Starting phenix.real_space_refine on Fri Mar 6 06:37:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c0m_30267/03_2026/7c0m_30267.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c0m_30267/03_2026/7c0m_30267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7c0m_30267/03_2026/7c0m_30267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c0m_30267/03_2026/7c0m_30267.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7c0m_30267/03_2026/7c0m_30267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c0m_30267/03_2026/7c0m_30267.map" } resolution = 3.9 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= 0.004 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 576 5.49 5 S 58 5.16 5 C 16996 2.51 5 N 5506 2.21 5 O 6678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29816 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 796 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 618 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 3013 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 366, 3004 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 12, 'TRANS': 353} Conformer: "B" Number of residues, atoms: 364, 2988 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 12, 'TRANS': 351} Chain breaks: 2 bond proxies already assigned to first conformer: 3037 Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13813 SG CYS K 396 74.336 42.987 112.768 1.00224.74 S ATOM 13819 SG CYS K 397 71.623 44.934 115.606 1.00228.17 S ATOM 13887 SG CYS K 404 74.626 45.271 115.000 1.00229.83 S Restraints were copied for chains: a, b, c, d, e, f, g, h, i, j, k Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ALEU K 387 " occ=0.50 ... (6 atoms not shown) pdb=" CD2ALEU K 387 " occ=0.50 residue: pdb=" N AGLU K 401 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU K 401 " occ=0.50 residue: pdb=" N ALEU k 387 " occ=0.50 ... (6 atoms not shown) pdb=" CD2ALEU k 387 " occ=0.50 residue: pdb=" N AGLU k 401 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU k 401 " occ=0.50 Time building chain proxies: 8.37, per 1000 atoms: 0.28 Number of scatterers: 29816 At special positions: 0 Unit cell: (163.8, 172.2, 150.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 58 16.00 P 576 15.00 O 6678 8.00 N 5506 7.00 C 16996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 397 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 396 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 404 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 390 " pdb=" ZN k 601 " pdb="ZN ZN k 601 " - pdb=" SG CYS k 397 " pdb="ZN ZN k 601 " - pdb=" SG CYS k 396 " pdb="ZN ZN k 601 " - pdb=" SG CYS k 404 " pdb="ZN ZN k 601 " - pdb=" NE2 HIS k 390 " Number of angles added : 6 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4208 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 28 sheets defined 64.0% alpha, 7.7% beta 282 base pairs and 500 stacking pairs defined. Time for finding SS restraints: 4.83 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.218A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.806A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.647A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.592A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 95 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'E' and resid 44 through 56 removed outlier: 4.026A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.805A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.409A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 39 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.617A pdb=" N ASN H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.774A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'K' and resid 161 through 175 removed outlier: 4.239A pdb=" N LEU K 165 " --> pdb=" O GLY K 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 198 Processing helix chain 'K' and resid 199 through 204 removed outlier: 6.165A pdb=" N ALA K 202 " --> pdb=" O CYS K 199 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG K 204 " --> pdb=" O SER K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 262 through 264 No H-bonds generated for 'chain 'K' and resid 262 through 264' Processing helix chain 'K' and resid 272 through 289 Processing helix chain 'K' and resid 345 through 354 Processing helix chain 'K' and resid 379 through 389 Processing helix chain 'K' and resid 405 through 424 Processing helix chain 'K' and resid 425 through 428 removed outlier: 3.749A pdb=" N LYS K 428 " --> pdb=" O LYS K 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 425 through 428' Processing helix chain 'K' and resid 434 through 449 removed outlier: 3.957A pdb=" N VAL K 438 " --> pdb=" O SER K 434 " (cutoff:3.500A) Processing helix chain 'K' and resid 451 through 458 removed outlier: 3.695A pdb=" N ASP K 456 " --> pdb=" O SER K 453 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ARG K 457 " --> pdb=" O GLN K 454 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LYS K 458 " --> pdb=" O TRP K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 478 removed outlier: 3.748A pdb=" N ASP K 465 " --> pdb=" O GLY K 461 " (cutoff:3.500A) Processing helix chain 'K' and resid 497 through 514 Processing helix chain 'K' and resid 517 through 522 removed outlier: 4.274A pdb=" N PHE K 522 " --> pdb=" O VAL K 518 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 57 Processing helix chain 'a' and resid 63 through 77 removed outlier: 4.218A pdb=" N ASP a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 removed outlier: 3.807A pdb=" N ASP a 106 " --> pdb=" O GLY a 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 120 through 132 Processing helix chain 'b' and resid 25 through 29 Processing helix chain 'b' and resid 30 through 42 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.646A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 94 Processing helix chain 'c' and resid 18 through 22 Processing helix chain 'c' and resid 26 through 36 Processing helix chain 'c' and resid 46 through 73 removed outlier: 3.592A pdb=" N TYR c 50 " --> pdb=" O GLY c 46 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 Processing helix chain 'c' and resid 90 through 95 Processing helix chain 'd' and resid 37 through 49 Processing helix chain 'd' and resid 55 through 84 Processing helix chain 'd' and resid 90 through 102 Processing helix chain 'd' and resid 103 through 124 Processing helix chain 'e' and resid 44 through 56 removed outlier: 4.027A pdb=" N LEU e 48 " --> pdb=" O GLY e 44 " (cutoff:3.500A) Processing helix chain 'e' and resid 63 through 76 removed outlier: 3.806A pdb=" N PHE e 67 " --> pdb=" O ARG e 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 132 Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 42 Processing helix chain 'f' and resid 49 through 76 Processing helix chain 'f' and resid 82 through 94 Processing helix chain 'g' and resid 16 through 21 Processing helix chain 'g' and resid 26 through 36 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.410A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 89 Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'h' and resid 39 through 49 Processing helix chain 'h' and resid 55 through 84 removed outlier: 3.617A pdb=" N ASN h 67 " --> pdb=" O ASN h 63 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN h 84 " --> pdb=" O LEU h 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 90 through 102 removed outlier: 3.774A pdb=" N ILE h 94 " --> pdb=" O THR h 90 " (cutoff:3.500A) Processing helix chain 'h' and resid 103 through 123 Processing helix chain 'k' and resid 161 through 175 removed outlier: 4.240A pdb=" N LEU k 165 " --> pdb=" O GLY k 161 " (cutoff:3.500A) Processing helix chain 'k' and resid 179 through 198 Processing helix chain 'k' and resid 199 through 204 removed outlier: 6.164A pdb=" N ALA k 202 " --> pdb=" O CYS k 199 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG k 204 " --> pdb=" O SER k 201 " (cutoff:3.500A) Processing helix chain 'k' and resid 262 through 264 No H-bonds generated for 'chain 'k' and resid 262 through 264' Processing helix chain 'k' and resid 272 through 289 Processing helix chain 'k' and resid 345 through 354 Processing helix chain 'k' and resid 379 through 389 Processing helix chain 'k' and resid 405 through 424 Processing helix chain 'k' and resid 425 through 428 removed outlier: 3.749A pdb=" N LYS k 428 " --> pdb=" O LYS k 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 425 through 428' Processing helix chain 'k' and resid 434 through 449 removed outlier: 3.957A pdb=" N VAL k 438 " --> pdb=" O SER k 434 " (cutoff:3.500A) Processing helix chain 'k' and resid 451 through 458 removed outlier: 3.695A pdb=" N ASP k 456 " --> pdb=" O SER k 453 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ARG k 457 " --> pdb=" O GLN k 454 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LYS k 458 " --> pdb=" O TRP k 455 " (cutoff:3.500A) Processing helix chain 'k' and resid 459 through 478 removed outlier: 3.748A pdb=" N ASP k 465 " --> pdb=" O GLY k 461 " (cutoff:3.500A) Processing helix chain 'k' and resid 497 through 514 Processing helix chain 'k' and resid 517 through 522 removed outlier: 4.274A pdb=" N PHE k 522 " --> pdb=" O VAL k 518 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.989A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.601A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.790A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.484A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 206 through 208 removed outlier: 6.608A pdb=" N PHE K 226 " --> pdb=" O ASP K 319 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR K 321 " --> pdb=" O PHE K 226 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL K 228 " --> pdb=" O THR K 321 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA K 323 " --> pdb=" O VAL K 228 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE K 230 " --> pdb=" O ALA K 323 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU K 325 " --> pdb=" O PHE K 230 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU K 232 " --> pdb=" O GLU K 325 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LEU K 322 " --> pdb=" O PRO K 361 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 206 through 208 removed outlier: 6.608A pdb=" N PHE K 226 " --> pdb=" O ASP K 319 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR K 321 " --> pdb=" O PHE K 226 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL K 228 " --> pdb=" O THR K 321 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA K 323 " --> pdb=" O VAL K 228 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE K 230 " --> pdb=" O ALA K 323 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU K 325 " --> pdb=" O PHE K 230 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU K 232 " --> pdb=" O GLU K 325 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 266 through 267 Processing sheet with id=AB5, first strand: chain 'K' and resid 364 through 365 removed outlier: 4.071A pdb=" N ALA K 364 " --> pdb=" O GLN K 371 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.989A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AB8, first strand: chain 'b' and resid 97 through 98 Processing sheet with id=AB9, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.601A pdb=" N ARG c 42 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AC2, first strand: chain 'c' and resid 100 through 102 Processing sheet with id=AC3, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.791A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AC5, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.484A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AC7, first strand: chain 'k' and resid 206 through 208 removed outlier: 6.608A pdb=" N PHE k 226 " --> pdb=" O ASP k 319 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR k 321 " --> pdb=" O PHE k 226 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL k 228 " --> pdb=" O THR k 321 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA k 323 " --> pdb=" O VAL k 228 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE k 230 " --> pdb=" O ALA k 323 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU k 325 " --> pdb=" O PHE k 230 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU k 232 " --> pdb=" O GLU k 325 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LEU k 322 " --> pdb=" O PRO k 361 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'k' and resid 206 through 208 removed outlier: 6.608A pdb=" N PHE k 226 " --> pdb=" O ASP k 319 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR k 321 " --> pdb=" O PHE k 226 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL k 228 " --> pdb=" O THR k 321 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA k 323 " --> pdb=" O VAL k 228 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE k 230 " --> pdb=" O ALA k 323 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU k 325 " --> pdb=" O PHE k 230 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU k 232 " --> pdb=" O GLU k 325 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'k' and resid 266 through 267 Processing sheet with id=AD1, first strand: chain 'k' and resid 364 through 365 removed outlier: 4.071A pdb=" N ALA k 364 " --> pdb=" O GLN k 371 " (cutoff:3.500A) 1090 hydrogen bonds defined for protein. 3186 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 724 hydrogen bonds 1448 hydrogen bond angles 0 basepair planarities 282 basepair parallelities 500 stacking parallelities Total time for adding SS restraints: 7.45 Time building geometry restraints manager: 3.44 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: 5715 1.33 - 1.45: 9947 1.45 - 1.57: 14640 1.57 - 1.69: 1152 1.69 - 1.81: 88 Bond restraints: 31542 Sorted by residual: bond pdb=" C HIS D 49 " pdb=" N PRO D 50 " ideal model delta sigma weight residual 1.336 1.301 0.035 1.08e-02 8.57e+03 1.04e+01 bond pdb=" C ARG h 86 " pdb=" N SER h 87 " ideal model delta sigma weight residual 1.332 1.287 0.045 1.40e-02 5.10e+03 1.03e+01 bond pdb=" C ARG H 86 " pdb=" N SER H 87 " ideal model delta sigma weight residual 1.332 1.288 0.044 1.40e-02 5.10e+03 1.01e+01 bond pdb=" C HIS d 49 " pdb=" N PRO d 50 " ideal model delta sigma weight residual 1.336 1.302 0.034 1.08e-02 8.57e+03 1.00e+01 bond pdb=" CB ASN d 63 " pdb=" CG ASN d 63 " ideal model delta sigma weight residual 1.516 1.461 0.055 2.50e-02 1.60e+03 4.82e+00 ... (remaining 31537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 42783 1.77 - 3.54: 2020 3.54 - 5.31: 163 5.31 - 7.09: 50 7.09 - 8.86: 12 Bond angle restraints: 45028 Sorted by residual: angle pdb=" O3' DA j 5 " pdb=" C3' DA j 5 " pdb=" C2' DA j 5 " ideal model delta sigma weight residual 111.50 102.64 8.86 1.50e+00 4.44e-01 3.49e+01 angle pdb=" O3' DA J 5 " pdb=" C3' DA J 5 " pdb=" C2' DA J 5 " ideal model delta sigma weight residual 111.50 102.65 8.85 1.50e+00 4.44e-01 3.48e+01 angle pdb=" O3' DA I 48 " pdb=" C3' DA I 48 " pdb=" C2' DA I 48 " ideal model delta sigma weight residual 111.50 103.19 8.31 1.50e+00 4.44e-01 3.07e+01 angle pdb=" O3' DA i 48 " pdb=" C3' DA i 48 " pdb=" C2' DA i 48 " ideal model delta sigma weight residual 111.50 103.22 8.28 1.50e+00 4.44e-01 3.05e+01 angle pdb=" N GLU K 233 " pdb=" CA GLU K 233 " pdb=" C GLU K 233 " ideal model delta sigma weight residual 111.11 117.41 -6.30 1.20e+00 6.94e-01 2.76e+01 ... (remaining 45023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.02: 14246 34.02 - 68.03: 3233 68.03 - 102.05: 83 102.05 - 136.07: 0 136.07 - 170.08: 4 Dihedral angle restraints: 17566 sinusoidal: 11056 harmonic: 6510 Sorted by residual: dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual -180.00 -158.02 -21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA PRO d 103 " pdb=" C PRO d 103 " pdb=" N GLY d 104 " pdb=" CA GLY d 104 " ideal model delta harmonic sigma weight residual 180.00 -158.08 -21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ASN k 389 " pdb=" C ASN k 389 " pdb=" N HIS k 390 " pdb=" CA HIS k 390 " ideal model delta harmonic sigma weight residual -180.00 -159.01 -20.99 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 17563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3813 0.054 - 0.108: 1128 0.108 - 0.162: 104 0.162 - 0.215: 14 0.215 - 0.269: 11 Chirality restraints: 5070 Sorted by residual: chirality pdb=" CA LYS K 428 " pdb=" N LYS K 428 " pdb=" C LYS K 428 " pdb=" CB LYS K 428 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA LYS k 428 " pdb=" N LYS k 428 " pdb=" C LYS k 428 " pdb=" CB LYS k 428 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ARG C 71 " pdb=" N ARG C 71 " pdb=" C ARG C 71 " pdb=" CB ARG C 71 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 5067 not shown) Planarity restraints: 3698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA j 5 " 0.002 2.00e-02 2.50e+03 3.09e-02 2.63e+01 pdb=" N9 DA j 5 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DA j 5 " 0.071 2.00e-02 2.50e+03 pdb=" N7 DA j 5 " -0.064 2.00e-02 2.50e+03 pdb=" C5 DA j 5 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA j 5 " 0.023 2.00e-02 2.50e+03 pdb=" N6 DA j 5 " -0.000 2.00e-02 2.50e+03 pdb=" N1 DA j 5 " 0.012 2.00e-02 2.50e+03 pdb=" C2 DA j 5 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DA j 5 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DA j 5 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 5 " 0.002 2.00e-02 2.50e+03 3.09e-02 2.63e+01 pdb=" N9 DA J 5 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DA J 5 " 0.072 2.00e-02 2.50e+03 pdb=" N7 DA J 5 " -0.063 2.00e-02 2.50e+03 pdb=" C5 DA J 5 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA J 5 " 0.022 2.00e-02 2.50e+03 pdb=" N6 DA J 5 " -0.000 2.00e-02 2.50e+03 pdb=" N1 DA J 5 " 0.012 2.00e-02 2.50e+03 pdb=" C2 DA J 5 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DA J 5 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DA J 5 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 16 " -0.002 2.00e-02 2.50e+03 1.99e-02 8.87e+00 pdb=" N1 DC I 16 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DC I 16 " -0.033 2.00e-02 2.50e+03 pdb=" O2 DC I 16 " 0.034 2.00e-02 2.50e+03 pdb=" N3 DC I 16 " -0.012 2.00e-02 2.50e+03 pdb=" C4 DC I 16 " -0.024 2.00e-02 2.50e+03 pdb=" N4 DC I 16 " 0.020 2.00e-02 2.50e+03 pdb=" C5 DC I 16 " 0.011 2.00e-02 2.50e+03 pdb=" C6 DC I 16 " 0.009 2.00e-02 2.50e+03 ... (remaining 3695 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 3532 2.73 - 3.27: 28511 3.27 - 3.82: 57214 3.82 - 4.36: 68318 4.36 - 4.90: 99719 Nonbonded interactions: 257294 Sorted by model distance: nonbonded pdb=" O GLU E 133 " pdb=" NE ARG E 134 " model vdw 2.189 3.120 nonbonded pdb=" O GLU e 133 " pdb=" NE ARG e 134 " model vdw 2.189 3.120 nonbonded pdb=" NH2 ARG E 63 " pdb=" O3' DA J 59 " model vdw 2.204 3.120 nonbonded pdb=" NH2 ARG e 63 " pdb=" O3' DA j 59 " model vdw 2.206 3.120 nonbonded pdb=" OH TYR H 40 " pdb=" OP1 DG I 121 " model vdw 2.231 3.040 ... (remaining 257289 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'F' selection = chain 'f' } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = chain 'K' selection = chain 'k' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.010 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 37.740 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.080 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: 40.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5662 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 : 0.012 0.293 31550 Z= 0.495 Angle : 0.917 45.671 45034 Z= 0.501 Chirality : 0.049 0.269 5070 Planarity : 0.005 0.049 3698 Dihedral : 27.368 170.083 13358 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.73 % Allowed : 6.13 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.16), residues: 2204 helix: -0.68 (0.12), residues: 1374 sheet: -1.23 (0.45), residues: 106 loop : -2.12 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 71 TYR 0.024 0.002 TYR C 50 PHE 0.017 0.002 PHE B 100 TRP 0.010 0.002 TRP k 330 HIS 0.009 0.002 HIS f 75 Details of bonding type rmsd covalent geometry : bond 0.01138 (31542) covalent geometry : angle 0.83440 (45028) hydrogen bonds : bond 0.11257 ( 1810) hydrogen bonds : angle 4.74794 ( 4634) metal coordination : bond 0.15904 ( 8) metal coordination : angle 32.89883 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.727 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: D 59 MET cc_start: 0.8011 (tpt) cc_final: 0.7665 (tpp) REVERT: K 465 ASP cc_start: 0.8700 (m-30) cc_final: 0.8260 (t0) REVERT: k 229 MET cc_start: 0.1669 (ptm) cc_final: 0.0500 (tpp) outliers start: 14 outliers final: 3 residues processed: 145 average time/residue: 0.2067 time to fit residues: 47.0191 Evaluate side-chains 61 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain K residue 429 HIS Chi-restraints excluded: chain d residue 118 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 108 ASN G 31 HIS G 73 ASN K 192 HIS K 210 ASN K 264 GLN K 289 ASN K 429 HIS K 437 HIS K 466 ASN ** K 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 513 ASN K 514 ASN a 39 HIS a 68 GLN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 47 GLN ** d 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 39 HIS e 108 ASN g 31 HIS k 210 ASN k 264 GLN k 289 ASN k 466 ASN k 482 ASN k 514 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.069086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.049305 restraints weight = 513838.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.046530 restraints weight = 295755.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.044973 restraints weight = 228300.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.045177 restraints weight = 192711.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.044961 restraints weight = 174219.842| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 31550 Z= 0.264 Angle : 0.693 9.690 45034 Z= 0.396 Chirality : 0.039 0.241 5070 Planarity : 0.005 0.051 3698 Dihedral : 30.447 179.680 8810 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.99 % Allowed : 10.97 % Favored : 88.05 % 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 are not related in a simple way. whole: 0.38 (0.18), residues: 2204 helix: 1.12 (0.13), residues: 1372 sheet: -0.65 (0.46), residues: 106 loop : -1.22 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 23 TYR 0.017 0.002 TYR H 40 PHE 0.030 0.002 PHE k 503 TRP 0.013 0.001 TRP k 343 HIS 0.009 0.001 HIS K 381 Details of bonding type rmsd covalent geometry : bond 0.00570 (31542) covalent geometry : angle 0.69029 (45028) hydrogen bonds : bond 0.06771 ( 1810) hydrogen bonds : angle 3.67004 ( 4634) metal coordination : bond 0.02002 ( 8) metal coordination : angle 5.00614 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8848 (mt-10) REVERT: A 90 MET cc_start: 0.8944 (mmt) cc_final: 0.8723 (mmt) REVERT: B 85 ASP cc_start: 0.7935 (m-30) cc_final: 0.7734 (t0) REVERT: D 59 MET cc_start: 0.8964 (tpt) cc_final: 0.8734 (tpp) REVERT: b 84 MET cc_start: 0.9332 (ptp) cc_final: 0.9045 (ptt) REVERT: d 47 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7752 (tm-30) REVERT: f 79 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8193 (ptpp) outliers start: 19 outliers final: 8 residues processed: 78 average time/residue: 0.1814 time to fit residues: 24.1260 Evaluate side-chains 61 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain d residue 47 GLN Chi-restraints excluded: chain f residue 79 LYS Chi-restraints excluded: chain k residue 395 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 211 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 106 optimal weight: 8.9990 chunk 213 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 218 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS E 68 GLN G 38 ASN ** K 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 82 HIS d 95 GLN g 38 ASN k 482 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.068482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.048156 restraints weight = 423502.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.047562 restraints weight = 255056.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.046726 restraints weight = 214244.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.046731 restraints weight = 200613.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.046667 restraints weight = 180906.686| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 31550 Z= 0.236 Angle : 0.644 10.097 45034 Z= 0.370 Chirality : 0.037 0.296 5070 Planarity : 0.004 0.055 3698 Dihedral : 30.595 176.904 8806 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.20 % Allowed : 13.51 % Favored : 85.29 % 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 are not related in a simple way. whole: 1.01 (0.18), residues: 2204 helix: 1.65 (0.13), residues: 1384 sheet: -0.90 (0.48), residues: 114 loop : -1.01 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG k 376 TYR 0.014 0.002 TYR k 358 PHE 0.030 0.002 PHE A 67 TRP 0.007 0.001 TRP K 343 HIS 0.007 0.001 HIS a 113 Details of bonding type rmsd covalent geometry : bond 0.00516 (31542) covalent geometry : angle 0.64194 (45028) hydrogen bonds : bond 0.05563 ( 1810) hydrogen bonds : angle 3.54400 ( 4634) metal coordination : bond 0.01850 ( 8) metal coordination : angle 4.28584 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 52 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8812 (mt-10) REVERT: A 90 MET cc_start: 0.9045 (mmt) cc_final: 0.8776 (mmt) REVERT: B 85 ASP cc_start: 0.8135 (m-30) cc_final: 0.7918 (t0) REVERT: D 59 MET cc_start: 0.8995 (tpt) cc_final: 0.8761 (tpp) outliers start: 23 outliers final: 14 residues processed: 70 average time/residue: 0.1825 time to fit residues: 21.7383 Evaluate side-chains 62 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain f residue 79 LYS Chi-restraints excluded: chain h residue 90 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 198 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 71 optimal weight: 50.0000 chunk 138 optimal weight: 9.9990 chunk 234 optimal weight: 30.0000 chunk 221 optimal weight: 30.0000 chunk 86 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 113 optimal weight: 50.0000 chunk 212 optimal weight: 30.0000 overall best weight: 10.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS H 49 HIS ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 GLN g 31 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.067147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.047319 restraints weight = 462783.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.046299 restraints weight = 276898.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.045928 restraints weight = 207918.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.045040 restraints weight = 216763.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.044865 restraints weight = 187566.048| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 31550 Z= 0.299 Angle : 0.680 8.926 45034 Z= 0.387 Chirality : 0.038 0.257 5070 Planarity : 0.005 0.061 3698 Dihedral : 30.780 172.225 8806 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.56 % Allowed : 14.40 % Favored : 84.04 % 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 are not related in a simple way. whole: 1.02 (0.18), residues: 2204 helix: 1.66 (0.13), residues: 1368 sheet: -0.87 (0.50), residues: 114 loop : -0.97 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG k 166 TYR 0.018 0.002 TYR B 88 PHE 0.022 0.002 PHE A 67 TRP 0.010 0.002 TRP K 375 HIS 0.008 0.001 HIS a 113 Details of bonding type rmsd covalent geometry : bond 0.00649 (31542) covalent geometry : angle 0.67876 (45028) hydrogen bonds : bond 0.07620 ( 1810) hydrogen bonds : angle 3.74803 ( 4634) metal coordination : bond 0.01780 ( 8) metal coordination : angle 3.27591 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 49 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8833 (mt-10) REVERT: B 85 ASP cc_start: 0.8392 (m-30) cc_final: 0.8185 (t70) REVERT: D 59 MET cc_start: 0.9106 (tpt) cc_final: 0.8840 (tpp) REVERT: k 229 MET cc_start: 0.1739 (tpp) cc_final: 0.0610 (mtt) outliers start: 30 outliers final: 18 residues processed: 73 average time/residue: 0.1845 time to fit residues: 23.0667 Evaluate side-chains 66 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain f residue 79 LYS Chi-restraints excluded: chain h residue 90 THR Chi-restraints excluded: chain k residue 440 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 103 optimal weight: 0.0570 chunk 221 optimal weight: 30.0000 chunk 242 optimal weight: 40.0000 chunk 125 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 231 optimal weight: 20.0000 chunk 244 optimal weight: 50.0000 chunk 182 optimal weight: 20.0000 chunk 99 optimal weight: 50.0000 overall best weight: 12.0114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN C 73 ASN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 55 GLN ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 47 GLN ** d 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 GLN g 31 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.066214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.046003 restraints weight = 486572.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.043883 restraints weight = 283468.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.042656 restraints weight = 224928.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.042192 restraints weight = 195124.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.042162 restraints weight = 183069.289| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 31550 Z= 0.323 Angle : 0.730 12.143 45034 Z= 0.412 Chirality : 0.040 0.244 5070 Planarity : 0.005 0.070 3698 Dihedral : 31.204 170.767 8806 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.23 % Allowed : 16.16 % Favored : 81.60 % 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 are not related in a simple way. whole: 0.65 (0.18), residues: 2204 helix: 1.30 (0.14), residues: 1374 sheet: -0.57 (0.52), residues: 106 loop : -1.05 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 55 TYR 0.020 0.002 TYR A 54 PHE 0.024 0.003 PHE K 280 TRP 0.015 0.002 TRP K 375 HIS 0.012 0.002 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00701 (31542) covalent geometry : angle 0.72838 (45028) hydrogen bonds : bond 0.07811 ( 1810) hydrogen bonds : angle 4.03061 ( 4634) metal coordination : bond 0.02089 ( 8) metal coordination : angle 3.84110 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 50 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8902 (mt-10) REVERT: A 107 THR cc_start: 0.9677 (OUTLIER) cc_final: 0.9379 (p) REVERT: B 85 ASP cc_start: 0.8438 (m-30) cc_final: 0.8130 (t0) REVERT: D 59 MET cc_start: 0.9023 (tpt) cc_final: 0.8796 (tpp) REVERT: f 79 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8421 (pttm) REVERT: h 59 MET cc_start: 0.6191 (tpt) cc_final: 0.5987 (tpt) REVERT: k 229 MET cc_start: 0.1718 (tpp) cc_final: 0.0711 (mtt) REVERT: k 298 MET cc_start: 0.5959 (ttm) cc_final: 0.5417 (tpt) outliers start: 43 outliers final: 23 residues processed: 87 average time/residue: 0.1714 time to fit residues: 25.6823 Evaluate side-chains 71 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 46 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 79 LYS Chi-restraints excluded: chain g residue 16 THR Chi-restraints excluded: chain h residue 90 THR Chi-restraints excluded: chain k residue 440 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 119 optimal weight: 10.0000 chunk 222 optimal weight: 20.0000 chunk 232 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 214 optimal weight: 20.0000 chunk 229 optimal weight: 20.0000 chunk 180 optimal weight: 30.0000 chunk 15 optimal weight: 3.9990 chunk 242 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.066943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.046312 restraints weight = 484318.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.044928 restraints weight = 259662.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.043631 restraints weight = 220436.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.043282 restraints weight = 184056.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.043311 restraints weight = 188983.044| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31550 Z= 0.188 Angle : 0.612 13.612 45034 Z= 0.355 Chirality : 0.036 0.224 5070 Planarity : 0.004 0.062 3698 Dihedral : 30.909 171.295 8806 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.99 % Allowed : 16.53 % Favored : 82.48 % 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 are not related in a simple way. whole: 1.35 (0.18), residues: 2204 helix: 1.92 (0.14), residues: 1368 sheet: -0.78 (0.51), residues: 104 loop : -0.83 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 92 TYR 0.018 0.001 TYR k 358 PHE 0.020 0.002 PHE A 67 TRP 0.031 0.002 TRP K 375 HIS 0.013 0.001 HIS K 381 Details of bonding type rmsd covalent geometry : bond 0.00403 (31542) covalent geometry : angle 0.61064 (45028) hydrogen bonds : bond 0.05068 ( 1810) hydrogen bonds : angle 3.54577 ( 4634) metal coordination : bond 0.01578 ( 8) metal coordination : angle 2.89753 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8944 (tt0) REVERT: A 107 THR cc_start: 0.9679 (OUTLIER) cc_final: 0.9392 (p) REVERT: A 120 MET cc_start: 0.8556 (mmt) cc_final: 0.8344 (mmm) REVERT: B 85 ASP cc_start: 0.8280 (m-30) cc_final: 0.7979 (t0) REVERT: D 59 MET cc_start: 0.9071 (tpt) cc_final: 0.8743 (tpp) REVERT: f 79 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8604 (ptpp) REVERT: f 84 MET cc_start: 0.9173 (pmm) cc_final: 0.8952 (pmm) REVERT: k 229 MET cc_start: 0.1858 (tpp) cc_final: 0.0899 (mtt) outliers start: 19 outliers final: 10 residues processed: 63 average time/residue: 0.1627 time to fit residues: 17.9310 Evaluate side-chains 58 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 79 LYS Chi-restraints excluded: chain g residue 16 THR Chi-restraints excluded: chain k residue 440 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 213 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 243 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 85 optimal weight: 30.0000 chunk 56 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 162 optimal weight: 30.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.066586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.046935 restraints weight = 550521.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.045649 restraints weight = 306548.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.044022 restraints weight = 255947.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.043322 restraints weight = 212579.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.043071 restraints weight = 191760.098| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 31550 Z= 0.222 Angle : 0.624 12.402 45034 Z= 0.360 Chirality : 0.036 0.222 5070 Planarity : 0.004 0.068 3698 Dihedral : 30.763 171.777 8806 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.46 % Allowed : 17.00 % Favored : 81.55 % 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 are not related in a simple way. whole: 1.32 (0.18), residues: 2204 helix: 1.87 (0.14), residues: 1376 sheet: -0.85 (0.50), residues: 104 loop : -0.80 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG e 129 TYR 0.017 0.002 TYR k 358 PHE 0.017 0.002 PHE A 67 TRP 0.026 0.002 TRP K 375 HIS 0.013 0.001 HIS K 381 Details of bonding type rmsd covalent geometry : bond 0.00482 (31542) covalent geometry : angle 0.62255 (45028) hydrogen bonds : bond 0.06121 ( 1810) hydrogen bonds : angle 3.57504 ( 4634) metal coordination : bond 0.01773 ( 8) metal coordination : angle 3.20001 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 47 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8981 (tt0) REVERT: A 107 THR cc_start: 0.9713 (OUTLIER) cc_final: 0.9395 (p) REVERT: A 120 MET cc_start: 0.8514 (mmt) cc_final: 0.8303 (mmm) REVERT: B 85 ASP cc_start: 0.8257 (m-30) cc_final: 0.7922 (t0) REVERT: D 59 MET cc_start: 0.8988 (tpt) cc_final: 0.8697 (tpp) REVERT: H 56 SER cc_start: 0.9324 (OUTLIER) cc_final: 0.9106 (p) REVERT: H 59 MET cc_start: 0.7991 (tpp) cc_final: 0.7721 (tpp) REVERT: a 90 MET cc_start: 0.9017 (mmm) cc_final: 0.8362 (ptt) REVERT: b 20 LYS cc_start: 0.2914 (OUTLIER) cc_final: 0.2167 (pttm) REVERT: f 79 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8379 (ptpp) REVERT: f 84 MET cc_start: 0.9127 (pmm) cc_final: 0.8922 (pmm) REVERT: h 59 MET cc_start: 0.6247 (tpt) cc_final: 0.5895 (tpt) REVERT: k 229 MET cc_start: 0.2035 (tpp) cc_final: 0.1073 (mtt) outliers start: 28 outliers final: 18 residues processed: 70 average time/residue: 0.1696 time to fit residues: 21.2228 Evaluate side-chains 69 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain b residue 20 LYS Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 79 LYS Chi-restraints excluded: chain g residue 16 THR Chi-restraints excluded: chain h residue 49 HIS Chi-restraints excluded: chain h residue 90 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 8 optimal weight: 6.9990 chunk 229 optimal weight: 20.0000 chunk 227 optimal weight: 20.0000 chunk 165 optimal weight: 0.5980 chunk 50 optimal weight: 8.9990 chunk 160 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 121 optimal weight: 50.0000 chunk 168 optimal weight: 20.0000 chunk 263 optimal weight: 0.6980 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.067197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.046283 restraints weight = 356030.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.045813 restraints weight = 216859.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.045453 restraints weight = 165837.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.045360 restraints weight = 165498.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.045411 restraints weight = 156531.675| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31550 Z= 0.164 Angle : 0.587 11.617 45034 Z= 0.341 Chirality : 0.036 0.390 5070 Planarity : 0.004 0.067 3698 Dihedral : 30.521 172.852 8806 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.25 % Allowed : 17.36 % Favored : 81.39 % 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 are not related in a simple way. whole: 1.63 (0.18), residues: 2204 helix: 2.14 (0.14), residues: 1374 sheet: -0.96 (0.49), residues: 104 loop : -0.68 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 129 TYR 0.027 0.001 TYR K 510 PHE 0.018 0.001 PHE A 67 TRP 0.024 0.002 TRP K 375 HIS 0.012 0.001 HIS K 381 Details of bonding type rmsd covalent geometry : bond 0.00352 (31542) covalent geometry : angle 0.58582 (45028) hydrogen bonds : bond 0.04644 ( 1810) hydrogen bonds : angle 3.37228 ( 4634) metal coordination : bond 0.01510 ( 8) metal coordination : angle 2.85553 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 49 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.9686 (OUTLIER) cc_final: 0.9395 (p) REVERT: A 120 MET cc_start: 0.8603 (mmt) cc_final: 0.8363 (mmm) REVERT: B 85 ASP cc_start: 0.8222 (m-30) cc_final: 0.7913 (t0) REVERT: D 59 MET cc_start: 0.8983 (tpt) cc_final: 0.8677 (tpp) REVERT: H 59 MET cc_start: 0.8190 (tpp) cc_final: 0.7826 (tpp) REVERT: b 20 LYS cc_start: 0.4485 (OUTLIER) cc_final: 0.4052 (pttm) REVERT: f 84 MET cc_start: 0.9450 (pmm) cc_final: 0.8941 (pmm) REVERT: k 229 MET cc_start: 0.1765 (tpp) cc_final: 0.0916 (mtt) outliers start: 24 outliers final: 17 residues processed: 70 average time/residue: 0.1531 time to fit residues: 19.4293 Evaluate side-chains 67 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain b residue 20 LYS Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain g residue 16 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 258 optimal weight: 20.0000 chunk 189 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 249 optimal weight: 50.0000 chunk 78 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.066602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.046897 restraints weight = 515978.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.045216 restraints weight = 294431.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.043972 restraints weight = 258292.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.044072 restraints weight = 201822.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.043742 restraints weight = 176860.887| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 31550 Z= 0.219 Angle : 0.615 12.737 45034 Z= 0.354 Chirality : 0.036 0.301 5070 Planarity : 0.004 0.071 3698 Dihedral : 30.523 172.116 8806 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.46 % Allowed : 17.15 % Favored : 81.39 % 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 are not related in a simple way. whole: 1.49 (0.18), residues: 2204 helix: 2.01 (0.14), residues: 1374 sheet: -0.99 (0.49), residues: 104 loop : -0.69 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 236 TYR 0.018 0.002 TYR k 358 PHE 0.015 0.002 PHE A 67 TRP 0.022 0.002 TRP K 375 HIS 0.012 0.001 HIS K 381 Details of bonding type rmsd covalent geometry : bond 0.00473 (31542) covalent geometry : angle 0.61403 (45028) hydrogen bonds : bond 0.05986 ( 1810) hydrogen bonds : angle 3.50256 ( 4634) metal coordination : bond 0.01800 ( 8) metal coordination : angle 3.10177 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 48 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8963 (tt0) REVERT: A 107 THR cc_start: 0.9684 (OUTLIER) cc_final: 0.9403 (p) REVERT: A 120 MET cc_start: 0.8586 (mmt) cc_final: 0.8360 (mmm) REVERT: B 85 ASP cc_start: 0.8353 (m-30) cc_final: 0.7998 (t0) REVERT: D 59 MET cc_start: 0.8965 (tpt) cc_final: 0.8674 (tpp) REVERT: H 56 SER cc_start: 0.9350 (OUTLIER) cc_final: 0.9100 (p) REVERT: H 59 MET cc_start: 0.8159 (tpp) cc_final: 0.7772 (tpp) REVERT: a 73 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: a 90 MET cc_start: 0.8610 (mmp) cc_final: 0.7882 (ptt) REVERT: b 20 LYS cc_start: 0.2989 (OUTLIER) cc_final: 0.2451 (pttm) REVERT: f 79 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8587 (ptpp) REVERT: f 84 MET cc_start: 0.9276 (pmm) cc_final: 0.8754 (pmm) REVERT: k 229 MET cc_start: 0.1835 (tpp) cc_final: 0.0872 (mtt) outliers start: 28 outliers final: 19 residues processed: 73 average time/residue: 0.1687 time to fit residues: 21.9461 Evaluate side-chains 71 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 47 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain a residue 73 GLU Chi-restraints excluded: chain b residue 20 LYS Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 79 LYS Chi-restraints excluded: chain g residue 16 THR Chi-restraints excluded: chain k residue 395 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 265 optimal weight: 50.0000 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 232 optimal weight: 30.0000 chunk 15 optimal weight: 7.9990 chunk 198 optimal weight: 0.1980 chunk 113 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN K 444 HIS ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.067086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.047761 restraints weight = 511536.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.045632 restraints weight = 295962.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.044049 restraints weight = 224947.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.043923 restraints weight = 192321.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.043699 restraints weight = 170736.326| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31550 Z= 0.148 Angle : 0.577 12.066 45034 Z= 0.335 Chirality : 0.035 0.314 5070 Planarity : 0.004 0.069 3698 Dihedral : 30.305 174.438 8806 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.83 % Allowed : 17.57 % Favored : 81.60 % 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 are not related in a simple way. whole: 1.82 (0.18), residues: 2204 helix: 2.28 (0.14), residues: 1376 sheet: -0.96 (0.49), residues: 104 loop : -0.57 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 40 TYR 0.017 0.001 TYR k 358 PHE 0.018 0.001 PHE A 67 TRP 0.021 0.001 TRP K 375 HIS 0.011 0.001 HIS K 381 Details of bonding type rmsd covalent geometry : bond 0.00314 (31542) covalent geometry : angle 0.57651 (45028) hydrogen bonds : bond 0.04192 ( 1810) hydrogen bonds : angle 3.25883 ( 4634) metal coordination : bond 0.01443 ( 8) metal coordination : angle 2.75987 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8577 (mmt) cc_final: 0.8372 (mmm) REVERT: B 85 ASP cc_start: 0.8149 (m-30) cc_final: 0.7841 (t0) REVERT: D 59 MET cc_start: 0.8910 (tpt) cc_final: 0.8582 (tpp) REVERT: a 90 MET cc_start: 0.8445 (mmp) cc_final: 0.7758 (ptm) REVERT: b 20 LYS cc_start: 0.1412 (OUTLIER) cc_final: 0.1105 (pttt) REVERT: f 84 MET cc_start: 0.9216 (pmm) cc_final: 0.8752 (pmm) REVERT: k 229 MET cc_start: 0.2235 (tpp) cc_final: 0.1479 (mtt) outliers start: 16 outliers final: 10 residues processed: 61 average time/residue: 0.1586 time to fit residues: 17.3563 Evaluate side-chains 58 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain b residue 20 LYS Chi-restraints excluded: chain g residue 16 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 11 optimal weight: 1.9990 chunk 213 optimal weight: 20.0000 chunk 230 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 216 optimal weight: 20.0000 chunk 205 optimal weight: 30.0000 chunk 100 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.066377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.046776 restraints weight = 524947.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.046178 restraints weight = 291430.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.045440 restraints weight = 225313.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.044732 restraints weight = 212325.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.044530 restraints weight = 184246.122| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31550 Z= 0.207 Angle : 0.604 12.978 45034 Z= 0.347 Chirality : 0.036 0.307 5070 Planarity : 0.004 0.072 3698 Dihedral : 30.331 172.673 8806 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.57 % Allowed : 17.57 % Favored : 81.86 % 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 are not related in a simple way. whole: 1.70 (0.18), residues: 2204 helix: 2.16 (0.14), residues: 1374 sheet: -0.95 (0.49), residues: 104 loop : -0.57 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 81 TYR 0.017 0.001 TYR k 358 PHE 0.014 0.001 PHE k 503 TRP 0.020 0.001 TRP K 375 HIS 0.011 0.001 HIS K 381 Details of bonding type rmsd covalent geometry : bond 0.00446 (31542) covalent geometry : angle 0.60291 (45028) hydrogen bonds : bond 0.05602 ( 1810) hydrogen bonds : angle 3.40950 ( 4634) metal coordination : bond 0.01724 ( 8) metal coordination : angle 2.95989 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8546.91 seconds wall clock time: 146 minutes 24.39 seconds (8784.39 seconds total)