Starting phenix.real_space_refine on Mon Jun 16 16:45:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u1q_41824/06_2025/8u1q_41824.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u1q_41824/06_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_41824/06_2025/8u1q_41824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u1q_41824/06_2025/8u1q_41824.map" model { file = "/net/cci-nas-00/data/ceres_data/8u1q_41824/06_2025/8u1q_41824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u1q_41824/06_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-5710/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: 8.34, 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: 4.31 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: 2.39 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: 6.80 Time building geometry restraints manager: 5.18 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: 0.16 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: 3.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 40.390 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.220 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:3.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.740 ------------------------------------------------------------------------------- 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 : 2.159 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: 0.3259 time to fit residues: 245.0605 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 : 2.065 ------------------------------------------------------------------------------- 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 = 0.156401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.134640 restraints weight = 25332.255| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.79 r_work: 0.3683 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- 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 20.138 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 0.00234 ( 4) link_NAG-ASN : angle 3.99544 ( 12) link_BETA1-4 : bond 0.00641 ( 4) link_BETA1-4 : angle 2.95473 ( 12) hydrogen bonds : bond 0.05216 ( 588) hydrogen bonds : angle 7.38906 ( 1500) SS BOND : bond 0.00310 ( 32) SS BOND : angle 1.16234 ( 64) covalent geometry : bond 0.00408 (19484) covalent geometry : angle 0.79244 (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 : 2.066 Fit side-chains REVERT: A 242 ASP cc_start: 0.6941 (t0) cc_final: 0.6667 (t0) REVERT: A 435 LYS cc_start: 0.7156 (mmtt) cc_final: 0.6909 (mmtm) REVERT: L 78 LEU cc_start: 0.7563 (tt) cc_final: 0.7184 (tt) REVERT: L 86 TYR cc_start: 0.7201 (m-80) cc_final: 0.6573 (m-80) REVERT: C 116 ARG cc_start: 0.8119 (mtp180) cc_final: 0.7908 (mtp180) REVERT: C 242 ASP cc_start: 0.6931 (t0) cc_final: 0.6656 (t0) REVERT: C 435 LYS cc_start: 0.7143 (mmtt) cc_final: 0.6916 (mmtm) REVERT: E 78 LEU cc_start: 0.7576 (tt) cc_final: 0.7192 (tt) REVERT: E 86 TYR cc_start: 0.7203 (m-80) cc_final: 0.6572 (m-80) REVERT: G 242 ASP cc_start: 0.6935 (t0) cc_final: 0.6658 (t0) REVERT: G 435 LYS cc_start: 0.7140 (mmtt) cc_final: 0.6918 (mmtm) REVERT: J 86 TYR cc_start: 0.7203 (m-80) cc_final: 0.6574 (m-80) REVERT: M 116 ARG cc_start: 0.8123 (mtp180) cc_final: 0.7912 (mtp180) REVERT: M 242 ASP cc_start: 0.6940 (t0) cc_final: 0.6666 (t0) REVERT: M 435 LYS cc_start: 0.7148 (mmtt) cc_final: 0.6924 (mmtm) REVERT: O 86 TYR cc_start: 0.7206 (m-80) cc_final: 0.6577 (m-80) outliers start: 48 outliers final: 21 residues processed: 387 average time/residue: 0.3613 time to fit residues: 215.6150 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 : 2.370 ------------------------------------------------------------------------------- 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: 5.9990 chunk 2 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 202 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 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: 0.6980 chunk 140 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN H 39 GLN H 100AASN L 6 GLN L 79 GLN C 230 ASN D 39 GLN D 100AASN E 6 GLN E 79 GLN G 230 ASN I 39 GLN I 100AASN J 6 GLN N 39 GLN N 100AASN O 6 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.152103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.130607 restraints weight = 25332.319| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.72 r_work: 0.3656 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3366 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= 0.209 Angle : 0.813 33.385 26476 Z= 0.387 Chirality : 0.049 0.182 2840 Planarity : 0.005 0.066 3356 Dihedral : 6.291 60.624 2844 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.77 % Favored : 92.90 % Rotamer: Outliers : 3.02 % Allowed : 9.06 % Favored : 87.91 % 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: -1.77 (0.15), residues: 2424 helix: None (None), residues: 0 sheet: -0.30 (0.16), residues: 936 loop : -1.85 (0.14), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 438 HIS 0.008 0.002 HIS A 101 PHE 0.022 0.002 PHE H 78 TYR 0.022 0.002 TYR D 53 ARG 0.005 0.001 ARG G 300 Details of bonding type rmsd link_NAG-ASN : bond 0.00824 ( 4) link_NAG-ASN : angle 2.67452 ( 12) link_BETA1-4 : bond 0.01008 ( 4) link_BETA1-4 : angle 2.03996 ( 12) hydrogen bonds : bond 0.04703 ( 588) hydrogen bonds : angle 6.83115 ( 1500) SS BOND : bond 0.00316 ( 32) SS BOND : angle 0.86225 ( 64) covalent geometry : bond 0.00491 (19484) covalent geometry : angle 0.81026 (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 416 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 354 time to evaluate : 3.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7502 (tp30) cc_final: 0.7271 (tp30) REVERT: A 308 GLU cc_start: 0.8495 (tm-30) cc_final: 0.7839 (tm-30) REVERT: A 428 GLU cc_start: 0.7520 (tt0) cc_final: 0.7254 (tt0) REVERT: H 75 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8142 (mtmt) REVERT: L 4 MET cc_start: 0.7403 (mmm) cc_final: 0.7137 (tpp) REVERT: L 86 TYR cc_start: 0.7313 (m-80) cc_final: 0.6543 (m-80) REVERT: C 116 ARG cc_start: 0.8358 (mtp180) cc_final: 0.8029 (mtp180) REVERT: C 308 GLU cc_start: 0.8491 (tm-30) cc_final: 0.7838 (tm-30) REVERT: D 75 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8143 (mtmt) REVERT: E 4 MET cc_start: 0.7411 (mmm) cc_final: 0.7144 (tpp) REVERT: E 86 TYR cc_start: 0.7321 (m-80) cc_final: 0.6547 (m-80) REVERT: G 308 GLU cc_start: 0.8485 (tm-30) cc_final: 0.7833 (tm-30) REVERT: I 75 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8138 (mtmt) REVERT: J 4 MET cc_start: 0.7409 (mmm) cc_final: 0.7140 (tpp) REVERT: J 86 TYR cc_start: 0.7273 (m-80) cc_final: 0.6491 (m-80) REVERT: M 116 ARG cc_start: 0.8356 (mtp180) cc_final: 0.8027 (mtp180) REVERT: M 308 GLU cc_start: 0.8505 (tm-30) cc_final: 0.7852 (tm-30) REVERT: N 75 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8141 (mtmt) REVERT: O 4 MET cc_start: 0.7408 (mmm) cc_final: 0.7143 (tpp) REVERT: O 86 TYR cc_start: 0.7273 (m-80) cc_final: 0.6487 (m-80) outliers start: 62 outliers final: 28 residues processed: 398 average time/residue: 0.4015 time to fit residues: 244.8183 Evaluate side-chains 339 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 307 time to evaluate : 2.209 ------------------------------------------------------------------------------- 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 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 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 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: 0.9980 chunk 71 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 232 optimal weight: 0.0000 chunk 94 optimal weight: 4.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100AASN D 100AASN ** G 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 100AASN M 230 ASN N 100AASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.148093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.126048 restraints weight = 25640.701| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.76 r_work: 0.3592 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19524 Z= 0.204 Angle : 0.776 33.511 26476 Z= 0.361 Chirality : 0.048 0.193 2840 Planarity : 0.005 0.068 3356 Dihedral : 6.199 60.255 2844 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.19 % Favored : 93.48 % Rotamer: Outliers : 3.02 % Allowed : 11.11 % Favored : 85.87 % 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: -1.86 (0.15), residues: 2424 helix: -3.27 (0.78), residues: 24 sheet: -0.26 (0.16), residues: 920 loop : -1.94 (0.14), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 177 HIS 0.007 0.002 HIS G 101 PHE 0.025 0.002 PHE E 83 TYR 0.018 0.002 TYR I 53 ARG 0.003 0.001 ARG A 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00416 ( 4) link_NAG-ASN : angle 2.64109 ( 12) link_BETA1-4 : bond 0.00517 ( 4) link_BETA1-4 : angle 1.45527 ( 12) hydrogen bonds : bond 0.04292 ( 588) hydrogen bonds : angle 6.72132 ( 1500) SS BOND : bond 0.00367 ( 32) SS BOND : angle 0.71942 ( 64) covalent geometry : bond 0.00485 (19484) covalent geometry : angle 0.77425 (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 400 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 338 time to evaluate : 2.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7605 (tp30) cc_final: 0.7336 (tp30) REVERT: A 308 GLU cc_start: 0.8500 (tm-30) cc_final: 0.7797 (tm-30) REVERT: A 428 GLU cc_start: 0.7557 (tt0) cc_final: 0.7323 (tt0) REVERT: H 5 GLN cc_start: 0.7202 (pt0) cc_final: 0.6996 (pt0) REVERT: L 4 MET cc_start: 0.7360 (mmm) cc_final: 0.6727 (tpp) REVERT: L 86 TYR cc_start: 0.7347 (m-80) cc_final: 0.6577 (m-80) REVERT: C 116 ARG cc_start: 0.8330 (mtp180) cc_final: 0.8020 (mtp180) REVERT: C 208 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7321 (tp30) REVERT: C 308 GLU cc_start: 0.8491 (tm-30) cc_final: 0.7789 (tm-30) REVERT: E 4 MET cc_start: 0.7355 (mmm) cc_final: 0.6726 (tpp) REVERT: E 86 TYR cc_start: 0.7356 (m-80) cc_final: 0.6582 (m-80) REVERT: G 208 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7302 (tp30) REVERT: G 308 GLU cc_start: 0.8484 (tm-30) cc_final: 0.7779 (tm-30) REVERT: I 5 GLN cc_start: 0.7208 (pt0) cc_final: 0.7004 (pt0) REVERT: J 4 MET cc_start: 0.7362 (mmm) cc_final: 0.6727 (tpp) REVERT: J 14 SER cc_start: 0.7449 (t) cc_final: 0.7143 (p) REVERT: J 86 TYR cc_start: 0.7341 (m-80) cc_final: 0.6580 (m-80) REVERT: M 116 ARG cc_start: 0.8328 (mtp180) cc_final: 0.8018 (mtp180) REVERT: M 208 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7316 (tp30) REVERT: M 308 GLU cc_start: 0.8496 (tm-30) cc_final: 0.7794 (tm-30) REVERT: O 4 MET cc_start: 0.7356 (mmm) cc_final: 0.6724 (tpp) REVERT: O 14 SER cc_start: 0.7448 (t) cc_final: 0.7143 (p) REVERT: O 86 TYR cc_start: 0.7340 (m-80) cc_final: 0.6572 (m-80) outliers start: 62 outliers final: 38 residues processed: 372 average time/residue: 0.3136 time to fit residues: 177.8600 Evaluate side-chains 352 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 314 time to evaluate : 2.044 ------------------------------------------------------------------------------- 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 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 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 73 THR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain J residue 85 ILE 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 73 THR Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain O residue 85 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 24 optimal weight: 0.0980 chunk 137 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100AASN L 6 GLN D 100AASN E 6 GLN ** G 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 100AASN J 6 GLN N 100AASN O 6 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.151040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.128841 restraints weight = 25809.537| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.81 r_work: 0.3624 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19524 Z= 0.135 Angle : 0.753 35.541 26476 Z= 0.338 Chirality : 0.047 0.201 2840 Planarity : 0.005 0.066 3356 Dihedral : 5.890 57.442 2844 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.77 % Favored : 92.90 % Rotamer: Outliers : 2.68 % Allowed : 12.38 % Favored : 84.94 % 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: -1.86 (0.15), residues: 2424 helix: -2.93 (0.89), residues: 24 sheet: -0.26 (0.17), residues: 912 loop : -1.94 (0.14), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 177 HIS 0.006 0.001 HIS M 101 PHE 0.029 0.002 PHE D 78 TYR 0.016 0.002 TYR N 53 ARG 0.005 0.000 ARG O 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 4) link_NAG-ASN : angle 2.21113 ( 12) link_BETA1-4 : bond 0.00730 ( 4) link_BETA1-4 : angle 1.24305 ( 12) hydrogen bonds : bond 0.03972 ( 588) hydrogen bonds : angle 6.50393 ( 1500) SS BOND : bond 0.00152 ( 32) SS BOND : angle 0.61117 ( 64) covalent geometry : bond 0.00312 (19484) covalent geometry : angle 0.75212 (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 402 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 347 time to evaluate : 2.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7665 (tp30) cc_final: 0.7364 (tp30) REVERT: A 308 GLU cc_start: 0.8507 (tm-30) cc_final: 0.7802 (tm-30) REVERT: A 428 GLU cc_start: 0.7456 (tt0) cc_final: 0.7202 (tt0) REVERT: H 5 GLN cc_start: 0.7070 (pt0) cc_final: 0.6863 (pt0) REVERT: L 4 MET cc_start: 0.7330 (mmm) cc_final: 0.6699 (tpp) REVERT: L 37 GLN cc_start: 0.8370 (tt0) cc_final: 0.7650 (tt0) REVERT: L 86 TYR cc_start: 0.7253 (m-80) cc_final: 0.6367 (m-80) REVERT: C 116 ARG cc_start: 0.8268 (mtp180) cc_final: 0.7999 (mtp180) REVERT: C 208 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7378 (tp30) REVERT: C 308 GLU cc_start: 0.8499 (tm-30) cc_final: 0.7798 (tm-30) REVERT: E 4 MET cc_start: 0.7327 (mmm) cc_final: 0.6701 (tpp) REVERT: E 37 GLN cc_start: 0.8368 (tt0) cc_final: 0.7654 (tt0) REVERT: E 86 TYR cc_start: 0.7263 (m-80) cc_final: 0.6374 (m-80) REVERT: G 208 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7372 (tp30) REVERT: G 308 GLU cc_start: 0.8495 (tm-30) cc_final: 0.7790 (tm-30) REVERT: I 5 GLN cc_start: 0.7080 (pt0) cc_final: 0.6872 (pt0) REVERT: J 4 MET cc_start: 0.7330 (mmm) cc_final: 0.6702 (tpp) REVERT: J 14 SER cc_start: 0.7398 (t) cc_final: 0.6623 (p) REVERT: J 37 GLN cc_start: 0.8362 (tt0) cc_final: 0.7641 (tt0) REVERT: J 86 TYR cc_start: 0.7249 (m-80) cc_final: 0.6364 (m-80) REVERT: M 116 ARG cc_start: 0.8263 (mtp180) cc_final: 0.7997 (mtp180) REVERT: M 208 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7370 (tp30) REVERT: M 308 GLU cc_start: 0.8493 (tm-30) cc_final: 0.7790 (tm-30) REVERT: O 4 MET cc_start: 0.7323 (mmm) cc_final: 0.6703 (tpp) REVERT: O 14 SER cc_start: 0.7394 (t) cc_final: 0.6616 (p) REVERT: O 37 GLN cc_start: 0.8360 (tt0) cc_final: 0.7645 (tt0) REVERT: O 86 TYR cc_start: 0.7249 (m-80) cc_final: 0.6366 (m-80) outliers start: 55 outliers final: 33 residues processed: 379 average time/residue: 0.3077 time to fit residues: 178.5778 Evaluate side-chains 357 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 324 time to evaluate : 2.295 ------------------------------------------------------------------------------- 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 13 LYS Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 83 THR 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 13 LYS Chi-restraints excluded: chain D residue 83 THR 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 456 TRP Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 69 ILE 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 13 LYS 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: 4.9990 chunk 134 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 44 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 0.2980 chunk 219 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.147282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.124921 restraints weight = 25911.380| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.80 r_work: 0.3573 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19524 Z= 0.217 Angle : 0.778 33.660 26476 Z= 0.360 Chirality : 0.049 0.218 2840 Planarity : 0.005 0.070 3356 Dihedral : 6.060 59.542 2844 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.30 % Favored : 92.37 % Rotamer: Outliers : 2.39 % Allowed : 12.43 % Favored : 85.19 % 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: -2.05 (0.16), residues: 2424 helix: -3.05 (0.86), residues: 24 sheet: -0.43 (0.16), residues: 920 loop : -2.05 (0.14), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 36 HIS 0.008 0.002 HIS G 101 PHE 0.022 0.002 PHE N 78 TYR 0.018 0.002 TYR G 296 ARG 0.005 0.001 ARG O 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 4) link_NAG-ASN : angle 2.53816 ( 12) link_BETA1-4 : bond 0.00462 ( 4) link_BETA1-4 : angle 1.17679 ( 12) hydrogen bonds : bond 0.04193 ( 588) hydrogen bonds : angle 6.63097 ( 1500) SS BOND : bond 0.00235 ( 32) SS BOND : angle 0.67751 ( 64) covalent geometry : bond 0.00520 (19484) covalent geometry : angle 0.77670 (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 393 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 344 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8281 (mmm160) REVERT: A 208 GLU cc_start: 0.7787 (tp30) cc_final: 0.7484 (tp30) REVERT: A 308 GLU cc_start: 0.8554 (tm-30) cc_final: 0.7841 (tm-30) REVERT: L 78 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7075 (tt) REVERT: L 86 TYR cc_start: 0.7242 (m-80) cc_final: 0.6324 (m-80) REVERT: C 116 ARG cc_start: 0.8394 (mtp180) cc_final: 0.8025 (mtp180) REVERT: C 208 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7204 (tp30) REVERT: C 308 GLU cc_start: 0.8531 (tm-30) cc_final: 0.7816 (tm-30) REVERT: E 78 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7074 (tt) REVERT: E 86 TYR cc_start: 0.7255 (m-80) cc_final: 0.6334 (m-80) REVERT: G 208 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7215 (tp30) REVERT: G 308 GLU cc_start: 0.8526 (tm-30) cc_final: 0.7814 (tm-30) REVERT: J 14 SER cc_start: 0.7718 (t) cc_final: 0.7364 (p) REVERT: J 86 TYR cc_start: 0.7227 (m-80) cc_final: 0.6325 (m-80) REVERT: M 116 ARG cc_start: 0.8397 (mtp180) cc_final: 0.8026 (mtp180) REVERT: M 208 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7216 (tp30) REVERT: M 308 GLU cc_start: 0.8542 (tm-30) cc_final: 0.7830 (tm-30) REVERT: O 14 SER cc_start: 0.7713 (t) cc_final: 0.7356 (p) REVERT: O 86 TYR cc_start: 0.7233 (m-80) cc_final: 0.6328 (m-80) outliers start: 49 outliers final: 32 residues processed: 374 average time/residue: 0.2954 time to fit residues: 172.6497 Evaluate side-chains 357 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 322 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG 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 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 353 VAL 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 353 VAL 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 353 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 20 optimal weight: 3.9990 chunk 176 optimal weight: 0.1980 chunk 160 optimal weight: 0.1980 chunk 112 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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 C 169 ASN D 100AASN E 38 GLN G 169 ASN I 100AASN J 38 GLN M 169 ASN N 100AASN O 38 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.150362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.128010 restraints weight = 25567.270| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.80 r_work: 0.3605 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19524 Z= 0.131 Angle : 0.751 35.939 26476 Z= 0.334 Chirality : 0.046 0.214 2840 Planarity : 0.005 0.065 3356 Dihedral : 5.773 56.866 2844 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.10 % Favored : 92.74 % Rotamer: Outliers : 2.10 % Allowed : 13.30 % 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: -1.94 (0.16), residues: 2424 helix: -2.74 (0.95), residues: 24 sheet: -0.31 (0.17), residues: 932 loop : -2.02 (0.14), residues: 1468 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 0.030 0.002 PHE J 83 TYR 0.016 0.002 TYR H 53 ARG 0.006 0.000 ARG O 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 4) link_NAG-ASN : angle 2.16939 ( 12) link_BETA1-4 : bond 0.00574 ( 4) link_BETA1-4 : angle 0.99318 ( 12) hydrogen bonds : bond 0.03817 ( 588) hydrogen bonds : angle 6.36438 ( 1500) SS BOND : bond 0.00206 ( 32) SS BOND : angle 0.70456 ( 64) covalent geometry : bond 0.00308 (19484) covalent geometry : angle 0.74964 (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: 43 poor density : 341 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7671 (tp30) cc_final: 0.7370 (tp30) REVERT: A 428 GLU cc_start: 0.7480 (tt0) cc_final: 0.7220 (tt0) REVERT: H 53 TYR cc_start: 0.8485 (p90) cc_final: 0.8194 (p90) REVERT: L 37 GLN cc_start: 0.8113 (tt0) cc_final: 0.7405 (tp40) REVERT: L 78 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.6989 (tt) REVERT: L 86 TYR cc_start: 0.7239 (m-80) cc_final: 0.6560 (m-80) REVERT: C 116 ARG cc_start: 0.8332 (mtp180) cc_final: 0.7988 (mtp180) REVERT: C 208 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7175 (tp30) REVERT: D 53 TYR cc_start: 0.8478 (p90) cc_final: 0.8186 (p90) REVERT: E 37 GLN cc_start: 0.8116 (tt0) cc_final: 0.7415 (tp40) REVERT: E 78 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.6984 (tt) REVERT: E 86 TYR cc_start: 0.7248 (m-80) cc_final: 0.6564 (m-80) REVERT: G 208 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7163 (tp30) REVERT: I 53 TYR cc_start: 0.8490 (p90) cc_final: 0.8200 (p90) REVERT: J 14 SER cc_start: 0.7602 (t) cc_final: 0.7195 (p) REVERT: J 37 GLN cc_start: 0.8156 (tt0) cc_final: 0.7478 (tp40) REVERT: J 86 TYR cc_start: 0.7200 (m-80) cc_final: 0.6530 (m-80) REVERT: M 116 ARG cc_start: 0.8332 (mtp180) cc_final: 0.7984 (mtp180) REVERT: M 208 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7177 (tp30) REVERT: N 53 TYR cc_start: 0.8490 (p90) cc_final: 0.8198 (p90) REVERT: O 14 SER cc_start: 0.7604 (t) cc_final: 0.7192 (p) REVERT: O 37 GLN cc_start: 0.8156 (tt0) cc_final: 0.7482 (tp40) REVERT: O 86 TYR cc_start: 0.7214 (m-80) cc_final: 0.6533 (m-80) outliers start: 43 outliers final: 32 residues processed: 368 average time/residue: 0.2924 time to fit residues: 167.7884 Evaluate side-chains 344 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 310 time to evaluate : 2.103 ------------------------------------------------------------------------------- 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 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 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 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 83 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 224 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3938 r_free = 0.3938 target = 0.144912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.123125 restraints weight = 25995.647| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.79 r_work: 0.3512 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 19524 Z= 0.323 Angle : 0.837 30.553 26476 Z= 0.404 Chirality : 0.052 0.289 2840 Planarity : 0.005 0.072 3356 Dihedral : 6.382 63.432 2844 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.66 % Favored : 91.01 % Rotamer: Outliers : 2.97 % Allowed : 13.06 % Favored : 83.97 % 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: -2.37 (0.16), residues: 2424 helix: -3.09 (0.84), residues: 24 sheet: -0.69 (0.17), residues: 924 loop : -2.24 (0.14), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 438 HIS 0.008 0.002 HIS A 101 PHE 0.026 0.003 PHE E 83 TYR 0.022 0.003 TYR N 96 ARG 0.005 0.001 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00041 ( 4) link_NAG-ASN : angle 2.82353 ( 12) link_BETA1-4 : bond 0.00413 ( 4) link_BETA1-4 : angle 1.27890 ( 12) hydrogen bonds : bond 0.04628 ( 588) hydrogen bonds : angle 6.77534 ( 1500) SS BOND : bond 0.00350 ( 32) SS BOND : angle 0.94120 ( 64) covalent geometry : bond 0.00773 (19484) covalent geometry : angle 0.83465 (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 390 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 329 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7846 (tp30) cc_final: 0.7537 (tp30) REVERT: A 286 THR cc_start: 0.9334 (t) cc_final: 0.9093 (m) REVERT: A 428 GLU cc_start: 0.7943 (tt0) cc_final: 0.7637 (tt0) REVERT: L 4 MET cc_start: 0.7021 (mmt) cc_final: 0.6800 (mmm) REVERT: L 37 GLN cc_start: 0.8297 (tt0) cc_final: 0.7424 (tp40) REVERT: L 78 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7011 (tt) REVERT: L 86 TYR cc_start: 0.7319 (m-80) cc_final: 0.6456 (m-80) REVERT: C 116 ARG cc_start: 0.8492 (mtp180) cc_final: 0.7964 (mtp180) REVERT: C 208 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7363 (tp30) REVERT: C 286 THR cc_start: 0.9333 (t) cc_final: 0.9096 (m) REVERT: E 4 MET cc_start: 0.7018 (mmt) cc_final: 0.6801 (mmm) REVERT: E 37 GLN cc_start: 0.8301 (tt0) cc_final: 0.7434 (tp40) REVERT: E 78 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.6997 (tt) REVERT: E 86 TYR cc_start: 0.7325 (m-80) cc_final: 0.6462 (m-80) REVERT: G 208 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7345 (tp30) REVERT: G 286 THR cc_start: 0.9331 (t) cc_final: 0.9090 (m) REVERT: J 4 MET cc_start: 0.7000 (mmt) cc_final: 0.6783 (mmm) REVERT: J 14 SER cc_start: 0.7744 (t) cc_final: 0.7420 (p) REVERT: J 86 TYR cc_start: 0.7303 (m-80) cc_final: 0.6487 (m-80) REVERT: M 116 ARG cc_start: 0.8489 (mtp180) cc_final: 0.7962 (mtp180) REVERT: M 208 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7373 (tp30) REVERT: M 286 THR cc_start: 0.9328 (t) cc_final: 0.9092 (m) REVERT: O 4 MET cc_start: 0.7008 (mmt) cc_final: 0.6791 (mmm) REVERT: O 14 SER cc_start: 0.7740 (t) cc_final: 0.7411 (p) REVERT: O 86 TYR cc_start: 0.7316 (m-80) cc_final: 0.6497 (m-80) outliers start: 61 outliers final: 50 residues processed: 368 average time/residue: 0.2856 time to fit residues: 164.3621 Evaluate side-chains 373 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 321 time to evaluate : 1.927 ------------------------------------------------------------------------------- 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 278 THR Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 348 ILE 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 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 278 THR Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 348 ILE 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 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 278 THR Chi-restraints excluded: chain G residue 317 MET Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 348 ILE 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 73 THR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain J residue 19 VAL 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 278 THR Chi-restraints excluded: chain M residue 317 MET Chi-restraints excluded: chain M residue 342 ASP Chi-restraints excluded: chain M residue 348 ILE 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 73 THR Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain O residue 19 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 97 optimal weight: 0.1980 chunk 181 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 214 optimal weight: 0.6980 chunk 190 optimal weight: 4.9990 chunk 205 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 183 optimal weight: 0.0470 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.149524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.127380 restraints weight = 25730.893| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.80 r_work: 0.3602 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19524 Z= 0.126 Angle : 0.762 35.823 26476 Z= 0.342 Chirality : 0.047 0.250 2840 Planarity : 0.005 0.066 3356 Dihedral : 5.769 56.828 2844 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.27 % Favored : 93.56 % Rotamer: Outliers : 2.19 % Allowed : 14.67 % Favored : 83.14 % 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: -2.72 (0.96), residues: 24 sheet: -0.36 (0.17), residues: 904 loop : -2.17 (0.14), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 177 HIS 0.005 0.001 HIS A 101 PHE 0.030 0.002 PHE E 83 TYR 0.020 0.002 TYR A 296 ARG 0.007 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 4) link_NAG-ASN : angle 2.19083 ( 12) link_BETA1-4 : bond 0.00480 ( 4) link_BETA1-4 : angle 0.90958 ( 12) hydrogen bonds : bond 0.03832 ( 588) hydrogen bonds : angle 6.29464 ( 1500) SS BOND : bond 0.00154 ( 32) SS BOND : angle 0.65805 ( 64) covalent geometry : bond 0.00291 (19484) covalent geometry : angle 0.76092 (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 375 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 330 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7771 (tp30) cc_final: 0.7517 (tp30) REVERT: A 286 THR cc_start: 0.9233 (t) cc_final: 0.8998 (m) REVERT: A 428 GLU cc_start: 0.7736 (tt0) cc_final: 0.7450 (tt0) REVERT: H 53 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.8179 (p90) REVERT: L 14 SER cc_start: 0.7480 (t) cc_final: 0.6951 (p) REVERT: L 37 GLN cc_start: 0.8135 (tt0) cc_final: 0.7296 (tp40) REVERT: L 78 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.6961 (tt) REVERT: L 86 TYR cc_start: 0.7243 (m-80) cc_final: 0.6405 (m-80) REVERT: C 116 ARG cc_start: 0.8412 (mtp180) cc_final: 0.7954 (mtp180) REVERT: C 208 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7253 (tp30) REVERT: C 286 THR cc_start: 0.9230 (t) cc_final: 0.9002 (m) REVERT: D 53 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.8172 (p90) REVERT: E 14 SER cc_start: 0.7484 (t) cc_final: 0.6956 (p) REVERT: E 37 GLN cc_start: 0.8136 (tt0) cc_final: 0.7306 (tp40) REVERT: E 78 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.6958 (tt) REVERT: E 86 TYR cc_start: 0.7253 (m-80) cc_final: 0.6414 (m-80) REVERT: G 208 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7253 (tp30) REVERT: G 286 THR cc_start: 0.9230 (t) cc_final: 0.8997 (m) REVERT: I 53 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.8183 (p90) REVERT: J 14 SER cc_start: 0.7650 (t) cc_final: 0.7300 (p) REVERT: J 37 GLN cc_start: 0.8047 (tt0) cc_final: 0.7222 (tp40) REVERT: J 86 TYR cc_start: 0.7131 (m-80) cc_final: 0.6686 (m-80) REVERT: M 116 ARG cc_start: 0.8409 (mtp180) cc_final: 0.7953 (mtp180) REVERT: M 208 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7257 (tp30) REVERT: M 286 THR cc_start: 0.9229 (t) cc_final: 0.9003 (m) REVERT: N 53 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.8177 (p90) REVERT: O 14 SER cc_start: 0.7648 (t) cc_final: 0.7295 (p) REVERT: O 37 GLN cc_start: 0.8055 (tt0) cc_final: 0.7228 (tp40) REVERT: O 86 TYR cc_start: 0.7129 (m-80) cc_final: 0.6688 (m-80) outliers start: 45 outliers final: 37 residues processed: 353 average time/residue: 0.3026 time to fit residues: 167.1082 Evaluate side-chains 373 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 330 time to evaluate : 2.210 ------------------------------------------------------------------------------- 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 429 MET Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 53 TYR 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 456 TRP Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 53 TYR 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 13 LYS Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 53 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain J residue 19 VAL 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 456 TRP Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 53 TYR Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain O residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 17 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 234 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 129 optimal weight: 0.3980 chunk 233 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 186 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 J 38 GLN O 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.149388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.127077 restraints weight = 25636.905| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.79 r_work: 0.3600 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4658 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= 0.142 Angle : 0.766 36.234 26476 Z= 0.341 Chirality : 0.048 0.420 2840 Planarity : 0.005 0.064 3356 Dihedral : 5.716 56.130 2844 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.18 % Favored : 92.66 % Rotamer: Outliers : 2.34 % Allowed : 14.28 % Favored : 83.38 % 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: None (None), residues: 0 sheet: -0.41 (0.17), residues: 912 loop : -2.16 (0.14), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 36 HIS 0.006 0.001 HIS A 101 PHE 0.028 0.002 PHE E 83 TYR 0.021 0.002 TYR M 296 ARG 0.011 0.001 ARG E 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 4) link_NAG-ASN : angle 2.09618 ( 12) link_BETA1-4 : bond 0.00451 ( 4) link_BETA1-4 : angle 0.89325 ( 12) hydrogen bonds : bond 0.03857 ( 588) hydrogen bonds : angle 6.19608 ( 1500) SS BOND : bond 0.00153 ( 32) SS BOND : angle 0.66993 ( 64) covalent geometry : bond 0.00338 (19484) covalent geometry : angle 0.76464 (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 378 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 330 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7781 (tp30) cc_final: 0.7532 (tp30) REVERT: A 286 THR cc_start: 0.9236 (t) cc_final: 0.9019 (m) REVERT: A 428 GLU cc_start: 0.7775 (tt0) cc_final: 0.7482 (tt0) REVERT: L 14 SER cc_start: 0.7476 (t) cc_final: 0.6947 (p) REVERT: L 37 GLN cc_start: 0.8085 (tt0) cc_final: 0.7278 (tp40) REVERT: L 61 ARG cc_start: 0.6393 (ptt-90) cc_final: 0.6117 (ptt-90) REVERT: L 78 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.6912 (tt) REVERT: L 86 TYR cc_start: 0.7287 (m-80) cc_final: 0.6491 (m-80) REVERT: C 116 ARG cc_start: 0.8417 (mtp180) cc_final: 0.7957 (mtp180) REVERT: C 208 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7191 (tp30) REVERT: C 286 THR cc_start: 0.9237 (t) cc_final: 0.9025 (m) REVERT: E 14 SER cc_start: 0.7468 (t) cc_final: 0.6937 (p) REVERT: E 37 GLN cc_start: 0.8084 (tt0) cc_final: 0.7281 (tp40) REVERT: E 61 ARG cc_start: 0.6391 (ptt-90) cc_final: 0.6113 (ptt-90) REVERT: E 78 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.6897 (tt) REVERT: E 86 TYR cc_start: 0.7296 (m-80) cc_final: 0.6497 (m-80) REVERT: E 94 TYR cc_start: 0.6911 (m-10) cc_final: 0.6711 (m-10) REVERT: G 208 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7197 (tp30) REVERT: G 286 THR cc_start: 0.9229 (t) cc_final: 0.9016 (m) REVERT: J 14 SER cc_start: 0.7686 (t) cc_final: 0.7350 (p) REVERT: J 61 ARG cc_start: 0.6338 (ptt-90) cc_final: 0.6037 (ptt-90) REVERT: M 116 ARG cc_start: 0.8416 (mtp180) cc_final: 0.7953 (mtp180) REVERT: M 208 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7205 (tp30) REVERT: M 286 THR cc_start: 0.9231 (t) cc_final: 0.9019 (m) REVERT: O 14 SER cc_start: 0.7686 (t) cc_final: 0.7348 (p) REVERT: O 61 ARG cc_start: 0.6327 (ptt-90) cc_final: 0.6029 (ptt-90) outliers start: 48 outliers final: 41 residues processed: 358 average time/residue: 0.2989 time to fit residues: 169.4075 Evaluate side-chains 363 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 320 time to evaluate : 2.015 ------------------------------------------------------------------------------- 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 429 MET Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 71 VAL 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 456 TRP Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 71 VAL 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 13 LYS Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain J residue 19 VAL 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 456 TRP Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain O residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 6 optimal weight: 0.9980 chunk 223 optimal weight: 0.8980 chunk 220 optimal weight: 0.8980 chunk 227 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 183 optimal weight: 0.2980 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 4 optimal weight: 0.0170 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.147278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.124340 restraints weight = 26654.128| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.91 r_work: 0.3532 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19524 Z= 0.130 Angle : 0.770 37.454 26476 Z= 0.341 Chirality : 0.047 0.335 2840 Planarity : 0.005 0.062 3356 Dihedral : 5.624 53.853 2844 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.10 % Favored : 92.74 % Rotamer: Outliers : 2.73 % Allowed : 13.94 % Favored : 83.33 % 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: -2.08 (0.16), residues: 2424 helix: None (None), residues: 0 sheet: -0.35 (0.17), residues: 912 loop : -2.16 (0.14), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 36 HIS 0.006 0.001 HIS A 101 PHE 0.028 0.002 PHE L 83 TYR 0.022 0.002 TYR D 59 ARG 0.010 0.000 ARG E 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 4) link_NAG-ASN : angle 1.97215 ( 12) link_BETA1-4 : bond 0.00496 ( 4) link_BETA1-4 : angle 0.82214 ( 12) hydrogen bonds : bond 0.03794 ( 588) hydrogen bonds : angle 6.13308 ( 1500) SS BOND : bond 0.00157 ( 32) SS BOND : angle 0.70469 ( 64) covalent geometry : bond 0.00313 (19484) covalent geometry : angle 0.76928 (26388) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9978.41 seconds wall clock time: 173 minutes 28.95 seconds (10408.95 seconds total)