7126 (p) REVERT: O 86 TYR cc_start: 0.7317 (m-80) cc_final: 0.6493 (m-80) outliers start: 66 outliers final: 40 residues processed: 378 average time/residue: 0.3349 time to fit residues: 192.9527 Evaluate side-chains 329 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 289 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain G residue 229 CYS Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 429 MET Chi-restraints excluded: chain G residue 456 TRP Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 278 THR Chi-restraints excluded: chain M residue 342 ASP Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain M residue 429 MET Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 83 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 34 optimal weight: 0.0040 chunk 37 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 205 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100AASN C 169 ASN D 100AASN ** G 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 100AASN M 169 ASN N 100AASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.150746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.128533 restraints weight = 25658.979| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.77 r_work: 0.3628 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19524 Z= 0.132 Angle : 0.759 35.574 26476 Z= 0.342 Chirality : 0.047 0.197 2840 Planarity : 0.005 0.068 3356 Dihedral : 5.965 57.908 2844 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.77 % Favored : 92.90 % Rotamer: Outliers : 2.63 % Allowed : 12.72 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -1.92 (0.16), residues: 2424 helix: -2.98 (0.87), residues: 24 sheet: -0.32 (0.16), residues: 928 loop : -1.98 (0.14), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 177 HIS 0.006 0.001 HIS A 101 PHE 0.029 0.002 PHE D 78 TYR 0.014 0.002 TYR I 53 ARG 0.005 0.000 ARG J 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00658 ( 4) link_NAG-ASN : angle 2.27930 ( 12) link_BETA1-4 : bond 0.00681 ( 4) link_BETA1-4 : angle 1.30221 ( 12) hydrogen bonds : bond 0.04022 ( 588) hydrogen bonds : angle 6.49684 ( 1500) SS BOND : bond 0.00219 ( 32) SS BOND : angle 0.62776 ( 64) covalent geometry : bond 0.00303 (19484) covalent geometry : angle 0.75790 (26388) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 343 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7324 (tp30) REVERT: A 308 GLU cc_start: 0.8527 (tm-30) cc_final: 0.7842 (tm-30) REVERT: A 428 GLU cc_start: 0.7462 (tt0) cc_final: 0.7246 (tt0) REVERT: H 5 GLN cc_start: 0.7106 (pt0) cc_final: 0.6875 (pt0) REVERT: L 37 GLN cc_start: 0.8389 (tt0) cc_final: 0.7804 (tt0) REVERT: L 86 TYR cc_start: 0.7271 (m-80) cc_final: 0.6432 (m-80) REVERT: C 116 ARG cc_start: 0.8283 (mtp180) cc_final: 0.8009 (mtp180) REVERT: C 208 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7333 (tp30) REVERT: C 308 GLU cc_start: 0.8513 (tm-30) cc_final: 0.7830 (tm-30) REVERT: E 37 GLN cc_start: 0.8388 (tt0) cc_final: 0.7807 (tt0) REVERT: E 86 TYR cc_start: 0.7281 (m-80) cc_final: 0.6443 (m-80) REVERT: G 208 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7339 (tp30) REVERT: G 308 GLU cc_start: 0.8516 (tm-30) cc_final: 0.7832 (tm-30) REVERT: I 5 GLN cc_start: 0.7116 (pt0) cc_final: 0.6884 (pt0) REVERT: J 14 SER cc_start: 0.7410 (t) cc_final: 0.7094 (p) REVERT: J 37 GLN cc_start: 0.8392 (tt0) cc_final: 0.7810 (tt0) REVERT: J 86 TYR cc_start: 0.7277 (m-80) cc_final: 0.6442 (m-80) REVERT: M 116 ARG cc_start: 0.8281 (mtp180) cc_final: 0.8008 (mtp180) REVERT: M 208 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7329 (tp30) REVERT: M 308 GLU cc_start: 0.8518 (tm-30) cc_final: 0.7835 (tm-30) REVERT: N 5 GLN cc_start: 0.7113 (pt0) cc_final: 0.6882 (pt0) REVERT: O 14 SER cc_start: 0.7416 (t) cc_final: 0.7099 (p) REVERT: O 37 GLN cc_start: 0.8389 (tt0) cc_final: 0.7814 (tt0) REVERT: O 86 TYR cc_start: 0.7281 (m-80) cc_final: 0.6445 (m-80) outliers start: 54 outliers final: 27 residues processed: 379 average time/residue: 0.2978 time to fit residues: 173.8700 Evaluate side-chains 348 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 321 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain G residue 229 CYS Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 456 TRP Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 342 ASP Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 83 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 88 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 0.0270 chunk 219 optimal weight: 3.9990 chunk 180 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 overall best weight: 1.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100AASN L 38 GLN D 100AASN E 38 GLN G 439 HIS I 100AASN J 38 GLN N 100AASN O 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.146291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.124193 restraints weight = 25768.151| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.77 r_work: 0.3566 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19524 Z= 0.217 Angle : 0.779 33.175 26476 Z= 0.362 Chirality : 0.049 0.220 2840 Planarity : 0.005 0.071 3356 Dihedral : 6.107 59.557 2844 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.76 % Favored : 91.91 % Rotamer: Outliers : 2.44 % Allowed : 12.04 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -2.12 (0.16), residues: 2424 helix: -2.96 (0.90), residues: 24 sheet: -0.56 (0.16), residues: 984 loop : -2.08 (0.14), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 177 HIS 0.008 0.002 HIS G 101 PHE 0.024 0.002 PHE D 78 TYR 0.018 0.002 TYR G 296 ARG 0.005 0.001 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 4) link_NAG-ASN : angle 2.57679 ( 12) link_BETA1-4 : bond 0.00440 ( 4) link_BETA1-4 : angle 1.20146 ( 12) hydrogen bonds : bond 0.04272 ( 588) hydrogen bonds : angle 6.60163 ( 1500) SS BOND : bond 0.00315 ( 32) SS BOND : angle 0.74043 ( 64) covalent geometry : bond 0.00517 (19484) covalent geometry : angle 0.77664 (26388) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 361 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7268 (tp30) REVERT: A 308 GLU cc_start: 0.8549 (tm-30) cc_final: 0.7856 (tm-30) REVERT: A 428 GLU cc_start: 0.7638 (tt0) cc_final: 0.7389 (tt0) REVERT: L 78 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7128 (tt) REVERT: L 83 PHE cc_start: 0.7605 (m-80) cc_final: 0.7400 (m-80) REVERT: L 86 TYR cc_start: 0.7241 (m-80) cc_final: 0.6381 (m-80) REVERT: C 116 ARG cc_start: 0.8406 (mtp180) cc_final: 0.8025 (mtp180) REVERT: C 208 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7289 (tp30) REVERT: C 308 GLU cc_start: 0.8525 (tm-30) cc_final: 0.7831 (tm-30) REVERT: E 78 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7125 (tt) REVERT: E 83 PHE cc_start: 0.7600 (m-80) cc_final: 0.7397 (m-80) REVERT: E 86 TYR cc_start: 0.7254 (m-80) cc_final: 0.6400 (m-80) REVERT: G 208 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7279 (tp30) REVERT: G 308 GLU cc_start: 0.8525 (tm-30) cc_final: 0.7831 (tm-30) REVERT: J 14 SER cc_start: 0.7451 (t) cc_final: 0.6667 (p) REVERT: J 86 TYR cc_start: 0.7232 (m-80) cc_final: 0.6396 (m-80) REVERT: M 116 ARG cc_start: 0.8403 (mtp180) cc_final: 0.8018 (mtp180) REVERT: M 208 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7286 (tp30) REVERT: M 308 GLU cc_start: 0.8537 (tm-30) cc_final: 0.7842 (tm-30) REVERT: O 14 SER cc_start: 0.7444 (t) cc_final: 0.6662 (p) REVERT: O 86 TYR cc_start: 0.7238 (m-80) cc_final: 0.6399 (m-80) outliers start: 50 outliers final: 36 residues processed: 387 average time/residue: 0.2785 time to fit residues: 169.3772 Evaluate side-chains 375 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 337 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain G residue 135 TYR Chi-restraints excluded: chain G residue 229 CYS Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 429 MET Chi-restraints excluded: chain G residue 456 TRP Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 342 ASP Chi-restraints excluded: chain M residue 429 MET Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 83 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 20 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 60 optimal weight: 0.0670 chunk 81 optimal weight: 0.5980 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN H 100AASN L 38 GLN D 100AASN E 38 GLN G 169 ASN I 100AASN J 38 GLN N 100AASN O 38 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.148855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.126709 restraints weight = 25506.148| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.78 r_work: 0.3600 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19524 Z= 0.149 Angle : 0.757 35.454 26476 Z= 0.340 Chirality : 0.047 0.219 2840 Planarity : 0.005 0.067 3356 Dihedral : 5.850 57.346 2844 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.10 % Favored : 92.74 % Rotamer: Outliers : 2.24 % Allowed : 12.96 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -2.04 (0.16), residues: 2424 helix: -2.79 (0.95), residues: 24 sheet: -0.47 (0.16), residues: 936 loop : -2.02 (0.14), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 36 HIS 0.006 0.001 HIS A 101 PHE 0.028 0.002 PHE J 83 TYR 0.015 0.002 TYR G 296 ARG 0.005 0.000 ARG J 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 4) link_NAG-ASN : angle 2.22851 ( 12) link_BETA1-4 : bond 0.00573 ( 4) link_BETA1-4 : angle 1.02057 ( 12) hydrogen bonds : bond 0.03953 ( 588) hydrogen bonds : angle 6.34988 ( 1500) SS BOND : bond 0.00207 ( 32) SS BOND : angle 0.76227 ( 64) covalent geometry : bond 0.00356 (19484) covalent geometry : angle 0.75542 (26388) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 338 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7286 (tp30) REVERT: A 428 GLU cc_start: 0.7558 (tt0) cc_final: 0.7305 (tt0) REVERT: L 37 GLN cc_start: 0.8130 (tt0) cc_final: 0.7376 (tp40) REVERT: L 78 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7053 (tt) REVERT: L 83 PHE cc_start: 0.7561 (m-80) cc_final: 0.7351 (m-80) REVERT: L 86 TYR cc_start: 0.7211 (m-80) cc_final: 0.6457 (m-80) REVERT: C 116 ARG cc_start: 0.8393 (mtp180) cc_final: 0.8016 (mtp180) REVERT: C 208 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7290 (tp30) REVERT: E 37 GLN cc_start: 0.8134 (tt0) cc_final: 0.7381 (tp40) REVERT: E 78 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7051 (tt) REVERT: E 83 PHE cc_start: 0.7561 (m-80) cc_final: 0.7353 (m-80) REVERT: E 86 TYR cc_start: 0.7237 (m-80) cc_final: 0.6480 (m-80) REVERT: G 208 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7298 (tp30) REVERT: J 14 SER cc_start: 0.7736 (t) cc_final: 0.7346 (p) REVERT: J 37 GLN cc_start: 0.8223 (tt0) cc_final: 0.7515 (tp40) REVERT: J 86 TYR cc_start: 0.7242 (m-80) cc_final: 0.6510 (m-80) REVERT: M 116 ARG cc_start: 0.8391 (mtp180) cc_final: 0.8010 (mtp180) REVERT: M 208 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7292 (tp30) REVERT: O 14 SER cc_start: 0.7740 (t) cc_final: 0.7350 (p) REVERT: O 37 GLN cc_start: 0.8222 (tt0) cc_final: 0.7519 (tp40) REVERT: O 86 TYR cc_start: 0.7248 (m-80) cc_final: 0.6511 (m-80) outliers start: 46 outliers final: 36 residues processed: 365 average time/residue: 0.2961 time to fit residues: 167.5382 Evaluate side-chains 349 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 311 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 428 GLU Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain G residue 135 TYR Chi-restraints excluded: chain G residue 229 CYS Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 428 GLU Chi-restraints excluded: chain G residue 429 MET Chi-restraints excluded: chain G residue 456 TRP Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 342 ASP Chi-restraints excluded: chain M residue 428 GLU Chi-restraints excluded: chain M residue 429 MET Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain O residue 85 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 38 optimal weight: 0.0470 chunk 183 optimal weight: 2.9990 chunk 85 optimal weight: 0.0570 chunk 117 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100AASN L 38 GLN D 100AASN E 38 GLN I 100AASN J 38 GLN N 100AASN O 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.147405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.125372 restraints weight = 25664.780| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.76 r_work: 0.3579 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19524 Z= 0.184 Angle : 0.773 34.444 26476 Z= 0.351 Chirality : 0.048 0.285 2840 Planarity : 0.005 0.067 3356 Dihedral : 5.926 58.238 2844 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.17 % Favored : 91.67 % Rotamer: Outliers : 2.14 % Allowed : 13.11 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -2.20 (0.16), residues: 2424 helix: -2.77 (0.96), residues: 24 sheet: -0.61 (0.17), residues: 936 loop : -2.11 (0.14), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 36 HIS 0.007 0.001 HIS A 101 PHE 0.027 0.002 PHE J 83 TYR 0.015 0.002 TYR N 53 ARG 0.006 0.000 ARG E 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 4) link_NAG-ASN : angle 2.24476 ( 12) link_BETA1-4 : bond 0.00343 ( 4) link_BETA1-4 : angle 0.98252 ( 12) hydrogen bonds : bond 0.04116 ( 588) hydrogen bonds : angle 6.35838 ( 1500) SS BOND : bond 0.00186 ( 32) SS BOND : angle 0.74983 ( 64) covalent geometry : bond 0.00441 (19484) covalent geometry : angle 0.77175 (26388) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 332 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7324 (tp30) REVERT: A 286 THR cc_start: 0.9240 (t) cc_final: 0.9020 (m) REVERT: L 37 GLN cc_start: 0.8139 (tt0) cc_final: 0.7381 (tt0) REVERT: L 78 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7065 (tt) REVERT: L 83 PHE cc_start: 0.7616 (m-80) cc_final: 0.7396 (m-80) REVERT: L 86 TYR cc_start: 0.7271 (m-80) cc_final: 0.6570 (m-80) REVERT: C 116 ARG cc_start: 0.8417 (mtp180) cc_final: 0.7992 (mtp180) REVERT: C 208 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7334 (tp30) REVERT: C 286 THR cc_start: 0.9242 (t) cc_final: 0.9024 (m) REVERT: E 78 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7061 (tt) REVERT: E 83 PHE cc_start: 0.7613 (m-80) cc_final: 0.7394 (m-80) REVERT: E 86 TYR cc_start: 0.7286 (m-80) cc_final: 0.6588 (m-80) REVERT: G 208 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7329 (tp30) REVERT: G 286 THR cc_start: 0.9235 (t) cc_final: 0.9014 (m) REVERT: J 14 SER cc_start: 0.7665 (t) cc_final: 0.7250 (p) REVERT: J 37 GLN cc_start: 0.8150 (tt0) cc_final: 0.7386 (tt0) REVERT: J 86 TYR cc_start: 0.7271 (m-80) cc_final: 0.6500 (m-80) REVERT: M 116 ARG cc_start: 0.8408 (mtp180) cc_final: 0.7981 (mtp180) REVERT: M 208 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7327 (tp30) REVERT: M 286 THR cc_start: 0.9234 (t) cc_final: 0.9014 (m) REVERT: O 14 SER cc_start: 0.7663 (t) cc_final: 0.7249 (p) REVERT: O 37 GLN cc_start: 0.8150 (tt0) cc_final: 0.7399 (tt0) REVERT: O 86 TYR cc_start: 0.7285 (m-80) cc_final: 0.6509 (m-80) outliers start: 44 outliers final: 36 residues processed: 360 average time/residue: 0.2799 time to fit residues: 158.8326 Evaluate side-chains 366 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 328 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 428 GLU Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain G residue 135 TYR Chi-restraints excluded: chain G residue 229 CYS Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 428 GLU Chi-restraints excluded: chain G residue 429 MET Chi-restraints excluded: chain G residue 456 TRP Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 342 ASP Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain M residue 428 GLU Chi-restraints excluded: chain M residue 429 MET Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain O residue 85 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 97 optimal weight: 5.9990 chunk 181 optimal weight: 0.0670 chunk 18 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 214 optimal weight: 0.9990 chunk 190 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 overall best weight: 0.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN E 38 GLN N 100AASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.146281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.123628 restraints weight = 26890.597| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.86 r_work: 0.3548 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19524 Z= 0.140 Angle : 0.762 36.314 26476 Z= 0.337 Chirality : 0.047 0.357 2840 Planarity : 0.004 0.064 3356 Dihedral : 5.712 55.919 2844 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.34 % Favored : 92.49 % Rotamer: Outliers : 2.00 % Allowed : 13.40 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -2.11 (0.16), residues: 2424 helix: -2.68 (0.95), residues: 24 sheet: -0.49 (0.17), residues: 932 loop : -2.09 (0.14), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 36 HIS 0.005 0.001 HIS A 101 PHE 0.027 0.002 PHE J 83 TYR 0.018 0.002 TYR E 94 ARG 0.007 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 4) link_NAG-ASN : angle 2.06013 ( 12) link_BETA1-4 : bond 0.00447 ( 4) link_BETA1-4 : angle 0.87502 ( 12) hydrogen bonds : bond 0.03828 ( 588) hydrogen bonds : angle 6.17287 ( 1500) SS BOND : bond 0.00219 ( 32) SS BOND : angle 0.74033 ( 64) covalent geometry : bond 0.00333 (19484) covalent geometry : angle 0.76060 (26388) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 318 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7317 (tp30) REVERT: A 286 THR cc_start: 0.9248 (t) cc_final: 0.9029 (m) REVERT: A 428 GLU cc_start: 0.7683 (tt0) cc_final: 0.7407 (tt0) REVERT: L 37 GLN cc_start: 0.8124 (tt0) cc_final: 0.7284 (tp40) REVERT: L 78 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.6929 (tt) REVERT: L 83 PHE cc_start: 0.7521 (m-80) cc_final: 0.7288 (m-80) REVERT: L 86 TYR cc_start: 0.7205 (m-80) cc_final: 0.6438 (m-80) REVERT: C 116 ARG cc_start: 0.8398 (mtp180) cc_final: 0.7966 (mtp180) REVERT: C 208 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7310 (tp30) REVERT: C 286 THR cc_start: 0.9246 (t) cc_final: 0.9034 (m) REVERT: E 37 GLN cc_start: 0.8071 (tt0) cc_final: 0.7152 (tp40) REVERT: E 78 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.6920 (tt) REVERT: E 83 PHE cc_start: 0.7504 (m-80) cc_final: 0.7274 (m-80) REVERT: E 86 TYR cc_start: 0.7168 (m-80) cc_final: 0.6585 (m-80) REVERT: G 208 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7329 (tp30) REVERT: G 286 THR cc_start: 0.9233 (t) cc_final: 0.9018 (m) REVERT: J 14 SER cc_start: 0.7655 (t) cc_final: 0.7278 (p) REVERT: J 37 GLN cc_start: 0.8177 (tt0) cc_final: 0.7450 (tp40) REVERT: J 86 TYR cc_start: 0.7244 (m-80) cc_final: 0.6570 (m-80) REVERT: M 116 ARG cc_start: 0.8396 (mtp180) cc_final: 0.7969 (mtp180) REVERT: M 208 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7311 (tp30) REVERT: M 286 THR cc_start: 0.9231 (t) cc_final: 0.9018 (m) REVERT: O 14 SER cc_start: 0.7659 (t) cc_final: 0.7282 (p) REVERT: O 37 GLN cc_start: 0.8187 (tt0) cc_final: 0.7470 (tp40) REVERT: O 86 TYR cc_start: 0.7247 (m-80) cc_final: 0.6576 (m-80) outliers start: 41 outliers final: 33 residues processed: 346 average time/residue: 0.2995 time to fit residues: 163.1570 Evaluate side-chains 343 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 308 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 428 GLU Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain G residue 135 TYR Chi-restraints excluded: chain G residue 229 CYS Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 428 GLU Chi-restraints excluded: chain G residue 456 TRP Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 342 ASP Chi-restraints excluded: chain M residue 428 GLU Chi-restraints excluded: chain M residue 429 MET Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 83 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 17 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 234 optimal weight: 0.5980 chunk 140 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 233 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100AASN L 38 GLN D 100AASN E 38 GLN I 100AASN J 38 GLN N 100AASN O 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.145133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.122530 restraints weight = 26782.836| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.85 r_work: 0.3535 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19524 Z= 0.167 Angle : 0.772 35.775 26476 Z= 0.345 Chirality : 0.048 0.347 2840 Planarity : 0.005 0.064 3356 Dihedral : 5.762 56.698 2844 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.92 % Favored : 91.91 % Rotamer: Outliers : 2.00 % Allowed : 13.74 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -2.20 (0.16), residues: 2424 helix: -2.66 (0.95), residues: 24 sheet: -0.57 (0.17), residues: 932 loop : -2.14 (0.14), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 36 HIS 0.007 0.001 HIS A 101 PHE 0.025 0.002 PHE J 83 TYR 0.017 0.002 TYR N 59 ARG 0.011 0.000 ARG E 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 4) link_NAG-ASN : angle 2.12627 ( 12) link_BETA1-4 : bond 0.00399 ( 4) link_BETA1-4 : angle 0.91551 ( 12) hydrogen bonds : bond 0.03911 ( 588) hydrogen bonds : angle 6.20551 ( 1500) SS BOND : bond 0.00273 ( 32) SS BOND : angle 0.78501 ( 64) covalent geometry : bond 0.00404 (19484) covalent geometry : angle 0.77074 (26388) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 342 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7284 (tp30) REVERT: A 286 THR cc_start: 0.9265 (t) cc_final: 0.9050 (m) REVERT: A 428 GLU cc_start: 0.7733 (tt0) cc_final: 0.7472 (tt0) REVERT: L 37 GLN cc_start: 0.8109 (tt0) cc_final: 0.7333 (tp40) REVERT: L 61 ARG cc_start: 0.6266 (ptt-90) cc_final: 0.6044 (ptt-90) REVERT: L 78 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.6946 (tt) REVERT: L 83 PHE cc_start: 0.7546 (m-80) cc_final: 0.7315 (m-80) REVERT: L 86 TYR cc_start: 0.7227 (m-80) cc_final: 0.6470 (m-80) REVERT: C 116 ARG cc_start: 0.8430 (mtp180) cc_final: 0.7965 (mtp180) REVERT: C 208 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7282 (tp30) REVERT: C 286 THR cc_start: 0.9253 (t) cc_final: 0.9044 (m) REVERT: E 37 GLN cc_start: 0.8054 (tt0) cc_final: 0.7035 (tp40) REVERT: E 61 ARG cc_start: 0.6263 (ptt-90) cc_final: 0.6016 (ptt-90) REVERT: E 78 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.6970 (tt) REVERT: E 83 PHE cc_start: 0.7524 (m-80) cc_final: 0.7296 (m-80) REVERT: E 86 TYR cc_start: 0.7171 (m-80) cc_final: 0.6463 (m-80) REVERT: G 208 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7294 (tp30) REVERT: G 286 THR cc_start: 0.9251 (t) cc_final: 0.9040 (m) REVERT: J 14 SER cc_start: 0.7658 (t) cc_final: 0.7262 (p) REVERT: J 37 GLN cc_start: 0.8131 (tt0) cc_final: 0.7341 (tt0) REVERT: J 61 ARG cc_start: 0.6333 (ptt-90) cc_final: 0.6080 (ptt-90) REVERT: J 86 TYR cc_start: 0.7232 (m-80) cc_final: 0.6548 (m-80) REVERT: M 116 ARG cc_start: 0.8426 (mtp180) cc_final: 0.7963 (mtp180) REVERT: M 208 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7273 (tp30) REVERT: M 286 THR cc_start: 0.9244 (t) cc_final: 0.9035 (m) REVERT: O 14 SER cc_start: 0.7670 (t) cc_final: 0.7275 (p) REVERT: O 37 GLN cc_start: 0.8138 (tt0) cc_final: 0.7354 (tt0) REVERT: O 61 ARG cc_start: 0.6351 (ptt-90) cc_final: 0.6097 (ptt-90) REVERT: O 86 TYR cc_start: 0.7235 (m-80) cc_final: 0.6553 (m-80) outliers start: 41 outliers final: 34 residues processed: 368 average time/residue: 0.2793 time to fit residues: 162.4041 Evaluate side-chains 373 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 337 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 428 GLU Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain G residue 135 TYR Chi-restraints excluded: chain G residue 229 CYS Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 428 GLU Chi-restraints excluded: chain G residue 456 TRP Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 342 ASP Chi-restraints excluded: chain M residue 428 GLU Chi-restraints excluded: chain M residue 429 MET Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 83 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 6 optimal weight: 0.9990 chunk 223 optimal weight: 0.9990 chunk 220 optimal weight: 1.9990 chunk 227 optimal weight: 10.0000 chunk 209 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 108 optimal weight: 0.0980 chunk 183 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN H 100AASN L 38 GLN D 100AASN E 38 GLN I 100AASN J 38 GLN N 100AASN O 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.146558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.124035 restraints weight = 26771.816| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.85 r_work: 0.3552 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19524 Z= 0.138 Angle : 0.765 37.065 26476 Z= 0.335 Chirality : 0.047 0.311 2840 Planarity : 0.005 0.062 3356 Dihedral : 5.631 54.597 2844 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.22 % Favored : 92.62 % Rotamer: Outliers : 2.00 % Allowed : 13.79 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -2.07 (0.16), residues: 2424 helix: None (None), residues: 0 sheet: -0.49 (0.17), residues: 924 loop : -2.06 (0.14), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 36 HIS 0.006 0.001 HIS A 101 PHE 0.027 0.002 PHE O 83 TYR 0.017 0.002 TYR G 296 ARG 0.009 0.000 ARG E 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00399 ( 4) link_NAG-ASN : angle 1.98268 ( 12) link_BETA1-4 : bond 0.00508 ( 4) link_BETA1-4 : angle 0.86551 ( 12) hydrogen bonds : bond 0.03716 ( 588) hydrogen bonds : angle 6.11751 ( 1500) SS BOND : bond 0.00238 ( 32) SS BOND : angle 0.86572 ( 64) covalent geometry : bond 0.00330 (19484) covalent geometry : angle 0.76419 (26388) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9532.13 seconds wall clock time: 166 minutes 13.13 seconds (9973.13 seconds total)