Starting phenix.real_space_refine on Thu Jun 26 14:46:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j99_36092/06_2025/8j99_36092_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j99_36092/06_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_36092/06_2025/8j99_36092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j99_36092/06_2025/8j99_36092.map" model { file = "/net/cci-nas-00/data/ceres_data/8j99_36092/06_2025/8j99_36092_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j99_36092/06_2025/8j99_36092_neut.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.22, per 1000 atoms: 0.56 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: 7.47 Conformation dependent library (CDL) restraints added in 3.7 seconds 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: 3.56 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: 11.39 Time building geometry restraints manager: 8.77 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: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.190 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 65.570 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.090 ------------------------------------------------------------------------------- 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 : 7.75 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.13), 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 TRP 0.007 0.001 TRP D 276 HIS 0.009 0.002 HIS K 531 PHE 0.013 0.001 PHE F 526 TYR 0.046 0.002 TYR E 636 ARG 0.016 0.001 ARG K 543 Details of bonding type rmsd hydrogen bonds : bond 0.12149 ( 1644) hydrogen bonds : angle 6.12960 ( 4596) covalent geometry : bond 0.00806 (31127) covalent geometry : angle 0.86267 (42089) *********************** 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 : 3.731 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: 1.8783 time to fit residues: 705.9409 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 : 3.316 ------------------------------------------------------------------------------- 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 324 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 196 optimal weight: 0.6980 chunk 155 optimal weight: 0.0670 chunk 300 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 chunk 348 optimal weight: 0.8980 overall best weight: 1.3322 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.113783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.081281 restraints weight = 72611.899| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.68 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31127 Z= 0.147 Angle : 0.579 10.553 42089 Z= 0.294 Chirality : 0.044 0.185 4608 Planarity : 0.004 0.081 5460 Dihedral : 10.081 87.059 4684 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.13 % Allowed : 6.84 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.14), residues: 3876 helix: 2.20 (0.13), residues: 1530 sheet: 1.41 (0.17), residues: 816 loop : 0.15 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 276 HIS 0.004 0.001 HIS E 531 PHE 0.011 0.001 PHE I 526 TYR 0.017 0.001 TYR C 590 ARG 0.005 0.000 ARG L 292 Details of bonding type rmsd hydrogen bonds : bond 0.04536 ( 1644) hydrogen bonds : angle 4.72983 ( 4596) covalent geometry : bond 0.00325 (31127) covalent geometry : angle 0.57918 (42089) *********************** 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 312 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 276 time to evaluate : 3.498 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: B 132 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8651 (tpt) REVERT: B 554 GLU cc_start: 0.8080 (pp20) cc_final: 0.7794 (pp20) REVERT: C 518 LYS cc_start: 0.8303 (tppp) cc_final: 0.8018 (mptp) REVERT: C 543 ARG cc_start: 0.9318 (mmm-85) cc_final: 0.9067 (mmm-85) REVERT: D 49 MET cc_start: 0.9071 (tpt) cc_final: 0.8720 (tpt) REVERT: F 543 ARG cc_start: 0.9391 (mmm-85) cc_final: 0.9149 (mmm-85) REVERT: F 556 LYS cc_start: 0.8135 (tttm) cc_final: 0.7929 (tppp) REVERT: G 554 GLU cc_start: 0.8111 (pp20) cc_final: 0.7751 (pp20) REVERT: G 555 LYS cc_start: 0.9078 (ptmm) cc_final: 0.8810 (ptmm) REVERT: H 49 MET cc_start: 0.9131 (tpt) cc_final: 0.8761 (tpt) REVERT: I 559 LYS cc_start: 0.8439 (mtmt) cc_final: 0.8128 (mmpt) REVERT: J 555 LYS cc_start: 0.9144 (ptmm) cc_final: 0.8926 (ptmm) REVERT: J 557 ASP cc_start: 0.9035 (m-30) cc_final: 0.8670 (m-30) REVERT: L 132 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8672 (tpt) REVERT: L 452 MET cc_start: 0.9287 (tpp) cc_final: 0.9079 (mmm) REVERT: L 554 GLU cc_start: 0.8086 (pp20) cc_final: 0.7860 (pp20) REVERT: L 555 LYS cc_start: 0.9008 (ptmm) cc_final: 0.8695 (ptmt) outliers start: 36 outliers final: 8 residues processed: 282 average time/residue: 1.7007 time to fit residues: 553.9417 Evaluate side-chains 259 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 249 time to evaluate : 3.372 ------------------------------------------------------------------------------- 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 266 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 381 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 356 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 380 optimal weight: 0.7980 chunk 238 optimal weight: 0.9990 chunk 219 optimal weight: 4.9990 chunk 128 optimal weight: 20.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 ASN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.114413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.081935 restraints weight = 72867.360| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.65 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1661 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= 0.127 Angle : 0.531 10.663 42089 Z= 0.269 Chirality : 0.043 0.177 4608 Planarity : 0.004 0.055 5460 Dihedral : 9.559 80.784 4677 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.10 % Allowed : 8.45 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.14), residues: 3876 helix: 2.44 (0.14), residues: 1530 sheet: 1.54 (0.17), residues: 786 loop : 0.07 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 276 HIS 0.008 0.001 HIS A 531 PHE 0.012 0.001 PHE F 526 TYR 0.020 0.001 TYR A 636 ARG 0.009 0.000 ARG C 544 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 1644) hydrogen bonds : angle 4.35734 ( 4596) covalent geometry : bond 0.00283 (31127) covalent geometry : angle 0.53072 (42089) *********************** 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 322 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 287 time to evaluate : 3.394 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: 0.9133 (OUTLIER) cc_final: 0.8719 (tpt) REVERT: B 213 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8615 (mtp) REVERT: B 554 GLU cc_start: 0.8108 (pp20) cc_final: 0.7864 (pp20) REVERT: C 570 HIS cc_start: 0.8229 (m-70) cc_final: 0.8005 (m-70) REVERT: D 49 MET cc_start: 0.9116 (tpt) cc_final: 0.8819 (tpt) REVERT: E 543 ARG cc_start: 0.9372 (mmm160) cc_final: 0.9035 (mmm-85) REVERT: E 556 LYS cc_start: 0.6747 (tptt) cc_final: 0.6521 (tptt) REVERT: E 617 THR cc_start: 0.6228 (OUTLIER) cc_final: 0.5927 (t) REVERT: F 556 LYS cc_start: 0.7983 (tttm) cc_final: 0.7726 (tptm) REVERT: G 204 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.9003 (mttp) REVERT: H 49 MET cc_start: 0.9122 (tpt) cc_final: 0.8796 (tpt) REVERT: J 555 LYS cc_start: 0.9301 (ptmm) cc_final: 0.9036 (ptmm) REVERT: J 557 ASP cc_start: 0.9012 (m-30) cc_final: 0.8659 (m-30) REVERT: L 132 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8740 (tpt) REVERT: L 213 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8603 (mtp) outliers start: 35 outliers final: 8 residues processed: 290 average time/residue: 1.7068 time to fit residues: 569.7538 Evaluate side-chains 254 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 240 time to evaluate : 3.586 ------------------------------------------------------------------------------- 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 266 HIS Chi-restraints excluded: chain E residue 617 THR Chi-restraints excluded: chain G residue 49 MET 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 213 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 34 optimal weight: 0.0000 chunk 305 optimal weight: 0.9990 chunk 377 optimal weight: 5.9990 chunk 286 optimal weight: 0.7980 chunk 253 optimal weight: 0.9990 chunk 291 optimal weight: 7.9990 chunk 272 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- 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 570 HIS F 603 ASN I 577 GLN I 603 ASN K 603 ASN L 102 GLN 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 = 0.114906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.082476 restraints weight = 72906.084| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.81 r_work: 0.2789 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 31127 Z= 0.104 Angle : 0.508 7.906 42089 Z= 0.259 Chirality : 0.043 0.172 4608 Planarity : 0.003 0.046 5460 Dihedral : 9.228 77.851 4677 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.13 % Allowed : 9.73 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.14), residues: 3876 helix: 2.51 (0.13), residues: 1530 sheet: 1.56 (0.17), residues: 786 loop : 0.01 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 276 HIS 0.003 0.000 HIS C 531 PHE 0.011 0.001 PHE E 526 TYR 0.018 0.001 TYR A 549 ARG 0.005 0.000 ARG C 544 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 1644) hydrogen bonds : angle 4.15146 ( 4596) covalent geometry : bond 0.00227 (31127) covalent geometry : angle 0.50828 (42089) *********************** 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 297 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 261 time to evaluate : 3.405 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: A 559 LYS cc_start: 0.8554 (mttt) cc_final: 0.8207 (mmpt) REVERT: B 213 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.9024 (mtp) REVERT: B 554 GLU cc_start: 0.8247 (pp20) cc_final: 0.7911 (pp20) REVERT: C 570 HIS cc_start: 0.8175 (m-70) cc_final: 0.7904 (m-70) REVERT: D 49 MET cc_start: 0.9220 (tpt) cc_final: 0.9008 (tpt) REVERT: D 110 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8714 (p0) REVERT: D 457 TYR cc_start: 0.9343 (m-80) cc_final: 0.8825 (m-80) REVERT: E 617 THR cc_start: 0.5957 (OUTLIER) cc_final: 0.5701 (t) REVERT: G 110 ASP cc_start: 0.9029 (OUTLIER) cc_final: 0.8524 (p0) REVERT: H 49 MET cc_start: 0.9209 (tpt) cc_final: 0.8967 (tpt) REVERT: H 110 ASP cc_start: 0.8934 (OUTLIER) cc_final: 0.8704 (p0) REVERT: H 161 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.8671 (ttp) REVERT: J 110 ASP cc_start: 0.9082 (OUTLIER) cc_final: 0.8529 (p0) REVERT: J 555 LYS cc_start: 0.9366 (ptmm) cc_final: 0.9148 (ptmm) REVERT: J 557 ASP cc_start: 0.9307 (m-30) cc_final: 0.9001 (m-30) REVERT: K 549 TYR cc_start: 0.7085 (t80) cc_final: 0.6824 (t80) REVERT: L 213 MET cc_start: 0.9264 (OUTLIER) cc_final: 0.9042 (mtp) REVERT: L 554 GLU cc_start: 0.8418 (pm20) cc_final: 0.8014 (pp20) outliers start: 36 outliers final: 7 residues processed: 274 average time/residue: 1.6120 time to fit residues: 514.8734 Evaluate side-chains 252 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 237 time to evaluate : 3.413 ------------------------------------------------------------------------------- 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 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 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 213 MET 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 212 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 278 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 131 optimal weight: 8.9990 chunk 185 optimal weight: 0.3980 chunk 188 optimal weight: 2.9990 chunk 301 optimal weight: 0.9990 chunk 294 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 ASN C 603 ASN D 102 GLN E 603 ASN F 584 GLN H 102 GLN I 603 ASN J 102 GLN K 603 ASN L 102 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.113358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.081010 restraints weight = 72749.363| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 3.54 r_work: 0.2823 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 31127 Z= 0.169 Angle : 0.536 10.366 42089 Z= 0.271 Chirality : 0.043 0.182 4608 Planarity : 0.003 0.040 5460 Dihedral : 9.290 76.507 4674 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.97 % Allowed : 11.11 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.14), residues: 3876 helix: 2.53 (0.13), residues: 1530 sheet: 1.43 (0.17), residues: 792 loop : 0.06 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 276 HIS 0.004 0.001 HIS A 531 PHE 0.010 0.001 PHE G 347 TYR 0.021 0.001 TYR F 549 ARG 0.008 0.000 ARG F 543 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 1644) hydrogen bonds : angle 4.12935 ( 4596) covalent geometry : bond 0.00392 (31127) covalent geometry : angle 0.53592 (42089) *********************** 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 282 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 251 time to evaluate : 3.721 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: 0.9247 (OUTLIER) cc_final: 0.8997 (mtp) REVERT: B 555 LYS cc_start: 0.8850 (ptmt) cc_final: 0.8563 (ttpp) REVERT: C 570 HIS cc_start: 0.8142 (m-70) cc_final: 0.7856 (m-70) REVERT: D 49 MET cc_start: 0.9285 (tpt) cc_final: 0.9051 (tpt) REVERT: D 110 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8679 (p0) REVERT: D 161 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8718 (ttp) REVERT: E 549 TYR cc_start: 0.7590 (t80) cc_final: 0.7381 (t80) REVERT: E 617 THR cc_start: 0.5846 (OUTLIER) cc_final: 0.5587 (t) REVERT: F 559 LYS cc_start: 0.6771 (mppt) cc_final: 0.6455 (ttpt) REVERT: G 110 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8522 (p0) REVERT: H 49 MET cc_start: 0.9299 (tpt) cc_final: 0.9065 (tpt) REVERT: H 110 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8641 (p0) REVERT: I 559 LYS cc_start: 0.8361 (ttpt) cc_final: 0.8034 (tppt) REVERT: J 110 ASP cc_start: 0.9076 (OUTLIER) cc_final: 0.8537 (p0) REVERT: J 554 GLU cc_start: 0.9046 (pm20) cc_final: 0.8517 (pm20) REVERT: J 555 LYS cc_start: 0.9436 (ptmm) cc_final: 0.9072 (ptmm) REVERT: J 557 ASP cc_start: 0.9306 (m-30) cc_final: 0.9014 (m-30) REVERT: K 549 TYR cc_start: 0.7165 (t80) cc_final: 0.6808 (t80) REVERT: L 213 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.9039 (mtp) REVERT: L 563 MET cc_start: 0.8919 (mmt) cc_final: 0.8441 (mmt) outliers start: 31 outliers final: 7 residues processed: 264 average time/residue: 1.6514 time to fit residues: 506.3052 Evaluate side-chains 244 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 229 time to evaluate : 3.788 ------------------------------------------------------------------------------- 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 213 MET 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 281 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 119 optimal weight: 0.5980 chunk 270 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 238 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 ASN A 570 HIS A 603 ASN C 584 GLN E 531 HIS E 603 ASN F 531 HIS F 584 GLN 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 = 0.3524 r_free = 0.3524 target = 0.112989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.080589 restraints weight = 72983.826| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.59 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31127 Z= 0.180 Angle : 0.542 8.004 42089 Z= 0.274 Chirality : 0.043 0.184 4608 Planarity : 0.003 0.040 5460 Dihedral : 9.400 76.871 4674 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.48 % Allowed : 10.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.14), residues: 3876 helix: 2.52 (0.13), residues: 1530 sheet: 1.36 (0.17), residues: 792 loop : 0.07 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 276 HIS 0.009 0.001 HIS C 531 PHE 0.010 0.001 PHE G 347 TYR 0.018 0.001 TYR A 549 ARG 0.005 0.000 ARG E 543 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 1644) hydrogen bonds : angle 4.10147 ( 4596) covalent geometry : bond 0.00419 (31127) covalent geometry : angle 0.54163 (42089) *********************** 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 290 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 243 time to evaluate : 3.481 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 543 ARG cc_start: 0.9236 (mmm-85) cc_final: 0.9017 (mmm-85) REVERT: A 559 LYS cc_start: 0.8577 (mttt) cc_final: 0.8204 (mmpt) REVERT: B 213 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8630 (mtp) REVERT: B 554 GLU cc_start: 0.8383 (pm20) cc_final: 0.7823 (pp20) REVERT: C 570 HIS cc_start: 0.8349 (m-70) cc_final: 0.8091 (m-70) REVERT: D 49 MET cc_start: 0.9137 (tpt) cc_final: 0.8835 (tpt) REVERT: D 110 ASP cc_start: 0.8921 (OUTLIER) cc_final: 0.8666 (p0) REVERT: E 549 TYR cc_start: 0.7261 (t80) cc_final: 0.7048 (t80) REVERT: E 556 LYS cc_start: 0.6812 (tptt) cc_final: 0.6529 (tptt) REVERT: E 570 HIS cc_start: 0.8411 (m-70) cc_final: 0.8047 (m-70) REVERT: E 617 THR cc_start: 0.6197 (OUTLIER) cc_final: 0.5897 (t) REVERT: F 559 LYS cc_start: 0.6947 (mppt) cc_final: 0.6463 (ttpt) REVERT: G 110 ASP cc_start: 0.8960 (OUTLIER) cc_final: 0.8458 (p0) REVERT: G 425 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8453 (tpt) REVERT: H 49 MET cc_start: 0.9156 (tpt) cc_final: 0.8869 (tpt) REVERT: H 110 ASP cc_start: 0.8865 (OUTLIER) cc_final: 0.8625 (p0) REVERT: I 559 LYS cc_start: 0.8448 (ttpt) cc_final: 0.8059 (tppt) REVERT: I 631 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7627 (pp) REVERT: J 110 ASP cc_start: 0.8959 (OUTLIER) cc_final: 0.8422 (p0) REVERT: J 425 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.8400 (tpt) REVERT: J 554 GLU cc_start: 0.8918 (pm20) cc_final: 0.8411 (pm20) REVERT: J 555 LYS cc_start: 0.9330 (ptmm) cc_final: 0.8984 (ptmm) REVERT: J 557 ASP cc_start: 0.9050 (m-30) cc_final: 0.8666 (m-30) REVERT: K 549 TYR cc_start: 0.7420 (t80) cc_final: 0.7213 (t80) REVERT: L 213 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8681 (mtp) REVERT: L 563 MET cc_start: 0.8931 (mmt) cc_final: 0.8436 (mmt) outliers start: 47 outliers final: 14 residues processed: 271 average time/residue: 1.6396 time to fit residues: 519.9724 Evaluate side-chains 238 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 3.577 ------------------------------------------------------------------------------- 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 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 266 HIS 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 266 HIS Chi-restraints excluded: chain J residue 425 MET Chi-restraints excluded: chain J residue 493 GLU Chi-restraints excluded: chain L residue 213 MET 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 57 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 264 optimal weight: 10.0000 chunk 343 optimal weight: 1.9990 chunk 271 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 314 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 HIS A 584 GLN A 603 ASN D 433 GLN E 603 ASN F 570 HIS G 433 GLN H 102 GLN I 603 ASN K 603 ASN L 433 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.112554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.081594 restraints weight = 72751.466| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.20 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31127 Z= 0.187 Angle : 0.558 10.782 42089 Z= 0.279 Chirality : 0.043 0.183 4608 Planarity : 0.003 0.040 5460 Dihedral : 9.441 76.827 4674 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.57 % Allowed : 10.86 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.14), residues: 3876 helix: 2.52 (0.13), residues: 1530 sheet: 1.30 (0.17), residues: 792 loop : 0.07 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 276 HIS 0.003 0.001 HIS J 285 PHE 0.010 0.001 PHE G 347 TYR 0.020 0.001 TYR C 549 ARG 0.004 0.000 ARG E 543 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 1644) hydrogen bonds : angle 4.07896 ( 4596) covalent geometry : bond 0.00434 (31127) covalent geometry : angle 0.55826 (42089) *********************** 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 272 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 222 time to evaluate : 3.347 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 543 ARG cc_start: 0.9261 (mmm-85) cc_final: 0.8998 (mmm-85) REVERT: A 559 LYS cc_start: 0.8569 (mttt) cc_final: 0.8188 (mmpt) REVERT: B 213 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8635 (mtp) REVERT: B 555 LYS cc_start: 0.8985 (ptmt) cc_final: 0.8519 (ptmm) REVERT: B 557 ASP cc_start: 0.9093 (m-30) cc_final: 0.8679 (m-30) REVERT: C 570 HIS cc_start: 0.8582 (m-70) cc_final: 0.8260 (m-70) REVERT: D 49 MET cc_start: 0.9164 (tpt) cc_final: 0.8879 (tpt) REVERT: D 110 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8651 (p0) REVERT: D 213 MET cc_start: 0.9078 (mmm) cc_final: 0.8573 (mmm) REVERT: D 554 GLU cc_start: 0.8725 (pm20) cc_final: 0.8398 (pm20) REVERT: E 570 HIS cc_start: 0.8522 (m-70) cc_final: 0.8215 (m-70) REVERT: E 617 THR cc_start: 0.6572 (OUTLIER) cc_final: 0.6248 (t) REVERT: F 559 LYS cc_start: 0.6997 (mppt) cc_final: 0.6438 (tppt) REVERT: G 110 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8436 (p0) REVERT: G 425 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8470 (tpt) REVERT: H 49 MET cc_start: 0.9179 (tpt) cc_final: 0.8898 (tpt) REVERT: H 110 ASP cc_start: 0.8858 (OUTLIER) cc_final: 0.8622 (p0) REVERT: I 559 LYS cc_start: 0.8493 (ttpt) cc_final: 0.8059 (tppt) REVERT: J 110 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8454 (p0) REVERT: J 425 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.8408 (tpt) REVERT: J 554 GLU cc_start: 0.8892 (pm20) cc_final: 0.8356 (pm20) REVERT: J 555 LYS cc_start: 0.9332 (ptmm) cc_final: 0.8974 (ptmm) REVERT: J 557 ASP cc_start: 0.9078 (m-30) cc_final: 0.8683 (m-30) REVERT: K 549 TYR cc_start: 0.7854 (t80) cc_final: 0.7636 (t80) REVERT: K 559 LYS cc_start: 0.8573 (mttt) cc_final: 0.8222 (mmpt) REVERT: L 213 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8647 (mtp) REVERT: L 563 MET cc_start: 0.8966 (mmt) cc_final: 0.8485 (mmt) outliers start: 50 outliers final: 26 residues processed: 255 average time/residue: 1.9056 time to fit residues: 571.1155 Evaluate side-chains 250 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 215 time to evaluate : 6.085 ------------------------------------------------------------------------------- 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 B residue 470 ILE Chi-restraints excluded: chain B residue 493 GLU 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 513 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 G residue 425 MET Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain G residue 493 GLU 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 H residue 493 GLU Chi-restraints excluded: chain I residue 522 MET 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 425 MET Chi-restraints excluded: chain J residue 493 GLU Chi-restraints excluded: chain L residue 213 MET Chi-restraints excluded: chain L residue 266 HIS Chi-restraints excluded: chain L residue 470 ILE Chi-restraints excluded: chain L residue 493 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 48 optimal weight: 0.9990 chunk 160 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 240 optimal weight: 2.9990 chunk 379 optimal weight: 3.9990 chunk 205 optimal weight: 0.0570 chunk 3 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 361 optimal weight: 3.9990 chunk 368 optimal weight: 3.9990 overall best weight: 0.8104 ------------------------------------------------------------------------------- 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 F 570 HIS H 102 GLN J 102 GLN K 603 ASN 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 = 0.114166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.082026 restraints weight = 72149.481| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 3.65 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 31127 Z= 0.107 Angle : 0.532 11.537 42089 Z= 0.264 Chirality : 0.042 0.175 4608 Planarity : 0.003 0.051 5460 Dihedral : 9.101 75.833 4672 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.38 % Allowed : 11.52 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.14), residues: 3876 helix: 2.60 (0.14), residues: 1530 sheet: 1.32 (0.17), residues: 792 loop : 0.06 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 276 HIS 0.006 0.001 HIS H 266 PHE 0.009 0.001 PHE G 347 TYR 0.019 0.001 TYR A 549 ARG 0.008 0.000 ARG E 543 Details of bonding type rmsd hydrogen bonds : bond 0.03464 ( 1644) hydrogen bonds : angle 3.93506 ( 4596) covalent geometry : bond 0.00240 (31127) covalent geometry : angle 0.53204 (42089) *********************** 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 273 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 229 time to evaluate : 3.374 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: A 559 LYS cc_start: 0.8561 (mttt) cc_final: 0.8182 (mmpt) REVERT: B 213 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8696 (mtp) REVERT: B 555 LYS cc_start: 0.8994 (ptmt) cc_final: 0.8777 (ptmm) REVERT: C 518 LYS cc_start: 0.8270 (tppp) cc_final: 0.8008 (mptp) REVERT: C 570 HIS cc_start: 0.8436 (m-70) cc_final: 0.8153 (m-70) REVERT: D 49 MET cc_start: 0.9128 (tpt) cc_final: 0.8890 (tpt) REVERT: D 110 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8613 (p0) REVERT: D 213 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8539 (mmm) REVERT: D 457 TYR cc_start: 0.9211 (m-80) cc_final: 0.8794 (m-80) REVERT: E 559 LYS cc_start: 0.8350 (ttpt) cc_final: 0.8018 (tppt) REVERT: E 617 THR cc_start: 0.6100 (OUTLIER) cc_final: 0.5803 (t) REVERT: G 110 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8405 (p0) REVERT: H 49 MET cc_start: 0.9144 (tpt) cc_final: 0.8879 (tpt) REVERT: H 110 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8613 (p0) REVERT: I 505 LYS cc_start: 0.6608 (OUTLIER) cc_final: 0.6375 (mmmt) REVERT: I 559 LYS cc_start: 0.8442 (ttpt) cc_final: 0.8048 (tppt) REVERT: I 631 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7562 (pp) REVERT: J 110 ASP cc_start: 0.8917 (OUTLIER) cc_final: 0.8380 (p0) REVERT: J 425 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.8454 (tpt) REVERT: J 554 GLU cc_start: 0.8913 (pm20) cc_final: 0.8371 (pm20) REVERT: J 555 LYS cc_start: 0.9355 (ptmm) cc_final: 0.8987 (ptmm) REVERT: J 557 ASP cc_start: 0.9044 (m-30) cc_final: 0.8654 (m-30) REVERT: K 559 LYS cc_start: 0.8661 (mttt) cc_final: 0.8283 (mmpt) REVERT: L 213 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8690 (mtp) REVERT: L 554 GLU cc_start: 0.8618 (pm20) cc_final: 0.8303 (pm20) REVERT: L 563 MET cc_start: 0.8871 (mmt) cc_final: 0.8428 (mmt) outliers start: 44 outliers final: 19 residues processed: 261 average time/residue: 1.5404 time to fit residues: 468.8243 Evaluate side-chains 241 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 211 time to evaluate : 2.977 ------------------------------------------------------------------------------- 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 213 MET Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain E residue 513 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 G residue 470 ILE Chi-restraints excluded: chain G residue 493 GLU 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 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 425 MET Chi-restraints excluded: chain J residue 493 GLU Chi-restraints excluded: chain L residue 213 MET Chi-restraints excluded: chain L residue 426 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 chunk 201 optimal weight: 0.9990 chunk 260 optimal weight: 10.0000 chunk 214 optimal weight: 0.4980 chunk 103 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 chunk 358 optimal weight: 10.0000 chunk 379 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS B 372 ASN D 102 GLN E 570 HIS F 570 HIS H 102 GLN H 433 GLN I 531 HIS J 102 GLN K 603 ASN L 266 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.113792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.081505 restraints weight = 71900.591| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.68 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2352 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= 0.130 Angle : 0.554 11.830 42089 Z= 0.274 Chirality : 0.043 0.178 4608 Planarity : 0.003 0.101 5460 Dihedral : 9.032 74.613 4670 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.13 % Allowed : 11.96 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.14), residues: 3876 helix: 2.57 (0.14), residues: 1530 sheet: 1.33 (0.17), residues: 804 loop : 0.01 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 276 HIS 0.010 0.001 HIS C 531 PHE 0.009 0.001 PHE G 347 TYR 0.020 0.001 TYR C 549 ARG 0.008 0.000 ARG E 543 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 1644) hydrogen bonds : angle 3.94877 ( 4596) covalent geometry : bond 0.00299 (31127) covalent geometry : angle 0.55433 (42089) *********************** 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 249 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 3.298 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: A 559 LYS cc_start: 0.8613 (mttt) cc_final: 0.8215 (mmpt) REVERT: B 213 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8707 (mtp) REVERT: B 555 LYS cc_start: 0.8989 (ptmt) cc_final: 0.8760 (ptmm) REVERT: C 518 LYS cc_start: 0.8259 (tppp) cc_final: 0.7995 (mptp) REVERT: C 570 HIS cc_start: 0.8443 (m-70) cc_final: 0.8176 (m-70) REVERT: D 49 MET cc_start: 0.9162 (tpt) cc_final: 0.8896 (tpt) REVERT: D 110 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8603 (p0) REVERT: D 161 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8211 (ttp) REVERT: D 213 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8546 (mmm) REVERT: E 559 LYS cc_start: 0.8351 (ttpt) cc_final: 0.8021 (tppt) REVERT: E 617 THR cc_start: 0.6076 (OUTLIER) cc_final: 0.5778 (t) REVERT: G 110 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8385 (p0) REVERT: H 49 MET cc_start: 0.9163 (tpt) cc_final: 0.8910 (tpt) REVERT: H 110 ASP cc_start: 0.8846 (OUTLIER) cc_final: 0.8607 (p0) REVERT: I 505 LYS cc_start: 0.6649 (OUTLIER) cc_final: 0.6424 (mmmt) REVERT: I 559 LYS cc_start: 0.8443 (ttpt) cc_final: 0.8040 (tppt) REVERT: J 110 ASP cc_start: 0.8928 (OUTLIER) cc_final: 0.8410 (p0) REVERT: J 425 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.8429 (tpt) REVERT: J 554 GLU cc_start: 0.8927 (pm20) cc_final: 0.8313 (pm20) REVERT: J 555 LYS cc_start: 0.9358 (ptmm) cc_final: 0.8991 (ptmm) REVERT: J 557 ASP cc_start: 0.9032 (m-30) cc_final: 0.8654 (m-30) REVERT: K 559 LYS cc_start: 0.8645 (mttt) cc_final: 0.8263 (mmpt) REVERT: L 213 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8745 (mtp) REVERT: L 473 MET cc_start: 0.8316 (ptp) cc_final: 0.7983 (ptm) REVERT: L 554 GLU cc_start: 0.8560 (pm20) cc_final: 0.8206 (pm20) REVERT: L 563 MET cc_start: 0.8880 (mmt) cc_final: 0.8444 (mmt) outliers start: 36 outliers final: 20 residues processed: 238 average time/residue: 1.4253 time to fit residues: 399.2443 Evaluate side-chains 241 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 210 time to evaluate : 3.431 ------------------------------------------------------------------------------- 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 407 PHE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain D residue 110 ASP 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 470 ILE Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain E residue 513 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 470 ILE Chi-restraints excluded: chain G residue 493 GLU 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 631 ILE 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 300 LEU Chi-restraints excluded: chain J residue 425 MET Chi-restraints excluded: chain J residue 493 GLU Chi-restraints excluded: chain L residue 213 MET Chi-restraints excluded: chain L residue 426 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 131 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 299 optimal weight: 3.9990 chunk 168 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 84 optimal weight: 0.0170 chunk 61 optimal weight: 0.0670 chunk 258 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN D 372 ASN E 570 HIS F 570 HIS H 102 GLN H 372 ASN J 102 GLN 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 = 0.3565 r_free = 0.3565 target = 0.115263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.083005 restraints weight = 71599.509| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.58 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31127 Z= 0.097 Angle : 0.540 11.445 42089 Z= 0.266 Chirality : 0.042 0.173 4608 Planarity : 0.003 0.083 5460 Dihedral : 8.663 73.090 4670 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.97 % Allowed : 12.31 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.14), residues: 3876 helix: 2.68 (0.14), residues: 1500 sheet: 1.40 (0.17), residues: 804 loop : -0.03 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 276 HIS 0.007 0.000 HIS H 266 PHE 0.008 0.001 PHE C 526 TYR 0.021 0.001 TYR A 549 ARG 0.014 0.000 ARG E 543 Details of bonding type rmsd hydrogen bonds : bond 0.03106 ( 1644) hydrogen bonds : angle 3.84566 ( 4596) covalent geometry : bond 0.00217 (31127) covalent geometry : angle 0.54014 (42089) ********************** 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 262 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 3.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ARG cc_start: 0.9250 (mmm-85) cc_final: 0.8852 (mmm160) REVERT: A 556 LYS cc_start: 0.7738 (tttp) cc_final: 0.7416 (tptt) REVERT: A 559 LYS cc_start: 0.8629 (mttt) cc_final: 0.8277 (mmpt) REVERT: B 213 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8596 (mtm) REVERT: C 518 LYS cc_start: 0.8290 (tppp) cc_final: 0.8081 (mptp) REVERT: C 570 HIS cc_start: 0.8515 (m-70) cc_final: 0.8256 (m-70) REVERT: D 49 MET cc_start: 0.9113 (tpt) cc_final: 0.8894 (tpt) REVERT: D 110 ASP cc_start: 0.8871 (OUTLIER) cc_final: 0.8594 (p0) REVERT: D 213 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8492 (mmm) REVERT: D 457 TYR cc_start: 0.9122 (m-80) cc_final: 0.8661 (m-80) REVERT: E 559 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7996 (tppt) REVERT: E 617 THR cc_start: 0.6089 (OUTLIER) cc_final: 0.5795 (t) REVERT: G 110 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8375 (p0) REVERT: H 49 MET cc_start: 0.9099 (tpt) cc_final: 0.8862 (tpt) REVERT: H 110 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8577 (p0) REVERT: I 505 LYS cc_start: 0.6643 (OUTLIER) cc_final: 0.6430 (mmmt) REVERT: I 559 LYS cc_start: 0.8450 (ttpt) cc_final: 0.8040 (tppt) REVERT: I 631 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7675 (pp) REVERT: J 110 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8428 (p0) REVERT: J 554 GLU cc_start: 0.8936 (pm20) cc_final: 0.8418 (pm20) REVERT: J 555 LYS cc_start: 0.9359 (ptmm) cc_final: 0.8946 (ptmm) REVERT: J 557 ASP cc_start: 0.9046 (m-30) cc_final: 0.8587 (m-30) REVERT: K 559 LYS cc_start: 0.8632 (mttt) cc_final: 0.8235 (mmpt) REVERT: L 213 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8640 (mtm) REVERT: L 555 LYS cc_start: 0.9126 (ptmt) cc_final: 0.8915 (ptmm) REVERT: L 563 MET cc_start: 0.8836 (mmt) cc_final: 0.8454 (mmt) outliers start: 31 outliers final: 14 residues processed: 253 average time/residue: 1.6485 time to fit residues: 484.6468 Evaluate side-chains 235 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 3.720 ------------------------------------------------------------------------------- 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 407 PHE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 213 MET 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 513 LEU Chi-restraints excluded: chain E residue 617 THR Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 407 PHE Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 470 ILE 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 300 LEU Chi-restraints excluded: chain J residue 493 GLU Chi-restraints excluded: chain L residue 213 MET Chi-restraints excluded: chain L residue 426 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 341 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 279 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 326 optimal weight: 10.0000 chunk 84 optimal weight: 0.1980 chunk 91 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 283 optimal weight: 0.7980 chunk 110 optimal weight: 0.1980 chunk 358 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 HIS F 570 HIS G 266 HIS J 266 HIS L 102 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.114824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.082448 restraints weight = 71718.491| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.75 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2577 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= 0.111 Angle : 0.558 11.305 42089 Z= 0.274 Chirality : 0.042 0.175 4608 Planarity : 0.003 0.063 5460 Dihedral : 8.540 73.828 4664 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.91 % Allowed : 12.53 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.14), residues: 3876 helix: 2.71 (0.14), residues: 1500 sheet: 1.39 (0.17), residues: 804 loop : -0.01 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 276 HIS 0.006 0.001 HIS J 266 PHE 0.008 0.001 PHE G 347 TYR 0.024 0.001 TYR C 549 ARG 0.006 0.000 ARG E 543 Details of bonding type rmsd hydrogen bonds : bond 0.03255 ( 1644) hydrogen bonds : angle 3.84255 ( 4596) covalent geometry : bond 0.00257 (31127) covalent geometry : angle 0.55751 (42089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17766.98 seconds wall clock time: 305 minutes 49.41 seconds (18349.41 seconds total)