Starting phenix.real_space_refine on Mon Aug 25 20:39:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j99_36092/08_2025/8j99_36092_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j99_36092/08_2025/8j99_36092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j99_36092/08_2025/8j99_36092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j99_36092/08_2025/8j99_36092.map" model { file = "/net/cci-nas-00/data/ceres_data/8j99_36092/08_2025/8j99_36092_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j99_36092/08_2025/8j99_36092_neut.cif" } resolution = 2.87 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= -0.001 sd= 0.030 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: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 156 5.16 5 C 19296 2.51 5 N 5280 2.21 5 O 5783 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30533 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1065 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain: "B" Number of atoms: 3970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3970 Classifications: {'peptide': 514} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 491} Chain breaks: 1 Chain: "C" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1065 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain: "D" Number of atoms: 3970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3970 Classifications: {'peptide': 514} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 491} Chain breaks: 1 Chain: "E" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1064 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1065 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain: "G" Number of atoms: 3970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3970 Classifications: {'peptide': 514} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 491} Chain breaks: 1 Chain: "H" Number of atoms: 3970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3970 Classifications: {'peptide': 514} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 491} Chain breaks: 1 Chain: "I" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1065 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain: "J" Number of atoms: 3970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3970 Classifications: {'peptide': 514} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 491} Chain breaks: 1 Chain: "K" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1065 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain: "L" Number of atoms: 3970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3970 Classifications: {'peptide': 514} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 491} Chain breaks: 1 Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'TW3': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'TW3': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'TW3': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'TW3': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'TW3': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'TW3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.60, per 1000 atoms: 0.22 Number of scatterers: 30533 At special positions: 0 Unit cell: (154.23, 136.77, 150.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 156 16.00 P 18 15.00 O 5783 8.00 N 5280 7.00 C 19296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.7 microseconds 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7116 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 24 sheets defined 45.9% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 504 through 530 removed outlier: 3.654A pdb=" N LEU A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A 529 " --> pdb=" O THR A 525 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 530 " --> pdb=" O PHE A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 539 Processing helix chain 'B' and resid 39 through 66 removed outlier: 3.989A pdb=" N GLY B 66 " --> pdb=" O HIS B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 78 Processing helix chain 'B' and resid 82 through 91 Processing helix chain 'B' and resid 114 through 117 Processing helix chain 'B' and resid 139 through 144 removed outlier: 4.029A pdb=" N GLY B 142 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 164 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.521A pdb=" N VAL B 184 " --> pdb=" O ARG B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 204 removed outlier: 4.213A pdb=" N THR B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE B 195 " --> pdb=" O PHE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 315 through 322 removed outlier: 4.237A pdb=" N GLY B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 339 removed outlier: 4.065A pdb=" N VAL B 334 " --> pdb=" O ASP B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 377 through 395 Processing helix chain 'B' and resid 414 through 432 removed outlier: 3.599A pdb=" N ILE B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 452 removed outlier: 4.016A pdb=" N TYR B 450 " --> pdb=" O GLY B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 458 Processing helix chain 'B' and resid 474 through 493 Processing helix chain 'B' and resid 498 through 517 Proline residue: B 508 - end of helix Processing helix chain 'B' and resid 518 through 525 removed outlier: 3.731A pdb=" N ARG B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 536 through 549 Processing helix chain 'C' and resid 504 through 530 removed outlier: 3.511A pdb=" N LEU C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 539 Processing helix chain 'D' and resid 39 through 66 removed outlier: 3.989A pdb=" N GLY D 66 " --> pdb=" O HIS D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 78 Processing helix chain 'D' and resid 82 through 91 Processing helix chain 'D' and resid 114 through 117 Processing helix chain 'D' and resid 139 through 144 removed outlier: 4.030A pdb=" N GLY D 142 " --> pdb=" O THR D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 164 Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing helix chain 'D' and resid 180 through 185 removed outlier: 3.521A pdb=" N VAL D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 204 removed outlier: 4.213A pdb=" N THR D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE D 195 " --> pdb=" O PHE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 227 Processing helix chain 'D' and resid 264 through 269 Processing helix chain 'D' and resid 279 through 293 Processing helix chain 'D' and resid 315 through 322 removed outlier: 4.237A pdb=" N GLY D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 339 removed outlier: 4.065A pdb=" N VAL D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 343 Processing helix chain 'D' and resid 377 through 395 Processing helix chain 'D' and resid 414 through 432 removed outlier: 3.599A pdb=" N ILE D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS D 424 " --> pdb=" O LYS D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 452 removed outlier: 4.016A pdb=" N TYR D 450 " --> pdb=" O GLY D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 458 Processing helix chain 'D' and resid 474 through 493 Processing helix chain 'D' and resid 498 through 517 Proline residue: D 508 - end of helix Processing helix chain 'D' and resid 518 through 525 removed outlier: 3.730A pdb=" N ARG D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 535 No H-bonds generated for 'chain 'D' and resid 533 through 535' Processing helix chain 'D' and resid 536 through 549 Processing helix chain 'E' and resid 504 through 530 removed outlier: 3.629A pdb=" N LEU E 508 " --> pdb=" O ALA E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 539 Processing helix chain 'F' and resid 504 through 530 removed outlier: 3.534A pdb=" N LEU F 508 " --> pdb=" O ALA F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 539 Processing helix chain 'G' and resid 39 through 66 removed outlier: 3.990A pdb=" N GLY G 66 " --> pdb=" O HIS G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 78 Processing helix chain 'G' and resid 82 through 91 Processing helix chain 'G' and resid 114 through 117 Processing helix chain 'G' and resid 139 through 144 removed outlier: 4.030A pdb=" N GLY G 142 " --> pdb=" O THR G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 164 Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 180 through 185 removed outlier: 3.520A pdb=" N VAL G 184 " --> pdb=" O ARG G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 204 removed outlier: 4.212A pdb=" N THR G 194 " --> pdb=" O HIS G 190 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE G 195 " --> pdb=" O PHE G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 227 Processing helix chain 'G' and resid 264 through 269 Processing helix chain 'G' and resid 279 through 293 Processing helix chain 'G' and resid 315 through 322 removed outlier: 4.237A pdb=" N GLY G 319 " --> pdb=" O ASP G 315 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 339 removed outlier: 4.065A pdb=" N VAL G 334 " --> pdb=" O ASP G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 343 Processing helix chain 'G' and resid 377 through 395 Processing helix chain 'G' and resid 414 through 432 removed outlier: 3.599A pdb=" N ILE G 418 " --> pdb=" O GLU G 414 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS G 424 " --> pdb=" O LYS G 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 446 through 452 removed outlier: 4.016A pdb=" N TYR G 450 " --> pdb=" O GLY G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 454 through 458 Processing helix chain 'G' and resid 474 through 493 Processing helix chain 'G' and resid 498 through 517 Proline residue: G 508 - end of helix Processing helix chain 'G' and resid 518 through 525 removed outlier: 3.731A pdb=" N ARG G 525 " --> pdb=" O TYR G 521 " (cutoff:3.500A) Processing helix chain 'G' and resid 533 through 535 No H-bonds generated for 'chain 'G' and resid 533 through 535' Processing helix chain 'G' and resid 536 through 549 Processing helix chain 'H' and resid 39 through 66 removed outlier: 3.989A pdb=" N GLY H 66 " --> pdb=" O HIS H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 78 Processing helix chain 'H' and resid 82 through 91 Processing helix chain 'H' and resid 114 through 117 Processing helix chain 'H' and resid 139 through 144 removed outlier: 4.029A pdb=" N GLY H 142 " --> pdb=" O THR H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 164 Processing helix chain 'H' and resid 177 through 179 No H-bonds generated for 'chain 'H' and resid 177 through 179' Processing helix chain 'H' and resid 180 through 185 removed outlier: 3.521A pdb=" N VAL H 184 " --> pdb=" O ARG H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 204 removed outlier: 4.213A pdb=" N THR H 194 " --> pdb=" O HIS H 190 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE H 195 " --> pdb=" O PHE H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 227 Processing helix chain 'H' and resid 264 through 269 Processing helix chain 'H' and resid 279 through 293 Processing helix chain 'H' and resid 315 through 322 removed outlier: 4.237A pdb=" N GLY H 319 " --> pdb=" O ASP H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 330 through 339 removed outlier: 4.065A pdb=" N VAL H 334 " --> pdb=" O ASP H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 343 Processing helix chain 'H' and resid 377 through 395 Processing helix chain 'H' and resid 414 through 432 removed outlier: 3.598A pdb=" N ILE H 418 " --> pdb=" O GLU H 414 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS H 424 " --> pdb=" O LYS H 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 446 through 452 removed outlier: 4.016A pdb=" N TYR H 450 " --> pdb=" O GLY H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 454 through 458 Processing helix chain 'H' and resid 474 through 493 Processing helix chain 'H' and resid 498 through 517 Proline residue: H 508 - end of helix Processing helix chain 'H' and resid 518 through 525 removed outlier: 3.731A pdb=" N ARG H 525 " --> pdb=" O TYR H 521 " (cutoff:3.500A) Processing helix chain 'H' and resid 533 through 535 No H-bonds generated for 'chain 'H' and resid 533 through 535' Processing helix chain 'H' and resid 536 through 549 Processing helix chain 'I' and resid 504 through 530 removed outlier: 3.635A pdb=" N LEU I 508 " --> pdb=" O ALA I 504 " (cutoff:3.500A) Processing helix chain 'I' and resid 535 through 539 Processing helix chain 'J' and resid 39 through 66 removed outlier: 3.989A pdb=" N GLY J 66 " --> pdb=" O HIS J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 78 Processing helix chain 'J' and resid 82 through 91 Processing helix chain 'J' and resid 114 through 117 Processing helix chain 'J' and resid 139 through 144 removed outlier: 4.029A pdb=" N GLY J 142 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 164 Processing helix chain 'J' and resid 177 through 179 No H-bonds generated for 'chain 'J' and resid 177 through 179' Processing helix chain 'J' and resid 180 through 185 removed outlier: 3.521A pdb=" N VAL J 184 " --> pdb=" O ARG J 180 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 204 removed outlier: 4.213A pdb=" N THR J 194 " --> pdb=" O HIS J 190 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE J 195 " --> pdb=" O PHE J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 227 Processing helix chain 'J' and resid 264 through 269 Processing helix chain 'J' and resid 279 through 293 Processing helix chain 'J' and resid 315 through 322 removed outlier: 4.237A pdb=" N GLY J 319 " --> pdb=" O ASP J 315 " (cutoff:3.500A) Processing helix chain 'J' and resid 330 through 339 removed outlier: 4.065A pdb=" N VAL J 334 " --> pdb=" O ASP J 330 " (cutoff:3.500A) Processing helix chain 'J' and resid 340 through 343 Processing helix chain 'J' and resid 377 through 395 Processing helix chain 'J' and resid 414 through 432 removed outlier: 3.599A pdb=" N ILE J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS J 424 " --> pdb=" O LYS J 420 " (cutoff:3.500A) Processing helix chain 'J' and resid 446 through 452 removed outlier: 4.016A pdb=" N TYR J 450 " --> pdb=" O GLY J 446 " (cutoff:3.500A) Processing helix chain 'J' and resid 454 through 458 Processing helix chain 'J' and resid 474 through 493 Processing helix chain 'J' and resid 498 through 517 Proline residue: J 508 - end of helix Processing helix chain 'J' and resid 518 through 525 removed outlier: 3.731A pdb=" N ARG J 525 " --> pdb=" O TYR J 521 " (cutoff:3.500A) Processing helix chain 'J' and resid 533 through 535 No H-bonds generated for 'chain 'J' and resid 533 through 535' Processing helix chain 'J' and resid 536 through 549 Processing helix chain 'K' and resid 504 through 530 removed outlier: 3.603A pdb=" N LEU K 508 " --> pdb=" O ALA K 504 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN K 529 " --> pdb=" O THR K 525 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA K 530 " --> pdb=" O PHE K 526 " (cutoff:3.500A) Processing helix chain 'K' and resid 535 through 539 Processing helix chain 'L' and resid 39 through 66 removed outlier: 3.989A pdb=" N GLY L 66 " --> pdb=" O HIS L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 78 Processing helix chain 'L' and resid 82 through 91 Processing helix chain 'L' and resid 114 through 117 Processing helix chain 'L' and resid 139 through 144 removed outlier: 4.029A pdb=" N GLY L 142 " --> pdb=" O THR L 139 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 164 Processing helix chain 'L' and resid 177 through 179 No H-bonds generated for 'chain 'L' and resid 177 through 179' Processing helix chain 'L' and resid 180 through 185 removed outlier: 3.521A pdb=" N VAL L 184 " --> pdb=" O ARG L 180 " (cutoff:3.500A) Processing helix chain 'L' and resid 190 through 204 removed outlier: 4.213A pdb=" N THR L 194 " --> pdb=" O HIS L 190 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE L 195 " --> pdb=" O PHE L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 221 through 227 Processing helix chain 'L' and resid 264 through 269 Processing helix chain 'L' and resid 279 through 293 Processing helix chain 'L' and resid 315 through 322 removed outlier: 4.237A pdb=" N GLY L 319 " --> pdb=" O ASP L 315 " (cutoff:3.500A) Processing helix chain 'L' and resid 330 through 339 removed outlier: 4.065A pdb=" N VAL L 334 " --> pdb=" O ASP L 330 " (cutoff:3.500A) Processing helix chain 'L' and resid 340 through 343 Processing helix chain 'L' and resid 377 through 395 Processing helix chain 'L' and resid 414 through 432 removed outlier: 3.599A pdb=" N ILE L 418 " --> pdb=" O GLU L 414 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS L 424 " --> pdb=" O LYS L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 446 through 452 removed outlier: 4.016A pdb=" N TYR L 450 " --> pdb=" O GLY L 446 " (cutoff:3.500A) Processing helix chain 'L' and resid 454 through 458 Processing helix chain 'L' and resid 474 through 493 Processing helix chain 'L' and resid 498 through 517 Proline residue: L 508 - end of helix Processing helix chain 'L' and resid 518 through 525 removed outlier: 3.731A pdb=" N ARG L 525 " --> pdb=" O TYR L 521 " (cutoff:3.500A) Processing helix chain 'L' and resid 533 through 535 No H-bonds generated for 'chain 'L' and resid 533 through 535' Processing helix chain 'L' and resid 536 through 549 Processing sheet with id=AA1, first strand: chain 'A' and resid 550 through 557 removed outlier: 4.931A pdb=" N THR A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.736A pdb=" N THR B 121 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ALA B 277 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE B 232 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 345 through 346 removed outlier: 7.747A pdb=" N LEU B 399 " --> pdb=" O PRO B 366 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLY B 368 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU B 401 " --> pdb=" O GLY B 368 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL B 370 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B 461 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 443 through 445 Processing sheet with id=AA5, first strand: chain 'C' and resid 550 through 557 removed outlier: 4.864A pdb=" N THR C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.735A pdb=" N THR D 121 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ALA D 277 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE D 232 " --> pdb=" O ALA D 277 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 345 through 346 removed outlier: 7.746A pdb=" N LEU D 399 " --> pdb=" O PRO D 366 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY D 368 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU D 401 " --> pdb=" O GLY D 368 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL D 370 " --> pdb=" O LEU D 401 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE D 461 " --> pdb=" O LYS D 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 443 through 445 Processing sheet with id=AA9, first strand: chain 'E' and resid 549 through 557 removed outlier: 4.552A pdb=" N TYR E 549 " --> pdb=" O TYR E 568 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N THR E 596 " --> pdb=" O LEU E 611 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 550 through 557 removed outlier: 4.833A pdb=" N THR F 596 " --> pdb=" O LEU F 611 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 98 through 100 removed outlier: 4.736A pdb=" N THR G 121 " --> pdb=" O LEU G 100 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ALA G 277 " --> pdb=" O ASN G 230 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE G 232 " --> pdb=" O ALA G 277 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 345 through 346 removed outlier: 7.746A pdb=" N LEU G 399 " --> pdb=" O PRO G 366 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLY G 368 " --> pdb=" O LEU G 399 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU G 401 " --> pdb=" O GLY G 368 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL G 370 " --> pdb=" O LEU G 401 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE G 461 " --> pdb=" O LYS G 436 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 443 through 445 Processing sheet with id=AB5, first strand: chain 'H' and resid 98 through 100 removed outlier: 4.737A pdb=" N THR H 121 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ALA H 277 " --> pdb=" O ASN H 230 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE H 232 " --> pdb=" O ALA H 277 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 345 through 346 removed outlier: 7.747A pdb=" N LEU H 399 " --> pdb=" O PRO H 366 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY H 368 " --> pdb=" O LEU H 399 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU H 401 " --> pdb=" O GLY H 368 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL H 370 " --> pdb=" O LEU H 401 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE H 461 " --> pdb=" O LYS H 436 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 443 through 445 Processing sheet with id=AB8, first strand: chain 'I' and resid 550 through 557 removed outlier: 4.878A pdb=" N THR I 596 " --> pdb=" O LEU I 611 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 98 through 100 removed outlier: 4.736A pdb=" N THR J 121 " --> pdb=" O LEU J 100 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ALA J 277 " --> pdb=" O ASN J 230 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE J 232 " --> pdb=" O ALA J 277 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 345 through 346 removed outlier: 7.747A pdb=" N LEU J 399 " --> pdb=" O PRO J 366 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY J 368 " --> pdb=" O LEU J 399 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU J 401 " --> pdb=" O GLY J 368 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL J 370 " --> pdb=" O LEU J 401 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE J 461 " --> pdb=" O LYS J 436 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 443 through 445 Processing sheet with id=AC3, first strand: chain 'K' and resid 549 through 557 removed outlier: 4.507A pdb=" N TYR K 549 " --> pdb=" O TYR K 568 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N THR K 596 " --> pdb=" O LEU K 611 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 98 through 100 removed outlier: 4.737A pdb=" N THR L 121 " --> pdb=" O LEU L 100 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ALA L 277 " --> pdb=" O ASN L 230 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE L 232 " --> pdb=" O ALA L 277 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 345 through 346 removed outlier: 7.747A pdb=" N LEU L 399 " --> pdb=" O PRO L 366 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY L 368 " --> pdb=" O LEU L 399 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU L 401 " --> pdb=" O GLY L 368 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL L 370 " --> pdb=" O LEU L 401 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE L 461 " --> pdb=" O LYS L 436 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 443 through 445 1644 hydrogen bonds defined for protein. 4596 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: 7.09 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7729 1.33 - 1.45: 5858 1.45 - 1.57: 17264 1.57 - 1.69: 30 1.69 - 1.81: 246 Bond restraints: 31127 Sorted by residual: bond pdb=" O14 TW3 B 801 " pdb=" P3 TW3 B 801 " ideal model delta sigma weight residual 1.688 1.611 0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" O14 TW3 D 801 " pdb=" P3 TW3 D 801 " ideal model delta sigma weight residual 1.688 1.611 0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" O14 TW3 J 801 " pdb=" P3 TW3 J 801 " ideal model delta sigma weight residual 1.688 1.611 0.077 2.00e-02 2.50e+03 1.46e+01 bond pdb=" O14 TW3 L 801 " pdb=" P3 TW3 L 801 " ideal model delta sigma weight residual 1.688 1.612 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" O14 TW3 G 801 " pdb=" P3 TW3 G 801 " ideal model delta sigma weight residual 1.688 1.612 0.076 2.00e-02 2.50e+03 1.46e+01 ... (remaining 31122 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 41239 2.55 - 5.11: 751 5.11 - 7.66: 65 7.66 - 10.22: 21 10.22 - 12.77: 13 Bond angle restraints: 42089 Sorted by residual: angle pdb=" N ASP G 274 " pdb=" CA ASP G 274 " pdb=" C ASP G 274 " ideal model delta sigma weight residual 113.41 105.61 7.80 1.22e+00 6.72e-01 4.09e+01 angle pdb=" N ASP B 274 " pdb=" CA ASP B 274 " pdb=" C ASP B 274 " ideal model delta sigma weight residual 113.41 105.65 7.76 1.22e+00 6.72e-01 4.04e+01 angle pdb=" N ASP H 274 " pdb=" CA ASP H 274 " pdb=" C ASP H 274 " ideal model delta sigma weight residual 113.41 105.66 7.75 1.22e+00 6.72e-01 4.04e+01 angle pdb=" N ASP J 274 " pdb=" CA ASP J 274 " pdb=" C ASP J 274 " ideal model delta sigma weight residual 113.41 105.67 7.74 1.22e+00 6.72e-01 4.03e+01 angle pdb=" N ASP L 274 " pdb=" CA ASP L 274 " pdb=" C ASP L 274 " ideal model delta sigma weight residual 113.41 105.67 7.74 1.22e+00 6.72e-01 4.02e+01 ... (remaining 42084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.26: 17399 19.26 - 38.51: 1200 38.51 - 57.77: 185 57.77 - 77.02: 49 77.02 - 96.28: 48 Dihedral angle restraints: 18881 sinusoidal: 7697 harmonic: 11184 Sorted by residual: dihedral pdb=" CA PHE H 185 " pdb=" C PHE H 185 " pdb=" N PRO H 186 " pdb=" CA PRO H 186 " ideal model delta harmonic sigma weight residual -180.00 -154.12 -25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA PHE J 185 " pdb=" C PHE J 185 " pdb=" N PRO J 186 " pdb=" CA PRO J 186 " ideal model delta harmonic sigma weight residual -180.00 -154.14 -25.86 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA PHE L 185 " pdb=" C PHE L 185 " pdb=" N PRO L 186 " pdb=" CA PRO L 186 " ideal model delta harmonic sigma weight residual -180.00 -154.15 -25.85 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 18878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3804 0.064 - 0.128: 671 0.128 - 0.192: 100 0.192 - 0.256: 28 0.256 - 0.320: 5 Chirality restraints: 4608 Sorted by residual: chirality pdb=" CA ASP I 580 " pdb=" N ASP I 580 " pdb=" C ASP I 580 " pdb=" CB ASP I 580 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA ILE E 618 " pdb=" N ILE E 618 " pdb=" C ILE E 618 " pdb=" CB ILE E 618 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA ILE C 578 " pdb=" N ILE C 578 " pdb=" C ILE C 578 " pdb=" CB ILE C 578 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 4605 not shown) Planarity restraints: 5460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 636 " -0.014 2.00e-02 2.50e+03 1.97e-02 7.77e+00 pdb=" CG TYR E 636 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR E 636 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR E 636 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR E 636 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR E 636 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR E 636 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR E 636 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7 TW3 H 801 " 0.021 2.00e-02 2.50e+03 1.78e-02 3.95e+00 pdb=" C8 TW3 H 801 " -0.010 2.00e-02 2.50e+03 pdb=" C9 TW3 H 801 " 0.017 2.00e-02 2.50e+03 pdb=" N1 TW3 H 801 " -0.027 2.00e-02 2.50e+03 pdb=" O2 TW3 H 801 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7 TW3 B 801 " 0.021 2.00e-02 2.50e+03 1.76e-02 3.87e+00 pdb=" C8 TW3 B 801 " -0.009 2.00e-02 2.50e+03 pdb=" C9 TW3 B 801 " 0.017 2.00e-02 2.50e+03 pdb=" N1 TW3 B 801 " -0.027 2.00e-02 2.50e+03 pdb=" O2 TW3 B 801 " -0.003 2.00e-02 2.50e+03 ... (remaining 5457 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 658 2.69 - 3.24: 31021 3.24 - 3.79: 48763 3.79 - 4.35: 62885 4.35 - 4.90: 106513 Nonbonded interactions: 249840 Sorted by model distance: nonbonded pdb=" OH TYR E 590 " pdb=" NZ LYS E 608 " model vdw 2.136 3.120 nonbonded pdb=" OH TYR C 590 " pdb=" NZ LYS C 608 " model vdw 2.137 3.120 nonbonded pdb=" O GLY D 117 " pdb=" OG1 THR D 149 " model vdw 2.151 3.040 nonbonded pdb=" O GLY B 117 " pdb=" OG1 THR B 149 " model vdw 2.152 3.040 nonbonded pdb=" O GLY G 117 " pdb=" OG1 THR G 149 " model vdw 2.152 3.040 ... (remaining 249835 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 501 through 637 or (resid 638 and (name N or name CA or na \ me C or name O or name CB )))) selection = (chain 'C' and (resid 501 through 637 or (resid 638 and (name N or name CA or na \ me C or name O or name CB )))) selection = chain 'E' selection = (chain 'F' and (resid 501 through 637 or (resid 638 and (name N or name CA or na \ me C or name O or name CB )))) selection = (chain 'I' and (resid 501 through 637 or (resid 638 and (name N or name CA or na \ me C or name O or name CB )))) selection = (chain 'K' and (resid 501 through 637 or (resid 638 and (name N or name CA or na \ me C or name O or name CB )))) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.190 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 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:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 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 : 0.008 0.077 31127 Z= 0.402 Angle : 0.863 12.772 42089 Z= 0.514 Chirality : 0.053 0.320 4608 Planarity : 0.004 0.042 5460 Dihedral : 14.453 96.278 11765 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.38 % Allowed : 1.19 % Favored : 98.43 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.13), residues: 3876 helix: 1.45 (0.13), residues: 1530 sheet: 1.50 (0.17), residues: 798 loop : 0.24 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 543 TYR 0.046 0.002 TYR E 636 PHE 0.013 0.001 PHE F 526 TRP 0.007 0.001 TRP D 276 HIS 0.009 0.002 HIS K 531 Details of bonding type rmsd covalent geometry : bond 0.00806 (31127) covalent geometry : angle 0.86267 (42089) hydrogen bonds : bond 0.12149 ( 1644) hydrogen bonds : angle 6.12960 ( 4596) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 324 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 VAL cc_start: 0.7993 (t) cc_final: 0.7701 (t) REVERT: B 452 MET cc_start: 0.9166 (mmm) cc_final: 0.8954 (mmm) REVERT: B 554 GLU cc_start: 0.7797 (pp20) cc_final: 0.7459 (pp20) REVERT: D 554 GLU cc_start: 0.7801 (pp20) cc_final: 0.7594 (pp20) REVERT: E 543 ARG cc_start: 0.9087 (mmm-85) cc_final: 0.8861 (mmm-85) REVERT: F 556 LYS cc_start: 0.8003 (tttm) cc_final: 0.7696 (tppp) REVERT: G 554 GLU cc_start: 0.7894 (pp20) cc_final: 0.7572 (pp20) REVERT: G 555 LYS cc_start: 0.8685 (ptmm) cc_final: 0.8432 (ptmm) REVERT: H 204 LYS cc_start: 0.9255 (mtmt) cc_final: 0.9025 (mttp) REVERT: H 554 GLU cc_start: 0.7797 (pp20) cc_final: 0.7424 (pp20) REVERT: I 522 MET cc_start: 0.7295 (mpp) cc_final: 0.7082 (mpp) REVERT: J 554 GLU cc_start: 0.7854 (pp20) cc_final: 0.7547 (pp20) REVERT: J 555 LYS cc_start: 0.8652 (ptmm) cc_final: 0.8296 (ptmm) REVERT: J 557 ASP cc_start: 0.8852 (m-30) cc_final: 0.8472 (m-30) REVERT: L 554 GLU cc_start: 0.7769 (pp20) cc_final: 0.7452 (pp20) outliers start: 12 outliers final: 10 residues processed: 330 average time/residue: 0.9446 time to fit residues: 353.7644 Evaluate side-chains 247 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 237 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 266 HIS Chi-restraints excluded: chain H residue 266 HIS Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain J residue 266 HIS Chi-restraints excluded: chain K residue 578 ILE Chi-restraints excluded: chain L residue 266 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.0670 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.5980 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 ASN B 24 HIS B 266 HIS C 570 HIS C 584 GLN C 603 ASN D 24 HIS D 266 HIS E 603 ASN F 570 HIS F 584 GLN F 603 ASN G 24 HIS G 266 HIS H 24 HIS H 266 HIS I 577 GLN I 584 GLN I 603 ASN J 24 HIS J 266 HIS J 285 HIS K 603 ASN L 24 HIS L 266 HIS L 285 HIS L 372 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.114159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.081491 restraints weight = 72838.373| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.72 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31127 Z= 0.131 Angle : 0.576 10.330 42089 Z= 0.293 Chirality : 0.044 0.184 4608 Planarity : 0.004 0.080 5460 Dihedral : 10.066 87.772 4684 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.16 % Allowed : 6.78 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.14), residues: 3876 helix: 2.23 (0.14), residues: 1530 sheet: 1.58 (0.17), residues: 798 loop : 0.13 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 292 TYR 0.016 0.001 TYR A 636 PHE 0.011 0.001 PHE J 347 TRP 0.009 0.001 TRP B 276 HIS 0.004 0.001 HIS E 531 Details of bonding type rmsd covalent geometry : bond 0.00279 (31127) covalent geometry : angle 0.57570 (42089) hydrogen bonds : bond 0.04534 ( 1644) hydrogen bonds : angle 4.74800 ( 4596) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 271 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8612 (tpt) REVERT: B 452 MET cc_start: 0.9430 (mmm) cc_final: 0.9226 (tpp) REVERT: B 554 GLU cc_start: 0.8082 (pp20) cc_final: 0.7791 (pp20) REVERT: C 518 LYS cc_start: 0.8306 (tppp) cc_final: 0.8024 (mptp) REVERT: C 543 ARG cc_start: 0.9304 (mmm-85) cc_final: 0.9050 (mmm-85) REVERT: D 457 TYR cc_start: 0.9308 (m-80) cc_final: 0.8776 (m-80) REVERT: F 543 ARG cc_start: 0.9388 (mmm-85) cc_final: 0.9115 (mmm-85) REVERT: G 554 GLU cc_start: 0.8108 (pp20) cc_final: 0.7746 (pp20) REVERT: G 555 LYS cc_start: 0.9042 (ptmm) cc_final: 0.8783 (ptmm) REVERT: H 49 MET cc_start: 0.9121 (tpt) cc_final: 0.8757 (tpt) REVERT: I 559 LYS cc_start: 0.8439 (mtmt) cc_final: 0.8132 (mmpt) REVERT: J 555 LYS cc_start: 0.9133 (ptmm) cc_final: 0.8911 (ptmm) REVERT: J 557 ASP cc_start: 0.9034 (m-30) cc_final: 0.8678 (m-30) REVERT: L 132 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8641 (tpt) REVERT: L 213 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8518 (mtp) REVERT: L 452 MET cc_start: 0.9281 (tpp) cc_final: 0.9052 (mmm) REVERT: L 554 GLU cc_start: 0.8077 (pp20) cc_final: 0.7858 (pp20) REVERT: L 555 LYS cc_start: 0.9006 (ptmm) cc_final: 0.8697 (ptmt) outliers start: 37 outliers final: 8 residues processed: 278 average time/residue: 0.8529 time to fit residues: 272.8380 Evaluate side-chains 259 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 248 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 266 HIS Chi-restraints excluded: chain H residue 266 HIS Chi-restraints excluded: chain I residue 633 VAL Chi-restraints excluded: chain J residue 266 HIS Chi-restraints excluded: chain L residue 132 MET Chi-restraints excluded: chain L residue 213 MET Chi-restraints excluded: chain L residue 266 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 353 optimal weight: 4.9990 chunk 376 optimal weight: 0.9990 chunk 249 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 324 optimal weight: 20.0000 chunk 221 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 316 optimal weight: 0.5980 chunk 281 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 GLN A 603 ASN C 584 GLN C 603 ASN E 603 ASN F 584 GLN F 603 ASN H 102 GLN I 584 GLN I 603 ASN J 102 GLN K 603 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.114936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.082901 restraints weight = 72725.678| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.54 r_work: 0.2792 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31127 Z= 0.114 Angle : 0.519 9.465 42089 Z= 0.263 Chirality : 0.043 0.174 4608 Planarity : 0.004 0.055 5460 Dihedral : 9.474 80.929 4677 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.10 % Allowed : 8.19 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.01 (0.14), residues: 3876 helix: 2.43 (0.14), residues: 1530 sheet: 1.59 (0.17), residues: 786 loop : 0.11 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 292 TYR 0.017 0.001 TYR A 636 PHE 0.012 0.001 PHE F 526 TRP 0.009 0.001 TRP B 276 HIS 0.005 0.001 HIS J 285 Details of bonding type rmsd covalent geometry : bond 0.00250 (31127) covalent geometry : angle 0.51895 (42089) hydrogen bonds : bond 0.03895 ( 1644) hydrogen bonds : angle 4.35164 ( 4596) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 294 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 MET cc_start: 0.9351 (OUTLIER) cc_final: 0.9048 (tpt) REVERT: B 554 GLU cc_start: 0.8279 (pp20) cc_final: 0.7986 (pp20) REVERT: C 570 HIS cc_start: 0.8200 (m-70) cc_final: 0.7969 (m-70) REVERT: D 457 TYR cc_start: 0.9363 (m-80) cc_final: 0.8852 (m-80) REVERT: E 556 LYS cc_start: 0.6551 (tptt) cc_final: 0.6320 (tptt) REVERT: E 617 THR cc_start: 0.6158 (OUTLIER) cc_final: 0.5861 (t) REVERT: G 204 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9129 (mttp) REVERT: H 49 MET cc_start: 0.9222 (tpt) cc_final: 0.8986 (tpt) REVERT: J 555 LYS cc_start: 0.9373 (ptmm) cc_final: 0.9120 (ptmm) REVERT: J 557 ASP cc_start: 0.9319 (m-30) cc_final: 0.9027 (m-30) REVERT: L 132 MET cc_start: 0.9374 (OUTLIER) cc_final: 0.9069 (tpt) outliers start: 35 outliers final: 7 residues processed: 296 average time/residue: 0.8827 time to fit residues: 298.6878 Evaluate side-chains 247 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 236 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain E residue 617 THR Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 266 HIS Chi-restraints excluded: chain H residue 266 HIS Chi-restraints excluded: chain I residue 633 VAL Chi-restraints excluded: chain J residue 266 HIS Chi-restraints excluded: chain L residue 132 MET Chi-restraints excluded: chain L residue 266 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 180 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 303 optimal weight: 0.5980 chunk 142 optimal weight: 6.9990 chunk 295 optimal weight: 3.9990 chunk 254 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 GLN A 603 ASN B 372 ASN C 603 ASN D 102 GLN E 603 ASN F 584 GLN F 603 ASN H 102 GLN I 577 GLN I 603 ASN K 603 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.114787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.082616 restraints weight = 72467.755| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.57 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31127 Z= 0.118 Angle : 0.521 7.370 42089 Z= 0.264 Chirality : 0.043 0.174 4608 Planarity : 0.003 0.045 5460 Dihedral : 9.247 78.153 4674 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.04 % Allowed : 9.64 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.03 (0.14), residues: 3876 helix: 2.51 (0.13), residues: 1530 sheet: 1.57 (0.17), residues: 786 loop : 0.08 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 292 TYR 0.017 0.001 TYR A 549 PHE 0.011 0.001 PHE F 526 TRP 0.008 0.001 TRP G 276 HIS 0.002 0.000 HIS G 62 Details of bonding type rmsd covalent geometry : bond 0.00265 (31127) covalent geometry : angle 0.52075 (42089) hydrogen bonds : bond 0.03711 ( 1644) hydrogen bonds : angle 4.20241 ( 4596) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 248 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8762 (tpt) REVERT: B 213 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8667 (mtm) REVERT: C 518 LYS cc_start: 0.8277 (tppp) cc_final: 0.8074 (mptp) REVERT: D 110 ASP cc_start: 0.8922 (OUTLIER) cc_final: 0.8645 (p0) REVERT: D 457 TYR cc_start: 0.9269 (m-80) cc_final: 0.8675 (m-80) REVERT: E 617 THR cc_start: 0.6198 (OUTLIER) cc_final: 0.5919 (t) REVERT: F 518 LYS cc_start: 0.8223 (tppp) cc_final: 0.7987 (mptp) REVERT: G 110 ASP cc_start: 0.8922 (OUTLIER) cc_final: 0.8437 (p0) REVERT: G 204 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8912 (mttp) REVERT: H 49 MET cc_start: 0.9095 (tpt) cc_final: 0.8800 (tpt) REVERT: H 110 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8634 (p0) REVERT: H 161 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8150 (ttp) REVERT: J 110 ASP cc_start: 0.8964 (OUTLIER) cc_final: 0.8429 (p0) REVERT: J 555 LYS cc_start: 0.9293 (ptmm) cc_final: 0.9022 (ptmm) REVERT: J 557 ASP cc_start: 0.9037 (m-30) cc_final: 0.8668 (m-30) REVERT: L 563 MET cc_start: 0.8878 (mmt) cc_final: 0.8326 (mmt) outliers start: 33 outliers final: 7 residues processed: 262 average time/residue: 0.7616 time to fit residues: 230.9801 Evaluate side-chains 254 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 238 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain E residue 617 THR Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 266 HIS Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 266 HIS Chi-restraints excluded: chain I residue 633 VAL Chi-restraints excluded: chain J residue 110 ASP Chi-restraints excluded: chain J residue 266 HIS Chi-restraints excluded: chain L residue 266 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 271 optimal weight: 4.9990 chunk 306 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 288 optimal weight: 9.9990 chunk 377 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 206 optimal weight: 0.6980 chunk 189 optimal weight: 4.9990 chunk 309 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 GLN A 603 ASN C 570 HIS C 584 GLN C 603 ASN D 102 GLN E 603 ASN F 531 HIS H 102 GLN I 603 ASN K 603 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.114261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.081767 restraints weight = 72826.361| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.74 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31127 Z= 0.131 Angle : 0.516 8.483 42089 Z= 0.261 Chirality : 0.043 0.177 4608 Planarity : 0.003 0.040 5460 Dihedral : 9.152 76.305 4674 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.04 % Allowed : 10.77 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.05 (0.14), residues: 3876 helix: 2.55 (0.13), residues: 1530 sheet: 1.49 (0.17), residues: 786 loop : 0.10 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 292 TYR 0.023 0.001 TYR C 549 PHE 0.010 0.001 PHE I 526 TRP 0.007 0.001 TRP G 276 HIS 0.006 0.001 HIS C 531 Details of bonding type rmsd covalent geometry : bond 0.00299 (31127) covalent geometry : angle 0.51576 (42089) hydrogen bonds : bond 0.03716 ( 1644) hydrogen bonds : angle 4.08635 ( 4596) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 253 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8613 (mtm) REVERT: D 110 ASP cc_start: 0.8930 (OUTLIER) cc_final: 0.8668 (p0) REVERT: D 161 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8179 (ttp) REVERT: E 617 THR cc_start: 0.6117 (OUTLIER) cc_final: 0.5827 (t) REVERT: G 110 ASP cc_start: 0.8934 (OUTLIER) cc_final: 0.8450 (p0) REVERT: H 49 MET cc_start: 0.9133 (tpt) cc_final: 0.8861 (tpt) REVERT: H 110 ASP cc_start: 0.8860 (OUTLIER) cc_final: 0.8630 (p0) REVERT: J 110 ASP cc_start: 0.8983 (OUTLIER) cc_final: 0.8439 (p0) REVERT: J 554 GLU cc_start: 0.8965 (pm20) cc_final: 0.8472 (pm20) REVERT: J 555 LYS cc_start: 0.9345 (ptmm) cc_final: 0.8999 (ptmm) REVERT: J 557 ASP cc_start: 0.9037 (m-30) cc_final: 0.8671 (m-30) REVERT: L 213 MET cc_start: 0.8934 (mtp) cc_final: 0.8689 (mmm) REVERT: L 563 MET cc_start: 0.8901 (mmt) cc_final: 0.8384 (mmt) outliers start: 33 outliers final: 7 residues processed: 264 average time/residue: 0.6908 time to fit residues: 212.1328 Evaluate side-chains 240 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 226 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain E residue 617 THR Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 266 HIS Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 266 HIS Chi-restraints excluded: chain I residue 633 VAL Chi-restraints excluded: chain J residue 110 ASP Chi-restraints excluded: chain J residue 266 HIS Chi-restraints excluded: chain L residue 266 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 118 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 158 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 352 optimal weight: 0.0470 chunk 96 optimal weight: 5.9990 chunk 362 optimal weight: 3.9990 chunk 186 optimal weight: 0.9990 chunk 221 optimal weight: 0.0980 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 HIS A 603 ASN C 570 HIS D 102 GLN E 603 ASN F 570 HIS I 603 ASN K 603 ASN L 102 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.115481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.082996 restraints weight = 72550.758| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.75 r_work: 0.2780 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 31127 Z= 0.097 Angle : 0.502 10.894 42089 Z= 0.253 Chirality : 0.042 0.173 4608 Planarity : 0.003 0.039 5460 Dihedral : 8.901 74.644 4674 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.10 % Allowed : 11.11 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.11 (0.14), residues: 3876 helix: 2.62 (0.13), residues: 1530 sheet: 1.51 (0.18), residues: 786 loop : 0.12 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 543 TYR 0.016 0.001 TYR F 549 PHE 0.009 0.001 PHE I 526 TRP 0.010 0.001 TRP J 276 HIS 0.002 0.000 HIS K 531 Details of bonding type rmsd covalent geometry : bond 0.00211 (31127) covalent geometry : angle 0.50184 (42089) hydrogen bonds : bond 0.03342 ( 1644) hydrogen bonds : angle 3.95928 ( 4596) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 253 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8959 (mmm) REVERT: D 110 ASP cc_start: 0.9015 (OUTLIER) cc_final: 0.8733 (p0) REVERT: D 213 MET cc_start: 0.9300 (mmm) cc_final: 0.8954 (mmm) REVERT: D 457 TYR cc_start: 0.9272 (m-80) cc_final: 0.8851 (m-80) REVERT: E 543 ARG cc_start: 0.9439 (mmm-85) cc_final: 0.9083 (mmm-85) REVERT: E 570 HIS cc_start: 0.8422 (m-70) cc_final: 0.8076 (m-70) REVERT: E 617 THR cc_start: 0.6008 (OUTLIER) cc_final: 0.5719 (t) REVERT: F 518 LYS cc_start: 0.8079 (tppp) cc_final: 0.7860 (mptp) REVERT: G 110 ASP cc_start: 0.9018 (OUTLIER) cc_final: 0.8520 (p0) REVERT: H 49 MET cc_start: 0.9200 (tpt) cc_final: 0.8994 (tpt) REVERT: H 110 ASP cc_start: 0.8964 (OUTLIER) cc_final: 0.8719 (p0) REVERT: I 505 LYS cc_start: 0.6476 (OUTLIER) cc_final: 0.6119 (mmmt) REVERT: I 559 LYS cc_start: 0.8384 (ttpt) cc_final: 0.8128 (mmpt) REVERT: J 110 ASP cc_start: 0.9079 (OUTLIER) cc_final: 0.8541 (p0) REVERT: J 554 GLU cc_start: 0.9051 (pm20) cc_final: 0.8541 (pm20) REVERT: J 555 LYS cc_start: 0.9411 (ptmm) cc_final: 0.9096 (ptmm) REVERT: J 557 ASP cc_start: 0.9295 (m-30) cc_final: 0.9004 (m-30) REVERT: K 549 TYR cc_start: 0.7127 (t80) cc_final: 0.6879 (t80) REVERT: L 213 MET cc_start: 0.9245 (mtp) cc_final: 0.8981 (mmm) REVERT: L 563 MET cc_start: 0.8858 (mmt) cc_final: 0.8409 (mmt) outliers start: 35 outliers final: 14 residues processed: 272 average time/residue: 0.6838 time to fit residues: 215.2695 Evaluate side-chains 247 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 226 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain E residue 617 THR Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 266 HIS Chi-restraints excluded: chain G residue 407 PHE Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 266 HIS Chi-restraints excluded: chain I residue 505 LYS Chi-restraints excluded: chain I residue 633 VAL Chi-restraints excluded: chain J residue 110 ASP Chi-restraints excluded: chain J residue 266 HIS Chi-restraints excluded: chain J residue 493 GLU Chi-restraints excluded: chain L residue 266 HIS Chi-restraints excluded: chain L residue 426 VAL Chi-restraints excluded: chain L residue 493 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 75 optimal weight: 9.9990 chunk 238 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 266 optimal weight: 8.9990 chunk 283 optimal weight: 2.9990 chunk 273 optimal weight: 4.9990 chunk 307 optimal weight: 6.9990 chunk 228 optimal weight: 8.9990 chunk 141 optimal weight: 30.0000 chunk 309 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 HIS A 603 ASN B 433 GLN C 584 GLN D 102 GLN D 433 GLN E 531 HIS E 603 ASN G 433 GLN H 102 GLN I 603 ASN J 102 GLN K 603 ASN L 102 GLN L 433 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.112029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.079484 restraints weight = 73584.357| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.62 r_work: 0.2787 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 31127 Z= 0.257 Angle : 0.604 8.651 42089 Z= 0.303 Chirality : 0.045 0.191 4608 Planarity : 0.003 0.039 5460 Dihedral : 9.532 76.737 4674 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.29 % Allowed : 11.18 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.14), residues: 3876 helix: 2.47 (0.13), residues: 1530 sheet: 1.39 (0.17), residues: 786 loop : 0.13 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 86 TYR 0.023 0.001 TYR B 457 PHE 0.011 0.001 PHE G 347 TRP 0.004 0.001 TRP H 527 HIS 0.004 0.001 HIS K 531 Details of bonding type rmsd covalent geometry : bond 0.00600 (31127) covalent geometry : angle 0.60375 (42089) hydrogen bonds : bond 0.04577 ( 1644) hydrogen bonds : angle 4.19580 ( 4596) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 224 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 LYS cc_start: 0.8556 (mttt) cc_final: 0.8187 (mmpt) REVERT: B 557 ASP cc_start: 0.9224 (m-30) cc_final: 0.8996 (m-30) REVERT: C 570 HIS cc_start: 0.8127 (m-70) cc_final: 0.7837 (m-70) REVERT: D 161 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.8780 (ttp) REVERT: D 213 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.8979 (mmm) REVERT: D 554 GLU cc_start: 0.8688 (pm20) cc_final: 0.8369 (pm20) REVERT: E 559 LYS cc_start: 0.8307 (ttpt) cc_final: 0.8029 (tppt) REVERT: E 570 HIS cc_start: 0.8387 (m-70) cc_final: 0.7969 (m-70) REVERT: E 617 THR cc_start: 0.5818 (OUTLIER) cc_final: 0.5556 (t) REVERT: F 559 LYS cc_start: 0.8323 (tppt) cc_final: 0.7951 (tppt) REVERT: F 570 HIS cc_start: 0.8129 (m-70) cc_final: 0.7846 (m-70) REVERT: G 425 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.8545 (tpt) REVERT: H 110 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8694 (p0) REVERT: H 213 MET cc_start: 0.9318 (OUTLIER) cc_final: 0.8993 (mmm) REVERT: I 559 LYS cc_start: 0.8412 (ttpt) cc_final: 0.8166 (mmpt) REVERT: J 425 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.8581 (tpt) REVERT: J 554 GLU cc_start: 0.9003 (pm20) cc_final: 0.8375 (pm20) REVERT: J 555 LYS cc_start: 0.9446 (ptmm) cc_final: 0.9046 (ptmm) REVERT: J 557 ASP cc_start: 0.9313 (m-30) cc_final: 0.9006 (m-30) REVERT: K 549 TYR cc_start: 0.7315 (t80) cc_final: 0.7075 (t80) REVERT: L 132 MET cc_start: 0.9331 (tpp) cc_final: 0.9066 (tpt) REVERT: L 213 MET cc_start: 0.9252 (mtp) cc_final: 0.8943 (mtm) REVERT: L 557 ASP cc_start: 0.9218 (m-30) cc_final: 0.8975 (m-30) REVERT: L 563 MET cc_start: 0.8953 (mmt) cc_final: 0.8528 (mmt) outliers start: 41 outliers final: 17 residues processed: 245 average time/residue: 0.6496 time to fit residues: 186.3031 Evaluate side-chains 244 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain E residue 617 THR Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 266 HIS Chi-restraints excluded: chain G residue 407 PHE Chi-restraints excluded: chain G residue 425 MET Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 213 MET Chi-restraints excluded: chain H residue 266 HIS Chi-restraints excluded: chain H residue 407 PHE Chi-restraints excluded: chain I residue 522 MET Chi-restraints excluded: chain I residue 633 VAL Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 266 HIS Chi-restraints excluded: chain J residue 425 MET Chi-restraints excluded: chain L residue 266 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 360 optimal weight: 2.9990 chunk 283 optimal weight: 0.7980 chunk 328 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 340 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 339 optimal weight: 0.6980 chunk 381 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 HIS A 603 ASN B 372 ASN D 102 GLN H 102 GLN I 603 ASN J 102 GLN K 603 ASN L 372 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.113913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.081752 restraints weight = 72214.190| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 3.43 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31127 Z= 0.121 Angle : 0.546 11.748 42089 Z= 0.270 Chirality : 0.043 0.177 4608 Planarity : 0.003 0.044 5460 Dihedral : 9.247 76.640 4674 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.07 % Allowed : 11.49 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.05 (0.14), residues: 3876 helix: 2.60 (0.14), residues: 1530 sheet: 1.35 (0.17), residues: 786 loop : 0.13 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 543 TYR 0.020 0.001 TYR F 549 PHE 0.009 0.001 PHE G 347 TRP 0.010 0.001 TRP L 276 HIS 0.003 0.001 HIS C 531 Details of bonding type rmsd covalent geometry : bond 0.00275 (31127) covalent geometry : angle 0.54619 (42089) hydrogen bonds : bond 0.03670 ( 1644) hydrogen bonds : angle 3.99856 ( 4596) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LYS cc_start: 0.7822 (tttp) cc_final: 0.7542 (tptt) REVERT: B 213 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8626 (mmm) REVERT: B 554 GLU cc_start: 0.8638 (pm20) cc_final: 0.8256 (pm20) REVERT: C 570 HIS cc_start: 0.8410 (m-70) cc_final: 0.8164 (m-70) REVERT: D 110 ASP cc_start: 0.8858 (OUTLIER) cc_final: 0.8588 (p0) REVERT: D 213 MET cc_start: 0.9105 (mmm) cc_final: 0.8640 (mmm) REVERT: E 543 ARG cc_start: 0.9378 (mmm-85) cc_final: 0.9026 (mmm-85) REVERT: E 559 LYS cc_start: 0.8427 (ttpt) cc_final: 0.8102 (tppt) REVERT: E 617 THR cc_start: 0.6217 (OUTLIER) cc_final: 0.5911 (t) REVERT: F 559 LYS cc_start: 0.8380 (tppt) cc_final: 0.7966 (tppt) REVERT: F 570 HIS cc_start: 0.8412 (m-70) cc_final: 0.8191 (m-70) REVERT: G 110 ASP cc_start: 0.8921 (OUTLIER) cc_final: 0.8404 (p0) REVERT: H 49 MET cc_start: 0.9144 (tpt) cc_final: 0.8845 (tpt) REVERT: I 505 LYS cc_start: 0.6663 (OUTLIER) cc_final: 0.6460 (mmmt) REVERT: I 559 LYS cc_start: 0.8457 (ttpt) cc_final: 0.8180 (mmpt) REVERT: J 110 ASP cc_start: 0.8925 (OUTLIER) cc_final: 0.8379 (p0) REVERT: J 554 GLU cc_start: 0.8925 (pm20) cc_final: 0.8360 (pm20) REVERT: J 555 LYS cc_start: 0.9354 (ptmm) cc_final: 0.8981 (ptmm) REVERT: J 557 ASP cc_start: 0.9055 (m-30) cc_final: 0.8652 (m-30) REVERT: L 213 MET cc_start: 0.8949 (mtp) cc_final: 0.8600 (mtm) REVERT: L 563 MET cc_start: 0.8882 (mmt) cc_final: 0.8459 (mmt) outliers start: 34 outliers final: 17 residues processed: 258 average time/residue: 0.6670 time to fit residues: 200.0208 Evaluate side-chains 248 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 225 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain E residue 598 LEU Chi-restraints excluded: chain E residue 617 THR Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 266 HIS Chi-restraints excluded: chain G residue 407 PHE Chi-restraints excluded: chain H residue 407 PHE Chi-restraints excluded: chain I residue 505 LYS Chi-restraints excluded: chain I residue 631 ILE Chi-restraints excluded: chain I residue 633 VAL Chi-restraints excluded: chain J residue 110 ASP Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 266 HIS Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 493 GLU Chi-restraints excluded: chain L residue 266 HIS Chi-restraints excluded: chain L residue 493 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 280 optimal weight: 3.9990 chunk 307 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 366 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 336 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 377 optimal weight: 4.9990 chunk 297 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 HIS A 603 ASN D 102 GLN E 570 HIS H 102 GLN H 266 HIS H 433 GLN I 531 HIS I 577 GLN I 603 ASN J 102 GLN K 603 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.113204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.081178 restraints weight = 72135.713| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.46 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31127 Z= 0.159 Angle : 0.566 10.781 42089 Z= 0.280 Chirality : 0.043 0.181 4608 Planarity : 0.003 0.064 5460 Dihedral : 9.226 75.524 4672 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.13 % Allowed : 11.71 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.01 (0.14), residues: 3876 helix: 2.57 (0.14), residues: 1530 sheet: 1.33 (0.17), residues: 786 loop : 0.12 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 543 TYR 0.023 0.001 TYR L 457 PHE 0.009 0.001 PHE G 347 TRP 0.008 0.001 TRP G 276 HIS 0.005 0.001 HIS H 266 Details of bonding type rmsd covalent geometry : bond 0.00370 (31127) covalent geometry : angle 0.56628 (42089) hydrogen bonds : bond 0.03860 ( 1644) hydrogen bonds : angle 4.01070 ( 4596) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8575 (mmm) REVERT: B 554 GLU cc_start: 0.8625 (pm20) cc_final: 0.8251 (pm20) REVERT: B 557 ASP cc_start: 0.9060 (m-30) cc_final: 0.8713 (m-30) REVERT: C 570 HIS cc_start: 0.8444 (m-70) cc_final: 0.8188 (m-70) REVERT: D 110 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8612 (p0) REVERT: E 617 THR cc_start: 0.6258 (OUTLIER) cc_final: 0.5944 (t) REVERT: F 559 LYS cc_start: 0.8421 (tppt) cc_final: 0.7995 (tppt) REVERT: F 570 HIS cc_start: 0.8408 (m-70) cc_final: 0.8174 (m-70) REVERT: G 110 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.8420 (p0) REVERT: G 425 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8421 (tpt) REVERT: H 49 MET cc_start: 0.9163 (tpt) cc_final: 0.8877 (tpt) REVERT: H 110 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8576 (p0) REVERT: I 505 LYS cc_start: 0.6702 (OUTLIER) cc_final: 0.6494 (mmmt) REVERT: I 559 LYS cc_start: 0.8462 (ttpt) cc_final: 0.8165 (mmpt) REVERT: J 110 ASP cc_start: 0.8935 (OUTLIER) cc_final: 0.8386 (p0) REVERT: J 554 GLU cc_start: 0.8913 (pm20) cc_final: 0.8217 (pm20) REVERT: J 555 LYS cc_start: 0.9347 (ptmm) cc_final: 0.8966 (ptmm) REVERT: J 557 ASP cc_start: 0.9052 (m-30) cc_final: 0.8649 (m-30) REVERT: L 213 MET cc_start: 0.8945 (mtp) cc_final: 0.8562 (mmm) REVERT: L 557 ASP cc_start: 0.9073 (m-30) cc_final: 0.8761 (m-30) REVERT: L 563 MET cc_start: 0.8919 (mmt) cc_final: 0.8448 (mmt) outliers start: 36 outliers final: 19 residues processed: 256 average time/residue: 0.6616 time to fit residues: 197.8757 Evaluate side-chains 249 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 222 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain E residue 598 LEU Chi-restraints excluded: chain E residue 617 THR Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 266 HIS Chi-restraints excluded: chain G residue 407 PHE Chi-restraints excluded: chain G residue 425 MET Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 407 PHE Chi-restraints excluded: chain H residue 470 ILE Chi-restraints excluded: chain I residue 505 LYS Chi-restraints excluded: chain I residue 522 MET Chi-restraints excluded: chain I residue 631 ILE Chi-restraints excluded: chain I residue 633 VAL Chi-restraints excluded: chain J residue 110 ASP Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 266 HIS Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 493 GLU Chi-restraints excluded: chain L residue 493 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 90 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 320 optimal weight: 20.0000 chunk 188 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 231 optimal weight: 0.0870 chunk 383 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 285 optimal weight: 3.9990 chunk 278 optimal weight: 0.9980 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 HIS A 603 ASN D 102 GLN E 570 HIS H 102 GLN I 577 GLN I 603 ASN J 102 GLN K 603 ASN ** L 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.114249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.081943 restraints weight = 71736.540| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.62 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31127 Z= 0.116 Angle : 0.551 10.940 42089 Z= 0.272 Chirality : 0.043 0.176 4608 Planarity : 0.003 0.085 5460 Dihedral : 8.997 74.777 4670 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.91 % Allowed : 12.12 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.02 (0.14), residues: 3876 helix: 2.59 (0.14), residues: 1530 sheet: 1.35 (0.18), residues: 786 loop : 0.10 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 543 TYR 0.022 0.001 TYR F 549 PHE 0.008 0.001 PHE G 347 TRP 0.011 0.001 TRP G 276 HIS 0.003 0.000 HIS L 266 Details of bonding type rmsd covalent geometry : bond 0.00265 (31127) covalent geometry : angle 0.55120 (42089) hydrogen bonds : bond 0.03488 ( 1644) hydrogen bonds : angle 3.92198 ( 4596) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8631 (mmm) REVERT: B 554 GLU cc_start: 0.8665 (pm20) cc_final: 0.8297 (pm20) REVERT: C 570 HIS cc_start: 0.8291 (m-70) cc_final: 0.8039 (m-70) REVERT: D 110 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8571 (p0) REVERT: D 213 MET cc_start: 0.9075 (mmm) cc_final: 0.8793 (mmm) REVERT: E 617 THR cc_start: 0.6040 (OUTLIER) cc_final: 0.5743 (t) REVERT: F 559 LYS cc_start: 0.8390 (tppt) cc_final: 0.7973 (tppt) REVERT: F 570 HIS cc_start: 0.8379 (m-70) cc_final: 0.8120 (m-70) REVERT: G 110 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8395 (p0) REVERT: G 554 GLU cc_start: 0.8949 (pm20) cc_final: 0.8445 (pm20) REVERT: H 49 MET cc_start: 0.9142 (tpt) cc_final: 0.8890 (tpt) REVERT: H 110 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8573 (p0) REVERT: I 559 LYS cc_start: 0.8436 (ttpt) cc_final: 0.8148 (mmpt) REVERT: J 110 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8379 (p0) REVERT: J 554 GLU cc_start: 0.8908 (pm20) cc_final: 0.8280 (pm20) REVERT: J 555 LYS cc_start: 0.9350 (ptmm) cc_final: 0.8986 (ptmm) REVERT: J 557 ASP cc_start: 0.9033 (m-30) cc_final: 0.8643 (m-30) REVERT: L 132 MET cc_start: 0.9054 (tpp) cc_final: 0.8789 (tpt) REVERT: L 213 MET cc_start: 0.8968 (mtp) cc_final: 0.8569 (mmm) REVERT: L 563 MET cc_start: 0.8860 (mmt) cc_final: 0.8410 (mmt) outliers start: 29 outliers final: 14 residues processed: 255 average time/residue: 0.7387 time to fit residues: 219.3950 Evaluate side-chains 249 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 229 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain E residue 598 LEU Chi-restraints excluded: chain E residue 617 THR Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 266 HIS Chi-restraints excluded: chain G residue 407 PHE Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 631 ILE Chi-restraints excluded: chain I residue 633 VAL Chi-restraints excluded: chain J residue 110 ASP Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 493 GLU Chi-restraints excluded: chain L residue 493 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 70 optimal weight: 8.9990 chunk 351 optimal weight: 5.9990 chunk 86 optimal weight: 0.0470 chunk 31 optimal weight: 0.7980 chunk 265 optimal weight: 7.9990 chunk 162 optimal weight: 0.4980 chunk 371 optimal weight: 5.9990 chunk 267 optimal weight: 8.9990 chunk 315 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 378 optimal weight: 2.9990 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS A 570 HIS D 102 GLN E 570 HIS I 603 ASN J 266 HIS L 266 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.114072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.081735 restraints weight = 71850.110| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.75 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31127 Z= 0.121 Angle : 0.553 10.714 42089 Z= 0.273 Chirality : 0.043 0.176 4608 Planarity : 0.003 0.074 5460 Dihedral : 8.894 73.802 4668 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.72 % Allowed : 12.40 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.02 (0.14), residues: 3876 helix: 2.59 (0.14), residues: 1530 sheet: 1.35 (0.18), residues: 786 loop : 0.10 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 543 TYR 0.023 0.001 TYR C 549 PHE 0.009 0.001 PHE G 347 TRP 0.010 0.001 TRP G 276 HIS 0.007 0.001 HIS L 266 Details of bonding type rmsd covalent geometry : bond 0.00279 (31127) covalent geometry : angle 0.55260 (42089) hydrogen bonds : bond 0.03514 ( 1644) hydrogen bonds : angle 3.89362 ( 4596) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8169.61 seconds wall clock time: 140 minutes 37.21 seconds (8437.21 seconds total)