Starting phenix.real_space_refine on Sat Oct 11 11:52:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tko_41355/10_2025/8tko_41355.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tko_41355/10_2025/8tko_41355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tko_41355/10_2025/8tko_41355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tko_41355/10_2025/8tko_41355.map" model { file = "/net/cci-nas-00/data/ceres_data/8tko_41355/10_2025/8tko_41355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tko_41355/10_2025/8tko_41355.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.031 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 1 5.49 5 S 37 5.16 5 C 8851 2.51 5 N 2628 2.21 5 O 2765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14282 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6747 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 900, 6697 Classifications: {'peptide': 900} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 46, 'TRANS': 853} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 900, 6697 Classifications: {'peptide': 900} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 46, 'TRANS': 853} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 6769 Chain: "B" Number of atoms: 6760 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 903, 6699 Classifications: {'peptide': 903} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 46, 'TRANS': 856} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 903, 6699 Classifications: {'peptide': 903} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 46, 'TRANS': 856} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 6760 Chain: "C" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 775 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4HH:plan-3': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N AASN A 48 " occ=0.42 ... (14 atoms not shown) pdb=" ND2BASN A 48 " occ=0.58 residue: pdb=" N AARG A 58 " occ=0.52 ... (20 atoms not shown) pdb=" NH2BARG A 58 " occ=0.48 residue: pdb=" N AGLU A 161 " occ=0.39 ... (16 atoms not shown) pdb=" OE2BGLU A 161 " occ=0.61 residue: pdb=" N AARG A 486 " occ=0.49 ... (20 atoms not shown) pdb=" NH2BARG A 486 " occ=0.51 residue: pdb=" N AARG B 13 " occ=0.45 ... (20 atoms not shown) pdb=" NH2BARG B 13 " occ=0.55 residue: pdb=" N AARG B 27 " occ=0.65 ... (20 atoms not shown) pdb=" NH2BARG B 27 " occ=0.35 residue: pdb=" N AASN B 48 " occ=0.47 ... (14 atoms not shown) pdb=" ND2BASN B 48 " occ=0.53 residue: pdb=" N AARG B 58 " occ=0.24 ... (20 atoms not shown) pdb=" NH2BARG B 58 " occ=0.76 residue: pdb=" N AGLU B 161 " occ=0.40 ... (16 atoms not shown) pdb=" OE2BGLU B 161 " occ=0.60 Time building chain proxies: 6.05, per 1000 atoms: 0.42 Number of scatterers: 14282 At special positions: 0 Unit cell: (93.654, 113.52, 196.768, 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 37 16.00 P 1 15.00 O 2765 8.00 N 2628 7.00 C 8851 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: 1.32 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3450 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 15 sheets defined 46.4% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.829A pdb=" N ASP A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 60 Processing helix chain 'A' and resid 74 through 79 removed outlier: 4.239A pdb=" N HIS A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 118 Processing helix chain 'A' and resid 119 through 136 removed outlier: 3.518A pdb=" N ARG A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.708A pdb=" N THR A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 191 removed outlier: 4.092A pdb=" N SER A 183 " --> pdb=" O PRO A 179 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 220 Processing helix chain 'A' and resid 236 through 246 removed outlier: 3.613A pdb=" N GLN A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 310 through 325 removed outlier: 3.521A pdb=" N GLN A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 358 Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 379 through 381 No H-bonds generated for 'chain 'A' and resid 379 through 381' Processing helix chain 'A' and resid 382 through 398 Processing helix chain 'A' and resid 414 through 418 removed outlier: 4.284A pdb=" N SER A 417 " --> pdb=" O ASP A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 498 removed outlier: 3.759A pdb=" N ARG A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 514 removed outlier: 4.001A pdb=" N ARG A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 541 removed outlier: 3.668A pdb=" N GLY A 541 " --> pdb=" O GLU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 Processing helix chain 'A' and resid 582 through 597 Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 619 through 640 Proline residue: A 625 - end of helix Processing helix chain 'A' and resid 653 through 663 removed outlier: 4.067A pdb=" N ALA A 657 " --> pdb=" O GLN A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 684 removed outlier: 3.628A pdb=" N LEU A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 702 Processing helix chain 'A' and resid 727 through 738 removed outlier: 3.759A pdb=" N ALA A 733 " --> pdb=" O GLY A 729 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS A 738 " --> pdb=" O PHE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 762 removed outlier: 3.597A pdb=" N VAL A 762 " --> pdb=" O ILE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 771 Processing helix chain 'A' and resid 792 through 796 Processing helix chain 'A' and resid 797 through 807 Processing helix chain 'A' and resid 811 through 822 Processing helix chain 'A' and resid 835 through 846 Processing helix chain 'A' and resid 864 through 877 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.641A pdb=" N VAL A 886 " --> pdb=" O ARG A 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.669A pdb=" N ASP B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.751A pdb=" N HIS B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 118 Processing helix chain 'B' and resid 119 through 136 removed outlier: 3.519A pdb=" N ARG B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 178 removed outlier: 3.714A pdb=" N THR B 175 " --> pdb=" O GLY B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 removed outlier: 3.902A pdb=" N SER B 183 " --> pdb=" O PRO B 179 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 204 through 220 removed outlier: 3.662A pdb=" N LYS B 219 " --> pdb=" O GLU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 245 removed outlier: 3.883A pdb=" N VAL B 240 " --> pdb=" O PRO B 236 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 245 " --> pdb=" O ASP B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 285 Processing helix chain 'B' and resid 310 through 326 removed outlier: 3.553A pdb=" N GLN B 314 " --> pdb=" O SER B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 357 removed outlier: 3.573A pdb=" N ILE B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 Processing helix chain 'B' and resid 383 through 398 Processing helix chain 'B' and resid 481 through 498 removed outlier: 3.641A pdb=" N ARG B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 527 through 541 Processing helix chain 'B' and resid 575 through 582 Processing helix chain 'B' and resid 582 through 592 removed outlier: 3.632A pdb=" N ALA B 586 " --> pdb=" O SER B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 600 Processing helix chain 'B' and resid 603 through 609 Processing helix chain 'B' and resid 619 through 640 Proline residue: B 625 - end of helix Processing helix chain 'B' and resid 653 through 662 removed outlier: 4.034A pdb=" N ALA B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 683 Processing helix chain 'B' and resid 696 through 704 Processing helix chain 'B' and resid 727 through 738 removed outlier: 3.966A pdb=" N GLU B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N CYS B 738 " --> pdb=" O PHE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 760 Processing helix chain 'B' and resid 762 through 770 Processing helix chain 'B' and resid 792 through 796 removed outlier: 4.228A pdb=" N GLU B 795 " --> pdb=" O ASP B 792 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 796 " --> pdb=" O GLY B 793 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 792 through 796' Processing helix chain 'B' and resid 797 through 806 Processing helix chain 'B' and resid 812 through 822 Processing helix chain 'B' and resid 835 through 846 Processing helix chain 'B' and resid 864 through 877 Processing helix chain 'B' and resid 883 through 888 Processing helix chain 'C' and resid 13 through 34 removed outlier: 3.589A pdb=" N THR C 31 " --> pdb=" O THR C 27 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 32 " --> pdb=" O SER C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 69 removed outlier: 3.698A pdb=" N ALA C 57 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 82 through 95 Processing helix chain 'C' and resid 163 through 168 Processing helix chain 'C' and resid 169 through 172 Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 199 removed outlier: 8.835A pdb=" N ILE A 197 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A 150 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL A 199 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU A 152 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A 270 " --> pdb=" O CYS A 41 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N CYS A 41 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU A 272 " --> pdb=" O MET A 39 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N MET A 39 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU A 274 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A 290 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE A 453 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER A 295 " --> pdb=" O HIS A 451 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N HIS A 451 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU A 297 " --> pdb=" O ASN A 449 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASN A 449 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 334 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 370 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LEU A 367 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AA4, first strand: chain 'A' and resid 399 through 400 Processing sheet with id=AA5, first strand: chain 'A' and resid 473 through 479 Processing sheet with id=AA6, first strand: chain 'A' and resid 647 through 650 removed outlier: 3.696A pdb=" N ALA A 647 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL A 561 " --> pdb=" O ILE A 827 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 691 through 692 removed outlier: 4.317A pdb=" N ALA A 691 " --> pdb=" O VAL A 724 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 782 through 783 removed outlier: 4.507A pdb=" N PHE A 782 " --> pdb=" O MET A 791 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N MET A 791 " --> pdb=" O PHE A 782 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 196 through 199 removed outlier: 8.999A pdb=" N ILE B 197 " --> pdb=" O THR B 148 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL B 150 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL B 199 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B 152 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL B 270 " --> pdb=" O CYS B 41 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N CYS B 41 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU B 272 " --> pdb=" O MET B 39 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N MET B 39 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 274 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B 290 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE B 453 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER B 295 " --> pdb=" O HIS B 451 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N HIS B 451 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU B 297 " --> pdb=" O ASN B 449 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN B 449 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA B 334 " --> pdb=" O ARG B 437 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 65 through 66 Processing sheet with id=AB2, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AB3, first strand: chain 'B' and resid 367 through 368 removed outlier: 6.009A pdb=" N LEU B 367 " --> pdb=" O ALA B 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AB5, first strand: chain 'B' and resid 473 through 479 Processing sheet with id=AB6, first strand: chain 'B' and resid 789 through 790 removed outlier: 3.584A pdb=" N ARG B 789 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL B 648 " --> pdb=" O HIS B 783 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VAL B 561 " --> pdb=" O ILE B 827 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1900 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: 2.69 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5094 1.34 - 1.46: 3022 1.46 - 1.58: 6376 1.58 - 1.70: 2 1.70 - 1.82: 63 Bond restraints: 14557 Sorted by residual: bond pdb=" N GLU A 577 " pdb=" CA GLU A 577 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.41e+00 bond pdb=" N MET A 574 " pdb=" CA MET A 574 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.30e+00 bond pdb=" N GLU B 577 " pdb=" CA GLU B 577 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.91e+00 bond pdb=" N GLN B 653 " pdb=" CA GLN B 653 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.62e+00 bond pdb=" N LEU B 578 " pdb=" CA LEU B 578 " ideal model delta sigma weight residual 1.459 1.485 -0.025 1.19e-02 7.06e+03 4.59e+00 ... (remaining 14552 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 19536 1.72 - 3.44: 230 3.44 - 5.17: 38 5.17 - 6.89: 6 6.89 - 8.61: 3 Bond angle restraints: 19813 Sorted by residual: angle pdb=" C ALA A 576 " pdb=" CA ALA A 576 " pdb=" CB ALA A 576 " ideal model delta sigma weight residual 117.23 111.54 5.69 1.36e+00 5.41e-01 1.75e+01 angle pdb=" CA ALA A 576 " pdb=" C ALA A 576 " pdb=" N GLU A 577 " ideal model delta sigma weight residual 119.98 117.13 2.85 8.50e-01 1.38e+00 1.13e+01 angle pdb=" N GLY A 573 " pdb=" CA GLY A 573 " pdb=" C GLY A 573 " ideal model delta sigma weight residual 115.72 111.28 4.44 1.51e+00 4.39e-01 8.64e+00 angle pdb=" CB MET A 690 " pdb=" CG MET A 690 " pdb=" SD MET A 690 " ideal model delta sigma weight residual 112.70 121.31 -8.61 3.00e+00 1.11e-01 8.23e+00 angle pdb=" N GLY A 726 " pdb=" CA GLY A 726 " pdb=" C GLY A 726 " ideal model delta sigma weight residual 110.71 115.05 -4.34 1.53e+00 4.27e-01 8.06e+00 ... (remaining 19808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 7895 17.89 - 35.79: 638 35.79 - 53.68: 144 53.68 - 71.58: 30 71.58 - 89.47: 12 Dihedral angle restraints: 8719 sinusoidal: 3325 harmonic: 5394 Sorted by residual: dihedral pdb=" CB GLU B 459 " pdb=" CG GLU B 459 " pdb=" CD GLU B 459 " pdb=" OE1 GLU B 459 " ideal model delta sinusoidal sigma weight residual 0.00 89.47 -89.47 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG A 536 " pdb=" CD ARG A 536 " pdb=" NE ARG A 536 " pdb=" CZ ARG A 536 " ideal model delta sinusoidal sigma weight residual -180.00 -136.39 -43.61 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CB GLU A 459 " pdb=" CG GLU A 459 " pdb=" CD GLU A 459 " pdb=" OE1 GLU A 459 " ideal model delta sinusoidal sigma weight residual 0.00 -86.81 86.81 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 8716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1567 0.036 - 0.071: 464 0.071 - 0.107: 150 0.107 - 0.142: 45 0.142 - 0.178: 2 Chirality restraints: 2228 Sorted by residual: chirality pdb=" CG LEU B 704 " pdb=" CB LEU B 704 " pdb=" CD1 LEU B 704 " pdb=" CD2 LEU B 704 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" CB ILE B 743 " pdb=" CA ILE B 743 " pdb=" CG1 ILE B 743 " pdb=" CG2 ILE B 743 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA MET B 574 " pdb=" N MET B 574 " pdb=" C MET B 574 " pdb=" CB MET B 574 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 2225 not shown) Planarity restraints: 2669 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 756 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.96e+00 pdb=" N PRO B 757 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 757 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 757 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 406 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.86e+00 pdb=" C VAL A 406 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL A 406 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A 407 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 49 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO A 50 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 50 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 50 " -0.023 5.00e-02 4.00e+02 ... (remaining 2666 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1422 2.74 - 3.28: 13990 3.28 - 3.82: 23349 3.82 - 4.36: 26131 4.36 - 4.90: 46892 Nonbonded interactions: 111784 Sorted by model distance: nonbonded pdb=" OE2 GLU B 828 " pdb=" OG SER B 830 " model vdw 2.204 3.040 nonbonded pdb=" OG SER B 254 " pdb=" O LYS B 373 " model vdw 2.260 3.040 nonbonded pdb=" OE1 GLU C 165 " pdb=" N ALA C 166 " model vdw 2.296 3.120 nonbonded pdb=" N GLU A 765 " pdb=" OE1 GLU A 765 " model vdw 2.314 3.120 nonbonded pdb=" O ARG B 732 " pdb=" OG SER B 735 " model vdw 2.316 3.040 ... (remaining 111779 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 5 through 12 or resid 14 through 26 or resid 28 through 47 \ or resid 49 through 57 or resid 59 through 160 or resid 162 through 462 or (res \ id 463 and (name N or name CA or name C or name O or name CB )) or resid 464 thr \ ough 470 or (resid 471 and (name N or name CA or name C or name O or name CB )) \ or resid 472 through 485 or resid 487 through 696 or (resid 697 through 699 and \ (name N or name CA or name C or name O or name CB )) or resid 700 through 745 or \ (resid 746 and (name N or name CA or name C or name O or name CB )) or resid 74 \ 7 through 910)) selection = (chain 'B' and (resid 5 through 12 or resid 14 through 26 or resid 28 through 47 \ or resid 49 through 57 or resid 59 through 160 or resid 162 through 485 or resi \ d 487 through 693 or resid 696 through 708 or resid 713 through 762 or (resid 76 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 764 through \ 910)) } 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=0.00 max=1.00 mean=0.99 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: 5.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.070 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 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 : 0.002 0.031 14557 Z= 0.126 Angle : 0.485 8.609 19813 Z= 0.256 Chirality : 0.040 0.178 2228 Planarity : 0.004 0.050 2669 Dihedral : 14.068 89.470 5269 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.67 % Favored : 95.28 % Rotamer: Outliers : 1.25 % Allowed : 9.38 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.20), residues: 1919 helix: 2.28 (0.20), residues: 770 sheet: 0.68 (0.38), residues: 196 loop : -1.02 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 806 TYR 0.009 0.001 TYR B 802 PHE 0.008 0.001 PHE B 264 TRP 0.006 0.001 TRP A 54 HIS 0.002 0.000 HIS B 876 Details of bonding type rmsd covalent geometry : bond 0.00249 (14557) covalent geometry : angle 0.48452 (19813) hydrogen bonds : bond 0.15907 ( 666) hydrogen bonds : angle 6.00785 ( 1900) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.659 Fit side-chains REVERT: B 18 ASP cc_start: 0.9039 (m-30) cc_final: 0.8767 (m-30) REVERT: B 574 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.6553 (mpt) REVERT: B 681 MET cc_start: 0.9157 (tmm) cc_final: 0.8956 (tmm) outliers start: 13 outliers final: 9 residues processed: 71 average time/residue: 0.1407 time to fit residues: 14.9438 Evaluate side-chains 71 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 165 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0470 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 0.0980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 708 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.068832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.043425 restraints weight = 212555.707| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 7.17 r_work: 0.2427 rms_B_bonded: 6.22 restraints_weight: 2.0000 r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2420 r_free = 0.2420 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2420 r_free = 0.2420 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.2420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14557 Z= 0.096 Angle : 0.479 7.739 19813 Z= 0.245 Chirality : 0.040 0.151 2228 Planarity : 0.004 0.051 2669 Dihedral : 4.306 61.155 2135 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.77 % Favored : 95.17 % Rotamer: Outliers : 1.18 % Allowed : 9.44 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.20), residues: 1919 helix: 2.63 (0.19), residues: 781 sheet: 0.59 (0.38), residues: 196 loop : -1.02 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 23 TYR 0.008 0.001 TYR B 802 PHE 0.009 0.001 PHE A 585 TRP 0.010 0.001 TRP B 571 HIS 0.002 0.000 HIS B 660 Details of bonding type rmsd covalent geometry : bond 0.00213 (14557) covalent geometry : angle 0.47917 (19813) hydrogen bonds : bond 0.03455 ( 666) hydrogen bonds : angle 4.32069 ( 1900) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.454 Fit side-chains REVERT: B 18 ASP cc_start: 0.9046 (m-30) cc_final: 0.8788 (m-30) REVERT: B 276 GLU cc_start: 0.9103 (tt0) cc_final: 0.8897 (tt0) REVERT: B 681 MET cc_start: 0.9225 (tmm) cc_final: 0.8950 (tmm) REVERT: C 23 ARG cc_start: 0.9206 (ttm-80) cc_final: 0.8910 (tpp80) outliers start: 12 outliers final: 6 residues processed: 70 average time/residue: 0.1324 time to fit residues: 13.8961 Evaluate side-chains 63 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 858 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 97 optimal weight: 0.0980 chunk 26 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 7 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.068707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.043371 restraints weight = 208712.836| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 7.10 r_work: 0.2427 rms_B_bonded: 6.20 restraints_weight: 2.0000 r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2420 r_free = 0.2420 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2420 r_free = 0.2420 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.2420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14557 Z= 0.093 Angle : 0.466 8.911 19813 Z= 0.236 Chirality : 0.040 0.187 2228 Planarity : 0.004 0.048 2669 Dihedral : 3.517 31.510 2120 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.40 % Favored : 95.55 % Rotamer: Outliers : 1.04 % Allowed : 10.00 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.20), residues: 1919 helix: 2.70 (0.19), residues: 783 sheet: 0.49 (0.37), residues: 196 loop : -1.05 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 23 TYR 0.008 0.001 TYR B 802 PHE 0.009 0.001 PHE A 585 TRP 0.008 0.001 TRP B 571 HIS 0.002 0.000 HIS B 660 Details of bonding type rmsd covalent geometry : bond 0.00215 (14557) covalent geometry : angle 0.46596 (19813) hydrogen bonds : bond 0.03167 ( 666) hydrogen bonds : angle 4.07101 ( 1900) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.486 Fit side-chains REVERT: B 18 ASP cc_start: 0.9049 (m-30) cc_final: 0.8799 (m-30) REVERT: B 241 ASP cc_start: 0.8918 (m-30) cc_final: 0.8633 (m-30) REVERT: B 574 MET cc_start: 0.8022 (mpt) cc_final: 0.7259 (mmt) REVERT: C 23 ARG cc_start: 0.9230 (ttm-80) cc_final: 0.8982 (tpp80) outliers start: 10 outliers final: 6 residues processed: 69 average time/residue: 0.1270 time to fit residues: 13.2529 Evaluate side-chains 62 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 858 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 189 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.066997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.041671 restraints weight = 205639.202| |-----------------------------------------------------------------------------| r_work (start): 0.2590 rms_B_bonded: 6.98 r_work: 0.2377 rms_B_bonded: 6.08 restraints_weight: 2.0000 r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2379 r_free = 0.2379 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2379 r_free = 0.2379 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.2379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14557 Z= 0.135 Angle : 0.490 7.773 19813 Z= 0.248 Chirality : 0.041 0.151 2228 Planarity : 0.004 0.048 2669 Dihedral : 3.702 35.871 2120 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.98 % Favored : 94.96 % Rotamer: Outliers : 1.32 % Allowed : 10.00 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.20), residues: 1919 helix: 2.71 (0.19), residues: 784 sheet: 0.32 (0.37), residues: 199 loop : -1.07 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 806 TYR 0.010 0.001 TYR B 641 PHE 0.011 0.001 PHE A 242 TRP 0.010 0.001 TRP B 571 HIS 0.003 0.001 HIS B 660 Details of bonding type rmsd covalent geometry : bond 0.00320 (14557) covalent geometry : angle 0.48959 (19813) hydrogen bonds : bond 0.03634 ( 666) hydrogen bonds : angle 4.11224 ( 1900) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.542 Fit side-chains REVERT: B 574 MET cc_start: 0.8289 (mpt) cc_final: 0.7440 (mmt) outliers start: 14 outliers final: 11 residues processed: 68 average time/residue: 0.1358 time to fit residues: 13.9708 Evaluate side-chains 67 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 858 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 90 optimal weight: 0.2980 chunk 131 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 180 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.068103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.042687 restraints weight = 192981.792| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 6.90 r_work: 0.2410 rms_B_bonded: 6.07 restraints_weight: 2.0000 r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2404 r_free = 0.2404 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2405 r_free = 0.2405 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14557 Z= 0.096 Angle : 0.469 8.217 19813 Z= 0.237 Chirality : 0.040 0.152 2228 Planarity : 0.004 0.047 2669 Dihedral : 3.591 37.963 2120 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.88 % Favored : 95.07 % Rotamer: Outliers : 1.25 % Allowed : 10.42 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.20), residues: 1919 helix: 2.73 (0.19), residues: 783 sheet: 0.33 (0.37), residues: 197 loop : -1.08 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 23 TYR 0.009 0.001 TYR B 802 PHE 0.009 0.001 PHE A 585 TRP 0.009 0.001 TRP B 571 HIS 0.003 0.000 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00224 (14557) covalent geometry : angle 0.46945 (19813) hydrogen bonds : bond 0.03065 ( 666) hydrogen bonds : angle 3.96245 ( 1900) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.578 Fit side-chains REVERT: B 574 MET cc_start: 0.8237 (mpt) cc_final: 0.7383 (mmt) outliers start: 13 outliers final: 10 residues processed: 69 average time/residue: 0.1283 time to fit residues: 13.6279 Evaluate side-chains 65 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 858 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 3 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 163 optimal weight: 0.0470 chunk 47 optimal weight: 0.0980 chunk 85 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.067763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.041890 restraints weight = 174276.046| |-----------------------------------------------------------------------------| r_work (start): 0.2573 rms_B_bonded: 6.87 r_work: 0.2354 rms_B_bonded: 6.16 restraints_weight: 2.0000 r_work (final): 0.2354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2399 r_free = 0.2399 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2399 r_free = 0.2399 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14557 Z= 0.098 Angle : 0.470 7.747 19813 Z= 0.237 Chirality : 0.040 0.163 2228 Planarity : 0.004 0.048 2669 Dihedral : 3.591 39.681 2120 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.72 % Favored : 95.23 % Rotamer: Outliers : 1.53 % Allowed : 10.28 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.20), residues: 1919 helix: 2.77 (0.19), residues: 782 sheet: 0.31 (0.37), residues: 197 loop : -1.08 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 59 TYR 0.010 0.001 TYR A 752 PHE 0.009 0.001 PHE A 585 TRP 0.008 0.001 TRP B 571 HIS 0.003 0.000 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00230 (14557) covalent geometry : angle 0.47029 (19813) hydrogen bonds : bond 0.03032 ( 666) hydrogen bonds : angle 3.93381 ( 1900) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.523 Fit side-chains REVERT: B 241 ASP cc_start: 0.8827 (m-30) cc_final: 0.8594 (m-30) REVERT: B 574 MET cc_start: 0.8143 (mpt) cc_final: 0.7804 (mmt) outliers start: 17 outliers final: 14 residues processed: 69 average time/residue: 0.1309 time to fit residues: 13.7607 Evaluate side-chains 69 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 167 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.066604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.040859 restraints weight = 155921.223| |-----------------------------------------------------------------------------| r_work (start): 0.2544 rms_B_bonded: 6.53 r_work: 0.2327 rms_B_bonded: 5.93 restraints_weight: 2.0000 r_work (final): 0.2327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2372 r_free = 0.2372 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2372 r_free = 0.2372 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14557 Z= 0.134 Angle : 0.493 8.038 19813 Z= 0.249 Chirality : 0.041 0.170 2228 Planarity : 0.004 0.047 2669 Dihedral : 3.710 47.384 2119 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.09 % Favored : 94.86 % Rotamer: Outliers : 1.46 % Allowed : 10.35 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.20), residues: 1919 helix: 2.72 (0.19), residues: 784 sheet: 0.27 (0.37), residues: 199 loop : -1.07 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 806 TYR 0.009 0.001 TYR B 802 PHE 0.010 0.001 PHE A 242 TRP 0.010 0.001 TRP B 571 HIS 0.003 0.001 HIS B 660 Details of bonding type rmsd covalent geometry : bond 0.00320 (14557) covalent geometry : angle 0.49300 (19813) hydrogen bonds : bond 0.03488 ( 666) hydrogen bonds : angle 4.00682 ( 1900) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.545 Fit side-chains REVERT: B 574 MET cc_start: 0.8149 (mpt) cc_final: 0.7809 (mmt) outliers start: 16 outliers final: 15 residues processed: 70 average time/residue: 0.1372 time to fit residues: 14.3014 Evaluate side-chains 70 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 167 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 75 optimal weight: 0.6980 chunk 132 optimal weight: 0.2980 chunk 162 optimal weight: 3.9990 chunk 21 optimal weight: 0.0030 chunk 147 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.068393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.043637 restraints weight = 197977.221| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 6.99 r_work: 0.2451 rms_B_bonded: 6.18 restraints_weight: 2.0000 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2447 r_free = 0.2447 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2447 r_free = 0.2447 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14557 Z= 0.095 Angle : 0.476 8.339 19813 Z= 0.239 Chirality : 0.040 0.179 2228 Planarity : 0.004 0.047 2669 Dihedral : 3.640 58.544 2119 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.77 % Favored : 95.17 % Rotamer: Outliers : 1.60 % Allowed : 10.21 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.20), residues: 1919 helix: 2.72 (0.19), residues: 788 sheet: 0.29 (0.37), residues: 197 loop : -1.09 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 77 TYR 0.009 0.001 TYR B 802 PHE 0.010 0.001 PHE A 585 TRP 0.009 0.001 TRP B 571 HIS 0.003 0.000 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00223 (14557) covalent geometry : angle 0.47650 (19813) hydrogen bonds : bond 0.02950 ( 666) hydrogen bonds : angle 3.88978 ( 1900) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.548 Fit side-chains REVERT: B 574 MET cc_start: 0.8333 (mpt) cc_final: 0.7498 (mmt) REVERT: C 16 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8282 (mm-30) REVERT: C 59 ARG cc_start: 0.9298 (mtm110) cc_final: 0.8993 (mtm110) outliers start: 18 outliers final: 16 residues processed: 71 average time/residue: 0.1405 time to fit residues: 14.9374 Evaluate side-chains 71 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 167 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 165 optimal weight: 0.9980 chunk 182 optimal weight: 0.0170 chunk 43 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 159 optimal weight: 0.3980 chunk 84 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.067992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.043292 restraints weight = 178725.007| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 6.73 r_work: 0.2453 rms_B_bonded: 6.02 restraints_weight: 2.0000 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2441 r_free = 0.2441 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2441 r_free = 0.2441 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14557 Z= 0.109 Angle : 0.483 9.191 19813 Z= 0.242 Chirality : 0.040 0.179 2228 Planarity : 0.004 0.047 2669 Dihedral : 3.561 46.730 2119 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.93 % Favored : 95.02 % Rotamer: Outliers : 1.60 % Allowed : 10.49 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.20), residues: 1919 helix: 2.72 (0.19), residues: 787 sheet: 0.28 (0.37), residues: 197 loop : -1.08 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 23 TYR 0.009 0.001 TYR B 641 PHE 0.009 0.001 PHE A 585 TRP 0.009 0.001 TRP B 571 HIS 0.002 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00259 (14557) covalent geometry : angle 0.48304 (19813) hydrogen bonds : bond 0.03135 ( 666) hydrogen bonds : angle 3.90957 ( 1900) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.440 Fit side-chains REVERT: B 574 MET cc_start: 0.8340 (mpt) cc_final: 0.8047 (mmt) REVERT: C 16 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8242 (mm-30) REVERT: C 59 ARG cc_start: 0.9304 (mtm110) cc_final: 0.8990 (mtm110) outliers start: 18 outliers final: 17 residues processed: 72 average time/residue: 0.1346 time to fit residues: 14.5076 Evaluate side-chains 72 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 167 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 140 optimal weight: 2.9990 chunk 142 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 chunk 115 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 189 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.068051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.043284 restraints weight = 194797.150| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 6.93 r_work: 0.2446 rms_B_bonded: 6.12 restraints_weight: 2.0000 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2440 r_free = 0.2440 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2440 r_free = 0.2440 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14557 Z= 0.103 Angle : 0.480 8.573 19813 Z= 0.241 Chirality : 0.040 0.180 2228 Planarity : 0.004 0.048 2669 Dihedral : 3.535 39.597 2119 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.93 % Favored : 95.02 % Rotamer: Outliers : 1.60 % Allowed : 10.62 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.20), residues: 1919 helix: 2.71 (0.19), residues: 788 sheet: 0.29 (0.37), residues: 197 loop : -1.09 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 77 TYR 0.009 0.001 TYR A 752 PHE 0.009 0.001 PHE A 585 TRP 0.009 0.001 TRP B 571 HIS 0.002 0.000 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00244 (14557) covalent geometry : angle 0.48036 (19813) hydrogen bonds : bond 0.03049 ( 666) hydrogen bonds : angle 3.88898 ( 1900) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.545 Fit side-chains REVERT: B 574 MET cc_start: 0.8327 (mpt) cc_final: 0.8035 (mmt) REVERT: C 16 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8248 (mm-30) REVERT: C 59 ARG cc_start: 0.9303 (mtm110) cc_final: 0.8992 (mtm110) outliers start: 18 outliers final: 16 residues processed: 70 average time/residue: 0.1363 time to fit residues: 14.3266 Evaluate side-chains 71 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 167 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 57 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 172 optimal weight: 0.8980 chunk 87 optimal weight: 0.0670 chunk 20 optimal weight: 0.9990 chunk 106 optimal weight: 0.0030 chunk 107 optimal weight: 0.6980 overall best weight: 0.4128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.068786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.043943 restraints weight = 196894.632| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 7.01 r_work: 0.2467 rms_B_bonded: 6.20 restraints_weight: 2.0000 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2450 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2450 r_free = 0.2450 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2450 r_free = 0.2450 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14557 Z= 0.092 Angle : 0.474 8.504 19813 Z= 0.237 Chirality : 0.040 0.176 2228 Planarity : 0.004 0.048 2669 Dihedral : 3.464 37.347 2119 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.98 % Favored : 94.96 % Rotamer: Outliers : 1.39 % Allowed : 10.69 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.20), residues: 1919 helix: 2.71 (0.19), residues: 789 sheet: 0.32 (0.37), residues: 197 loop : -1.08 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 77 TYR 0.008 0.001 TYR B 802 PHE 0.010 0.001 PHE A 585 TRP 0.008 0.001 TRP B 571 HIS 0.003 0.000 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00216 (14557) covalent geometry : angle 0.47444 (19813) hydrogen bonds : bond 0.02886 ( 666) hydrogen bonds : angle 3.85023 ( 1900) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4069.13 seconds wall clock time: 70 minutes 10.61 seconds (4210.61 seconds total)