Starting phenix.real_space_refine on Sat Oct 11 23:24:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u1q_41824/10_2025/8u1q_41824.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u1q_41824/10_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_41824/10_2025/8u1q_41824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u1q_41824/10_2025/8u1q_41824.map" model { file = "/net/cci-nas-00/data/ceres_data/8u1q_41824/10_2025/8u1q_41824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u1q_41824/10_2025/8u1q_41824.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.059 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: "H" 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: "L" 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} 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 Restraints were copied for chains: C, G, M, D, I, N, E, J, O, F, K, P Time building chain proxies: 3.57, per 1000 atoms: 0.19 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=40, 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 H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.02 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.02 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " 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: 1.58 Conformation dependent library (CDL) restraints added in 796.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.85 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: 3.67 Time building geometry restraints manager: 2.15 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: 11116 15.96 - 31.92: 380 31.92 - 47.88: 92 47.88 - 63.84: 60 63.84 - 79.80: 32 Dihedral angle restraints: 11680 sinusoidal: 4716 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 11677 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: 2.18 - 2.73: 2544 2.73 - 3.27: 16632 3.27 - 3.81: 31180 3.81 - 4.36: 41952 4.36 - 4.90: 68444 Nonbonded interactions: 160752 Sorted by model distance: nonbonded pdb=" OH TYR C 135 " pdb=" O ILE G 98 " model vdw 2.182 3.040 nonbonded pdb=" O ILE A 98 " pdb=" OH TYR M 135 " model vdw 2.182 3.040 nonbonded pdb=" OH TYR A 135 " pdb=" O ILE C 98 " model vdw 2.182 3.040 nonbonded pdb=" OH TYR G 135 " pdb=" O ILE M 98 " model vdw 2.182 3.040 nonbonded pdb=" OG1 THR C 241 " pdb=" OG SER C 249 " model vdw 2.391 3.040 ... (remaining 160747 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' selection = chain 'M' } ncs_group { reference = chain 'H' selection = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'L' selection = chain 'E' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'K' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 17.490 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.400 ------------------------------------------------------------------------------- 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 19532 Z= 1.210 Angle : 2.086 63.784 26492 Z= 1.322 Chirality : 0.108 0.496 2840 Planarity : 0.010 0.088 3356 Dihedral : 10.357 79.802 7168 Min Nonbonded Distance : 2.182 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (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 ARG 0.012 0.002 ARG A 260 TYR 0.072 0.009 TYR I 52 PHE 0.030 0.006 PHE E 98 TRP 0.070 0.010 TRP C 456 HIS 0.017 0.003 HIS C 273 Details of bonding type rmsd covalent geometry : bond 0.02125 (19484) covalent geometry : angle 1.92610 (26388) SS BOND : bond 0.19777 ( 40) SS BOND : angle 14.56923 ( 80) hydrogen bonds : bond 0.17002 ( 588) hydrogen bonds : angle 9.18637 ( 1500) link_BETA1-4 : bond 0.06911 ( 4) link_BETA1-4 : angle 4.24575 ( 12) link_NAG-ASN : bond 0.10366 ( 4) link_NAG-ASN : angle 3.71335 ( 12) *********************** 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 : 0.653 Fit side-chains REVERT: C 116 ARG cc_start: 0.8039 (mtp180) cc_final: 0.7838 (mmm160) REVERT: G 116 ARG cc_start: 0.8043 (mtp180) cc_final: 0.7840 (mmm160) REVERT: M 116 ARG cc_start: 0.8041 (mtp180) cc_final: 0.7840 (mmm160) outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 0.1474 time to fit residues: 112.1455 Evaluate side-chains 303 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 L 79 GLN C 294 ASN D 77 GLN G 294 ASN I 77 GLN M 294 ASN N 77 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.155619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.134297 restraints weight = 25184.284| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.73 r_work: 0.3694 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19532 Z= 0.192 Angle : 0.808 18.809 26492 Z= 0.425 Chirality : 0.050 0.164 2840 Planarity : 0.005 0.053 3356 Dihedral : 6.610 62.005 2844 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.40 % Favored : 94.10 % Rotamer: Outliers : 2.14 % Allowed : 7.46 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.16), residues: 2424 helix: None (None), residues: 0 sheet: 0.17 (0.17), residues: 912 loop : -1.39 (0.14), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 300 TYR 0.023 0.002 TYR H 34 PHE 0.028 0.002 PHE O 83 TRP 0.014 0.002 TRP N 103 HIS 0.017 0.002 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00436 (19484) covalent geometry : angle 0.79900 (26388) SS BOND : bond 0.00500 ( 40) SS BOND : angle 1.36430 ( 80) hydrogen bonds : bond 0.05484 ( 588) hydrogen bonds : angle 7.47871 ( 1500) link_BETA1-4 : bond 0.00609 ( 4) link_BETA1-4 : angle 3.05258 ( 12) link_NAG-ASN : bond 0.00932 ( 4) link_NAG-ASN : angle 3.93181 ( 12) *********************** 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 403 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 359 time to evaluate : 0.549 Fit side-chains REVERT: A 242 ASP cc_start: 0.6938 (t0) cc_final: 0.6660 (t0) REVERT: A 435 LYS cc_start: 0.7169 (mmtt) cc_final: 0.6928 (mmtm) REVERT: H 72 ASP cc_start: 0.6543 (t0) cc_final: 0.6270 (t0) REVERT: L 86 TYR cc_start: 0.7203 (m-80) cc_final: 0.6549 (m-80) REVERT: C 242 ASP cc_start: 0.6922 (t0) cc_final: 0.6644 (t0) REVERT: C 435 LYS cc_start: 0.7155 (mmtt) cc_final: 0.6939 (mmtm) REVERT: D 72 ASP cc_start: 0.6548 (t0) cc_final: 0.6275 (t0) REVERT: E 86 TYR cc_start: 0.7202 (m-80) cc_final: 0.6552 (m-80) REVERT: G 242 ASP cc_start: 0.6929 (t0) cc_final: 0.6651 (t0) REVERT: G 435 LYS cc_start: 0.7154 (mmtt) cc_final: 0.6942 (mmtm) REVERT: I 72 ASP cc_start: 0.6539 (t0) cc_final: 0.6268 (t0) REVERT: J 86 TYR cc_start: 0.7211 (m-80) cc_final: 0.6561 (m-80) REVERT: M 242 ASP cc_start: 0.6934 (t0) cc_final: 0.6655 (t0) REVERT: M 435 LYS cc_start: 0.7159 (mmtt) cc_final: 0.6943 (mmtm) REVERT: N 72 ASP cc_start: 0.6555 (t0) cc_final: 0.6280 (t0) REVERT: O 86 TYR cc_start: 0.7210 (m-80) cc_final: 0.6553 (m-80) outliers start: 44 outliers final: 25 residues processed: 383 average time/residue: 0.1404 time to fit residues: 83.3339 Evaluate side-chains 336 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 311 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 348 ILE 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 348 ILE 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 348 ILE 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 348 ILE 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 88 optimal weight: 0.7980 chunk 227 optimal weight: 10.0000 chunk 229 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 171 optimal weight: 0.0970 chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 100AASN L 6 GLN D 39 GLN D 100AASN E 6 GLN G 294 ASN I 39 GLN I 100AASN J 6 GLN M 294 ASN N 39 GLN N 100AASN O 6 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.153245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.131119 restraints weight = 25511.831| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.82 r_work: 0.3621 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19532 Z= 0.195 Angle : 0.798 32.634 26492 Z= 0.381 Chirality : 0.049 0.176 2840 Planarity : 0.005 0.061 3356 Dihedral : 6.265 60.769 2844 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.31 % Favored : 93.36 % Rotamer: Outliers : 2.68 % Allowed : 9.36 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.16), residues: 2424 helix: None (None), residues: 0 sheet: -0.15 (0.17), residues: 944 loop : -1.79 (0.14), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 61 TYR 0.021 0.002 TYR D 53 PHE 0.020 0.002 PHE O 83 TRP 0.012 0.002 TRP A 438 HIS 0.007 0.002 HIS M 101 Details of bonding type rmsd covalent geometry : bond 0.00461 (19484) covalent geometry : angle 0.79511 (26388) SS BOND : bond 0.00370 ( 40) SS BOND : angle 0.89376 ( 80) hydrogen bonds : bond 0.04647 ( 588) hydrogen bonds : angle 6.84742 ( 1500) link_BETA1-4 : bond 0.00859 ( 4) link_BETA1-4 : angle 2.16781 ( 12) link_NAG-ASN : bond 0.00833 ( 4) link_NAG-ASN : angle 2.67515 ( 12) *********************** 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 407 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 352 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 ASP cc_start: 0.7100 (t0) cc_final: 0.6874 (t0) REVERT: A 308 GLU cc_start: 0.8505 (tm-30) cc_final: 0.7837 (tm-30) REVERT: H 75 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8041 (mtmt) REVERT: L 86 TYR cc_start: 0.7453 (m-80) cc_final: 0.6806 (m-80) REVERT: C 242 ASP cc_start: 0.7106 (t0) cc_final: 0.6881 (t0) REVERT: C 308 GLU cc_start: 0.8511 (tm-30) cc_final: 0.7846 (tm-30) REVERT: D 75 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8033 (mtmt) REVERT: E 61 ARG cc_start: 0.6139 (ptt-90) cc_final: 0.5852 (ptt-90) REVERT: E 86 TYR cc_start: 0.7463 (m-80) cc_final: 0.6812 (m-80) REVERT: G 242 ASP cc_start: 0.7109 (t0) cc_final: 0.6885 (t0) REVERT: G 308 GLU cc_start: 0.8506 (tm-30) cc_final: 0.7843 (tm-30) REVERT: I 75 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8034 (mtmt) REVERT: J 61 ARG cc_start: 0.6133 (ptt-90) cc_final: 0.5846 (ptt-90) REVERT: J 86 TYR cc_start: 0.7463 (m-80) cc_final: 0.6809 (m-80) REVERT: M 242 ASP cc_start: 0.7096 (t0) cc_final: 0.6871 (t0) REVERT: M 308 GLU cc_start: 0.8523 (tm-30) cc_final: 0.7857 (tm-30) REVERT: N 75 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8042 (mtmt) REVERT: O 61 ARG cc_start: 0.6139 (ptt-90) cc_final: 0.5852 (ptt-90) REVERT: O 86 TYR cc_start: 0.7453 (m-80) cc_final: 0.6808 (m-80) outliers start: 55 outliers final: 32 residues processed: 391 average time/residue: 0.1401 time to fit residues: 84.1678 Evaluate side-chains 351 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 315 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 348 ILE 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 348 ILE 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 348 ILE 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 348 ILE 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 79 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 181 optimal weight: 0.0060 chunk 117 optimal weight: 0.0970 chunk 147 optimal weight: 3.9990 overall best weight: 1.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 100AASN L 6 GLN D 39 GLN D 100AASN E 6 GLN E 79 GLN I 39 GLN I 100AASN J 6 GLN J 79 GLN N 39 GLN N 100AASN O 6 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.151451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.129321 restraints weight = 25645.433| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.79 r_work: 0.3584 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19532 Z= 0.189 Angle : 0.776 33.624 26492 Z= 0.361 Chirality : 0.048 0.196 2840 Planarity : 0.005 0.066 3356 Dihedral : 6.127 59.099 2844 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.27 % Favored : 93.40 % Rotamer: Outliers : 3.02 % Allowed : 11.35 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.16), residues: 2424 helix: -3.21 (0.80), residues: 24 sheet: -0.28 (0.17), residues: 944 loop : -1.88 (0.14), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 327 TYR 0.019 0.002 TYR I 53 PHE 0.026 0.002 PHE L 83 TRP 0.011 0.001 TRP A 177 HIS 0.007 0.002 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00450 (19484) covalent geometry : angle 0.77341 (26388) SS BOND : bond 0.00347 ( 40) SS BOND : angle 0.88468 ( 80) hydrogen bonds : bond 0.04275 ( 588) hydrogen bonds : angle 6.67144 ( 1500) link_BETA1-4 : bond 0.00591 ( 4) link_BETA1-4 : angle 1.56382 ( 12) link_NAG-ASN : bond 0.00515 ( 4) link_NAG-ASN : angle 2.55672 ( 12) *********************** 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 393 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 331 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 GLU cc_start: 0.8513 (tm-30) cc_final: 0.7790 (tm-30) REVERT: H 5 GLN cc_start: 0.7122 (pt0) cc_final: 0.6850 (pt0) REVERT: L 14 SER cc_start: 0.7390 (t) cc_final: 0.7008 (p) REVERT: L 86 TYR cc_start: 0.7344 (m-80) cc_final: 0.6615 (m-80) REVERT: C 308 GLU cc_start: 0.8494 (tm-30) cc_final: 0.7772 (tm-30) REVERT: D 5 GLN cc_start: 0.7134 (pt0) cc_final: 0.6861 (pt0) REVERT: E 14 SER cc_start: 0.7394 (t) cc_final: 0.7032 (p) REVERT: E 86 TYR cc_start: 0.7354 (m-80) cc_final: 0.6628 (m-80) REVERT: G 308 GLU cc_start: 0.8497 (tm-30) cc_final: 0.7775 (tm-30) REVERT: I 5 GLN cc_start: 0.7136 (pt0) cc_final: 0.6864 (pt0) REVERT: J 14 SER cc_start: 0.7398 (t) cc_final: 0.7038 (p) REVERT: J 86 TYR cc_start: 0.7350 (m-80) cc_final: 0.6625 (m-80) REVERT: M 308 GLU cc_start: 0.8505 (tm-30) cc_final: 0.7782 (tm-30) REVERT: N 5 GLN cc_start: 0.7125 (pt0) cc_final: 0.6850 (pt0) REVERT: O 14 SER cc_start: 0.7391 (t) cc_final: 0.7029 (p) REVERT: O 86 TYR cc_start: 0.7341 (m-80) cc_final: 0.6614 (m-80) outliers start: 62 outliers final: 45 residues processed: 375 average time/residue: 0.1482 time to fit residues: 85.4004 Evaluate side-chains 356 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 311 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 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 15 SER Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 85 ILE 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 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 15 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 85 ILE 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 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 15 SER 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 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 15 SER 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 70 optimal weight: 0.3980 chunk 189 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 130 optimal weight: 0.0170 chunk 160 optimal weight: 0.0020 chunk 106 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.8830 ------------------------------------------------------------------------------- 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 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 = 0.4036 r_free = 0.4036 target = 0.152714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.130946 restraints weight = 25400.795| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.74 r_work: 0.3621 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19532 Z= 0.153 Angle : 0.761 35.248 26492 Z= 0.344 Chirality : 0.047 0.198 2840 Planarity : 0.005 0.065 3356 Dihedral : 5.908 57.525 2844 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.93 % Favored : 92.74 % Rotamer: Outliers : 3.17 % Allowed : 11.55 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.16), residues: 2424 helix: -3.04 (0.85), residues: 24 sheet: -0.34 (0.17), residues: 944 loop : -1.90 (0.14), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 61 TYR 0.016 0.002 TYR I 53 PHE 0.022 0.002 PHE L 83 TRP 0.011 0.001 TRP G 177 HIS 0.006 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00358 (19484) covalent geometry : angle 0.75910 (26388) SS BOND : bond 0.00291 ( 40) SS BOND : angle 0.76591 ( 80) hydrogen bonds : bond 0.04001 ( 588) hydrogen bonds : angle 6.42945 ( 1500) link_BETA1-4 : bond 0.00586 ( 4) link_BETA1-4 : angle 1.28689 ( 12) link_NAG-ASN : bond 0.00584 ( 4) link_NAG-ASN : angle 2.23912 ( 12) *********************** 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 404 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 339 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8410 (mmm160) REVERT: A 208 GLU cc_start: 0.7560 (tp30) cc_final: 0.7313 (tp30) REVERT: A 308 GLU cc_start: 0.8489 (tm-30) cc_final: 0.7769 (tm-30) REVERT: H 5 GLN cc_start: 0.7120 (pt0) cc_final: 0.6911 (pt0) REVERT: L 14 SER cc_start: 0.7379 (t) cc_final: 0.7051 (p) REVERT: L 86 TYR cc_start: 0.7334 (m-80) cc_final: 0.6577 (m-80) REVERT: C 208 GLU cc_start: 0.7569 (tp30) cc_final: 0.7328 (tp30) REVERT: C 308 GLU cc_start: 0.8493 (tm-30) cc_final: 0.7772 (tm-30) REVERT: D 5 GLN cc_start: 0.7134 (pt0) cc_final: 0.6926 (pt0) REVERT: E 14 SER cc_start: 0.7396 (t) cc_final: 0.7080 (p) REVERT: E 86 TYR cc_start: 0.7350 (m-80) cc_final: 0.6586 (m-80) REVERT: G 208 GLU cc_start: 0.7571 (tp30) cc_final: 0.7330 (tp30) REVERT: G 308 GLU cc_start: 0.8485 (tm-30) cc_final: 0.7764 (tm-30) REVERT: I 5 GLN cc_start: 0.7126 (pt0) cc_final: 0.6916 (pt0) REVERT: J 14 SER cc_start: 0.7402 (t) cc_final: 0.7086 (p) REVERT: J 86 TYR cc_start: 0.7344 (m-80) cc_final: 0.6576 (m-80) REVERT: M 208 GLU cc_start: 0.7554 (tp30) cc_final: 0.7318 (tp30) REVERT: M 308 GLU cc_start: 0.8488 (tm-30) cc_final: 0.7767 (tm-30) REVERT: N 5 GLN cc_start: 0.7122 (pt0) cc_final: 0.6915 (pt0) REVERT: O 14 SER cc_start: 0.7393 (t) cc_final: 0.7078 (p) REVERT: O 86 TYR cc_start: 0.7341 (m-80) cc_final: 0.6577 (m-80) outliers start: 65 outliers final: 42 residues processed: 379 average time/residue: 0.1375 time to fit residues: 81.4014 Evaluate side-chains 350 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 307 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG 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 348 ILE Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 85 ILE 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 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 69 ILE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 85 ILE 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 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 69 ILE 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 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 69 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 171 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 179 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100AASN L 6 GLN C 230 ASN D 100AASN E 6 GLN G 230 ASN I 100AASN J 6 GLN M 230 ASN N 100AASN O 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.147878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.125365 restraints weight = 25496.617| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.74 r_work: 0.3587 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19532 Z= 0.196 Angle : 0.770 33.669 26492 Z= 0.354 Chirality : 0.048 0.210 2840 Planarity : 0.005 0.066 3356 Dihedral : 5.984 58.346 2844 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.68 % Favored : 92.99 % Rotamer: Outliers : 2.92 % Allowed : 11.84 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.16), residues: 2424 helix: -3.03 (0.86), residues: 24 sheet: -0.26 (0.17), residues: 908 loop : -2.03 (0.14), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 61 TYR 0.017 0.002 TYR H 53 PHE 0.018 0.002 PHE J 83 TRP 0.010 0.001 TRP A 177 HIS 0.007 0.002 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00466 (19484) covalent geometry : angle 0.76851 (26388) SS BOND : bond 0.00475 ( 40) SS BOND : angle 0.77690 ( 80) hydrogen bonds : bond 0.04111 ( 588) hydrogen bonds : angle 6.46748 ( 1500) link_BETA1-4 : bond 0.00502 ( 4) link_BETA1-4 : angle 1.15791 ( 12) link_NAG-ASN : bond 0.00358 ( 4) link_NAG-ASN : angle 2.36253 ( 12) *********************** 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 382 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 322 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7651 (tp30) cc_final: 0.7415 (tp30) REVERT: A 308 GLU cc_start: 0.8527 (tm-30) cc_final: 0.7829 (tm-30) REVERT: L 14 SER cc_start: 0.7409 (t) cc_final: 0.6627 (p) REVERT: L 86 TYR cc_start: 0.7319 (m-80) cc_final: 0.6854 (m-80) REVERT: C 208 GLU cc_start: 0.7654 (tp30) cc_final: 0.7422 (tp30) REVERT: C 308 GLU cc_start: 0.8513 (tm-30) cc_final: 0.7817 (tm-30) REVERT: E 14 SER cc_start: 0.7418 (t) cc_final: 0.6629 (p) REVERT: E 86 TYR cc_start: 0.7318 (m-80) cc_final: 0.6857 (m-80) REVERT: G 208 GLU cc_start: 0.7646 (tp30) cc_final: 0.7417 (tp30) REVERT: G 308 GLU cc_start: 0.8515 (tm-30) cc_final: 0.7822 (tm-30) REVERT: J 14 SER cc_start: 0.7425 (t) cc_final: 0.6642 (p) REVERT: J 86 TYR cc_start: 0.7311 (m-80) cc_final: 0.6851 (m-80) REVERT: M 208 GLU cc_start: 0.7655 (tp30) cc_final: 0.7419 (tp30) REVERT: M 308 GLU cc_start: 0.8534 (tm-30) cc_final: 0.7839 (tm-30) REVERT: O 14 SER cc_start: 0.7418 (t) cc_final: 0.6637 (p) REVERT: O 86 TYR cc_start: 0.7316 (m-80) cc_final: 0.6849 (m-80) outliers start: 60 outliers final: 43 residues processed: 367 average time/residue: 0.1315 time to fit residues: 76.4413 Evaluate side-chains 350 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 307 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 348 ILE Chi-restraints excluded: chain A residue 353 VAL 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 85 ILE 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 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 85 ILE 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 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 85 ILE Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 342 ASP Chi-restraints excluded: chain M residue 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 85 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 87 optimal weight: 0.8980 chunk 129 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 230 ASN H 100AASN L 6 GLN L 38 GLN C 169 ASN D 100AASN E 6 GLN E 38 GLN I 100AASN J 6 GLN J 38 GLN M 169 ASN N 100AASN O 6 GLN O 38 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.148139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.125756 restraints weight = 25675.325| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.75 r_work: 0.3591 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19532 Z= 0.170 Angle : 0.763 34.544 26492 Z= 0.346 Chirality : 0.047 0.217 2840 Planarity : 0.005 0.064 3356 Dihedral : 5.869 57.487 2844 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.89 % Favored : 92.78 % Rotamer: Outliers : 2.68 % Allowed : 12.43 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.16), residues: 2424 helix: -2.93 (0.90), residues: 24 sheet: -0.34 (0.17), residues: 924 loop : -2.01 (0.14), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 61 TYR 0.017 0.002 TYR I 53 PHE 0.030 0.002 PHE E 83 TRP 0.011 0.001 TRP A 177 HIS 0.007 0.002 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00407 (19484) covalent geometry : angle 0.76150 (26388) SS BOND : bond 0.00251 ( 40) SS BOND : angle 0.77703 ( 80) hydrogen bonds : bond 0.03933 ( 588) hydrogen bonds : angle 6.35267 ( 1500) link_BETA1-4 : bond 0.00475 ( 4) link_BETA1-4 : angle 1.04955 ( 12) link_NAG-ASN : bond 0.00424 ( 4) link_NAG-ASN : angle 2.24869 ( 12) *********************** 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 379 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 324 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7720 (tp30) cc_final: 0.7481 (tp30) REVERT: L 14 SER cc_start: 0.7734 (t) cc_final: 0.7328 (p) REVERT: L 37 GLN cc_start: 0.8135 (tt0) cc_final: 0.7384 (tp40) REVERT: L 86 TYR cc_start: 0.7323 (m-80) cc_final: 0.6680 (m-80) REVERT: C 208 GLU cc_start: 0.7733 (tp30) cc_final: 0.7492 (tp30) REVERT: E 14 SER cc_start: 0.7736 (t) cc_final: 0.7332 (p) REVERT: E 37 GLN cc_start: 0.8141 (tt0) cc_final: 0.7394 (tp40) REVERT: E 86 TYR cc_start: 0.7327 (m-80) cc_final: 0.6689 (m-80) REVERT: G 208 GLU cc_start: 0.7716 (tp30) cc_final: 0.7479 (tp30) REVERT: J 14 SER cc_start: 0.7748 (t) cc_final: 0.7345 (p) REVERT: J 37 GLN cc_start: 0.8141 (tt0) cc_final: 0.7388 (tp40) REVERT: J 86 TYR cc_start: 0.7328 (m-80) cc_final: 0.6688 (m-80) REVERT: M 208 GLU cc_start: 0.7716 (tp30) cc_final: 0.7477 (tp30) REVERT: O 14 SER cc_start: 0.7742 (t) cc_final: 0.7342 (p) REVERT: O 37 GLN cc_start: 0.8137 (tt0) cc_final: 0.7383 (tp40) REVERT: O 86 TYR cc_start: 0.7322 (m-80) cc_final: 0.6679 (m-80) outliers start: 55 outliers final: 42 residues processed: 356 average time/residue: 0.1309 time to fit residues: 74.1938 Evaluate side-chains 350 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 308 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 348 ILE Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 85 ILE 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 348 ILE Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 85 ILE 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 348 ILE Chi-restraints excluded: chain G residue 429 MET Chi-restraints excluded: chain G residue 456 TRP Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 342 ASP Chi-restraints excluded: chain M residue 348 ILE Chi-restraints excluded: chain M residue 429 MET Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain O residue 85 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 49 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 201 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 193 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.149028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.127123 restraints weight = 25529.174| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.74 r_work: 0.3597 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19532 Z= 0.198 Angle : 0.773 33.128 26492 Z= 0.357 Chirality : 0.048 0.224 2840 Planarity : 0.005 0.064 3356 Dihedral : 5.962 58.506 2844 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.84 % Favored : 91.83 % Rotamer: Outliers : 2.34 % Allowed : 12.82 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.16), residues: 2424 helix: -2.91 (0.91), residues: 24 sheet: -0.36 (0.17), residues: 920 loop : -2.08 (0.14), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 61 TYR 0.016 0.002 TYR M 143 PHE 0.027 0.002 PHE J 83 TRP 0.010 0.001 TRP A 438 HIS 0.007 0.002 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00480 (19484) covalent geometry : angle 0.77150 (26388) SS BOND : bond 0.00260 ( 40) SS BOND : angle 0.78101 ( 80) hydrogen bonds : bond 0.04019 ( 588) hydrogen bonds : angle 6.35935 ( 1500) link_BETA1-4 : bond 0.00404 ( 4) link_BETA1-4 : angle 1.05603 ( 12) link_NAG-ASN : bond 0.00260 ( 4) link_NAG-ASN : angle 2.35412 ( 12) *********************** 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 391 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 343 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7706 (tp30) cc_final: 0.7474 (tp30) REVERT: L 14 SER cc_start: 0.7688 (t) cc_final: 0.7305 (p) REVERT: L 37 GLN cc_start: 0.8089 (tt0) cc_final: 0.7255 (tp40) REVERT: L 86 TYR cc_start: 0.7294 (m-80) cc_final: 0.6486 (m-80) REVERT: C 208 GLU cc_start: 0.7719 (tp30) cc_final: 0.7485 (tp30) REVERT: E 14 SER cc_start: 0.7686 (t) cc_final: 0.7298 (p) REVERT: E 37 GLN cc_start: 0.8095 (tt0) cc_final: 0.7264 (tp40) REVERT: E 86 TYR cc_start: 0.7295 (m-80) cc_final: 0.6490 (m-80) REVERT: G 208 GLU cc_start: 0.7713 (tp30) cc_final: 0.7483 (tp30) REVERT: J 14 SER cc_start: 0.7697 (t) cc_final: 0.7308 (p) REVERT: J 37 GLN cc_start: 0.8089 (tt0) cc_final: 0.7252 (tp40) REVERT: J 86 TYR cc_start: 0.7293 (m-80) cc_final: 0.6486 (m-80) REVERT: M 208 GLU cc_start: 0.7703 (tp30) cc_final: 0.7474 (tp30) REVERT: O 14 SER cc_start: 0.7693 (t) cc_final: 0.7307 (p) REVERT: O 37 GLN cc_start: 0.8087 (tt0) cc_final: 0.7252 (tp40) REVERT: O 86 TYR cc_start: 0.7295 (m-80) cc_final: 0.6485 (m-80) outliers start: 48 outliers final: 37 residues processed: 365 average time/residue: 0.1289 time to fit residues: 74.8983 Evaluate side-chains 364 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 327 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 348 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain H residue 18 LEU 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 348 ILE Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 69 ILE 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 348 ILE Chi-restraints excluded: chain G residue 456 TRP Chi-restraints excluded: chain I residue 18 LEU 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 348 ILE Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 83 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 222 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 232 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 226 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 202 optimal weight: 0.0980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.148306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.126028 restraints weight = 25387.830| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.77 r_work: 0.3578 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19532 Z= 0.155 Angle : 0.766 35.048 26492 Z= 0.345 Chirality : 0.048 0.383 2840 Planarity : 0.005 0.062 3356 Dihedral : 5.803 56.902 2844 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.05 % Favored : 92.78 % Rotamer: Outliers : 2.63 % Allowed : 13.16 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.16), residues: 2424 helix: -2.73 (0.96), residues: 24 sheet: -0.29 (0.17), residues: 912 loop : -2.07 (0.14), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 61 TYR 0.015 0.002 TYR M 296 PHE 0.027 0.002 PHE J 83 TRP 0.012 0.001 TRP A 177 HIS 0.006 0.002 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00372 (19484) covalent geometry : angle 0.76505 (26388) SS BOND : bond 0.00220 ( 40) SS BOND : angle 0.73343 ( 80) hydrogen bonds : bond 0.03796 ( 588) hydrogen bonds : angle 6.18269 ( 1500) link_BETA1-4 : bond 0.00474 ( 4) link_BETA1-4 : angle 0.92979 ( 12) link_NAG-ASN : bond 0.00386 ( 4) link_NAG-ASN : angle 2.17668 ( 12) *********************** 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 396 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 342 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7729 (tp30) cc_final: 0.7506 (tp30) REVERT: A 286 THR cc_start: 0.9225 (t) cc_final: 0.9004 (m) REVERT: L 14 SER cc_start: 0.7679 (t) cc_final: 0.7322 (p) REVERT: L 37 GLN cc_start: 0.8134 (tt0) cc_final: 0.7348 (tp40) REVERT: L 86 TYR cc_start: 0.7293 (m-80) cc_final: 0.6533 (m-80) REVERT: C 208 GLU cc_start: 0.7744 (tp30) cc_final: 0.7522 (tp30) REVERT: C 286 THR cc_start: 0.9221 (t) cc_final: 0.9002 (m) REVERT: E 14 SER cc_start: 0.7679 (t) cc_final: 0.7330 (p) REVERT: E 37 GLN cc_start: 0.8135 (tt0) cc_final: 0.7353 (tp40) REVERT: E 61 ARG cc_start: 0.6375 (ptt-90) cc_final: 0.6084 (ptt-90) REVERT: E 86 TYR cc_start: 0.7297 (m-80) cc_final: 0.6540 (m-80) REVERT: G 208 GLU cc_start: 0.7733 (tp30) cc_final: 0.7513 (tp30) REVERT: G 286 THR cc_start: 0.9219 (t) cc_final: 0.9002 (m) REVERT: J 14 SER cc_start: 0.7683 (t) cc_final: 0.7334 (p) REVERT: J 37 GLN cc_start: 0.8131 (tt0) cc_final: 0.7346 (tp40) REVERT: J 61 ARG cc_start: 0.6382 (ptt-90) cc_final: 0.6091 (ptt-90) REVERT: J 86 TYR cc_start: 0.7293 (m-80) cc_final: 0.6533 (m-80) REVERT: M 208 GLU cc_start: 0.7730 (tp30) cc_final: 0.7507 (tp30) REVERT: M 286 THR cc_start: 0.9217 (t) cc_final: 0.8999 (m) REVERT: O 14 SER cc_start: 0.7682 (t) cc_final: 0.7332 (p) REVERT: O 37 GLN cc_start: 0.8130 (tt0) cc_final: 0.7344 (tp40) REVERT: O 61 ARG cc_start: 0.6382 (ptt-90) cc_final: 0.6092 (ptt-90) REVERT: O 86 TYR cc_start: 0.7294 (m-80) cc_final: 0.6533 (m-80) outliers start: 54 outliers final: 49 residues processed: 376 average time/residue: 0.1280 time to fit residues: 77.2705 Evaluate side-chains 388 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 339 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 348 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 33 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 348 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 33 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 348 ILE Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 456 TRP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain J residue 33 LEU 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 348 ILE Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain O residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 206 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 188 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 124 optimal weight: 0.0870 chunk 80 optimal weight: 3.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.145786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.123750 restraints weight = 25828.993| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.72 r_work: 0.3588 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19532 Z= 0.225 Angle : 0.803 33.660 26492 Z= 0.369 Chirality : 0.051 0.389 2840 Planarity : 0.005 0.064 3356 Dihedral : 5.990 59.085 2844 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.75 % Favored : 90.92 % Rotamer: Outliers : 2.78 % Allowed : 12.96 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.16), residues: 2424 helix: -2.87 (0.92), residues: 24 sheet: -0.49 (0.17), residues: 916 loop : -2.14 (0.14), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 61 TYR 0.023 0.002 TYR O 94 PHE 0.025 0.002 PHE J 83 TRP 0.011 0.002 TRP A 438 HIS 0.008 0.002 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00544 (19484) covalent geometry : angle 0.80101 (26388) SS BOND : bond 0.00282 ( 40) SS BOND : angle 0.82087 ( 80) hydrogen bonds : bond 0.04055 ( 588) hydrogen bonds : angle 6.32751 ( 1500) link_BETA1-4 : bond 0.00337 ( 4) link_BETA1-4 : angle 1.02698 ( 12) link_NAG-ASN : bond 0.00228 ( 4) link_NAG-ASN : angle 2.41288 ( 12) ********************** 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 404 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 347 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7847 (tp30) cc_final: 0.7596 (tp30) REVERT: A 286 THR cc_start: 0.9225 (t) cc_final: 0.9005 (m) REVERT: H 98 LYS cc_start: 0.7839 (pttm) cc_final: 0.7312 (pttm) REVERT: L 14 SER cc_start: 0.7750 (t) cc_final: 0.7364 (p) REVERT: L 37 GLN cc_start: 0.8126 (tt0) cc_final: 0.7276 (tt0) REVERT: L 61 ARG cc_start: 0.6805 (ptt-90) cc_final: 0.6495 (ptt-90) REVERT: L 86 TYR cc_start: 0.7264 (m-80) cc_final: 0.6586 (m-80) REVERT: C 208 GLU cc_start: 0.7847 (tp30) cc_final: 0.7596 (tp30) REVERT: C 286 THR cc_start: 0.9223 (t) cc_final: 0.9002 (m) REVERT: D 98 LYS cc_start: 0.7841 (pttm) cc_final: 0.7312 (pttm) REVERT: E 14 SER cc_start: 0.7742 (t) cc_final: 0.7351 (p) REVERT: E 37 GLN cc_start: 0.8134 (tt0) cc_final: 0.7279 (tt0) REVERT: E 61 ARG cc_start: 0.6800 (ptt-90) cc_final: 0.6511 (ptt-90) REVERT: E 86 TYR cc_start: 0.7263 (m-80) cc_final: 0.6585 (m-80) REVERT: G 208 GLU cc_start: 0.7848 (tp30) cc_final: 0.7597 (tp30) REVERT: G 286 THR cc_start: 0.9222 (t) cc_final: 0.9000 (m) REVERT: I 98 LYS cc_start: 0.7839 (pttm) cc_final: 0.7302 (pttm) REVERT: J 14 SER cc_start: 0.7740 (t) cc_final: 0.7352 (p) REVERT: J 37 GLN cc_start: 0.8128 (tt0) cc_final: 0.7272 (tt0) REVERT: J 61 ARG cc_start: 0.6813 (ptt-90) cc_final: 0.6525 (ptt-90) REVERT: J 86 TYR cc_start: 0.7263 (m-80) cc_final: 0.6584 (m-80) REVERT: M 208 GLU cc_start: 0.7844 (tp30) cc_final: 0.7587 (tp30) REVERT: M 286 THR cc_start: 0.9222 (t) cc_final: 0.9002 (m) REVERT: N 98 LYS cc_start: 0.7843 (pttm) cc_final: 0.7309 (pttm) REVERT: O 14 SER cc_start: 0.7747 (t) cc_final: 0.7361 (p) REVERT: O 37 GLN cc_start: 0.8127 (tt0) cc_final: 0.7270 (tt0) REVERT: O 61 ARG cc_start: 0.6812 (ptt-90) cc_final: 0.6523 (ptt-90) REVERT: O 86 TYR cc_start: 0.7265 (m-80) cc_final: 0.6586 (m-80) outliers start: 57 outliers final: 49 residues processed: 380 average time/residue: 0.1220 time to fit residues: 74.5584 Evaluate side-chains 391 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 342 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 348 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 33 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 348 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 33 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 348 ILE Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 456 TRP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain J residue 33 LEU 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 348 ILE Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain O residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 186 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN L 38 GLN E 38 GLN J 38 GLN O 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.147688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.125937 restraints weight = 25548.878| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.71 r_work: 0.3592 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19532 Z= 0.151 Angle : 0.780 35.693 26492 Z= 0.351 Chirality : 0.048 0.355 2840 Planarity : 0.005 0.062 3356 Dihedral : 5.825 56.411 2844 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.43 % Favored : 92.41 % Rotamer: Outliers : 2.44 % Allowed : 13.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.12 (0.16), residues: 2424 helix: -2.69 (0.97), residues: 24 sheet: -0.42 (0.17), residues: 920 loop : -2.15 (0.14), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 61 TYR 0.017 0.002 TYR A 296 PHE 0.027 0.002 PHE L 83 TRP 0.011 0.001 TRP A 177 HIS 0.006 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00361 (19484) covalent geometry : angle 0.77813 (26388) SS BOND : bond 0.00219 ( 40) SS BOND : angle 0.84191 ( 80) hydrogen bonds : bond 0.03802 ( 588) hydrogen bonds : angle 6.16091 ( 1500) link_BETA1-4 : bond 0.00462 ( 4) link_BETA1-4 : angle 0.91093 ( 12) link_NAG-ASN : bond 0.00401 ( 4) link_NAG-ASN : angle 2.14931 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4611.28 seconds wall clock time: 80 minutes 0.82 seconds (4800.82 seconds total)