Starting phenix.real_space_refine on Mon Sep 14 07:09:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7c0m_30267/09_2026/7c0m_30267.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c0m_30267/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7c0m_30267/09_2026/7c0m_30267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c0m_30267/09_2026/7c0m_30267.map" model { file = "/net/cci-nas-00/data/ceres_data/7c0m_30267/09_2026/7c0m_30267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c0m_30267/09_2026/7c0m_30267.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7c0m_30267/09_2026/7c0m_30267.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7c0m_30267/09_2026/7c0m_30267.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 8.98, per 1000 atoms: 0.30 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: 2.64 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: 4.34 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: 6.98 Time building geometry restraints manager: 3.52 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=" C3' DC I 69 " pdb=" O3' DC I 69 " ideal model delta sigma weight residual 1.435 1.370 0.065 1.30e-02 5.92e+03 2.50e+01 bond pdb=" C3' DC i 69 " pdb=" O3' DC i 69 " ideal model delta sigma weight residual 1.435 1.371 0.064 1.30e-02 5.92e+03 2.46e+01 bond pdb=" C3' DG j 81 " pdb=" O3' DG j 81 " ideal model delta sigma weight residual 1.435 1.375 0.060 1.30e-02 5.92e+03 2.15e+01 bond pdb=" C3' DG J 81 " pdb=" O3' DG J 81 " ideal model delta sigma weight residual 1.435 1.375 0.060 1.30e-02 5.92e+03 2.11e+01 bond pdb=" C3' DG i 100 " pdb=" O3' DG i 100 " ideal model delta sigma weight residual 1.435 1.376 0.059 1.30e-02 5.92e+03 2.03e+01 ... (remaining 31537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 40622 1.57 - 3.15: 3991 3.15 - 4.72: 330 4.72 - 6.30: 64 6.30 - 7.87: 21 Bond angle restraints: 45028 Sorted by residual: angle pdb=" O4' DA j 116 " pdb=" C4' DA j 116 " pdb=" C3' DA j 116 " ideal model delta sigma weight residual 106.00 102.55 3.45 6.00e-01 2.78e+00 3.30e+01 angle pdb=" O4' DA J 116 " pdb=" C4' DA J 116 " pdb=" C3' DA J 116 " ideal model delta sigma weight residual 106.00 102.56 3.44 6.00e-01 2.78e+00 3.29e+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 angle pdb=" N SER h 123 " pdb=" CA SER h 123 " pdb=" C SER h 123 " ideal model delta sigma weight residual 110.43 116.84 -6.41 1.31e+00 5.83e-01 2.39e+01 angle pdb=" N SER H 123 " pdb=" CA SER H 123 " pdb=" C SER H 123 " ideal model delta sigma weight residual 110.43 116.84 -6.41 1.31e+00 5.83e-01 2.39e+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: 3465 0.054 - 0.108: 1294 0.108 - 0.162: 285 0.162 - 0.215: 19 0.215 - 0.269: 7 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: 0.05 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 37.400 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.070 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.590 ------------------------------------------------------------------------------- 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= 0.819 Angle : 1.016 45.671 45034 Z= 0.739 Chirality : 0.056 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/Z covalent geometry : bond 0.01190 / 0.82 (31542) covalent geometry : angle 0.94288 / 0.73 (45028) hydrogen bonds : bond 0.11257 / 7.63 ( 1810) hydrogen bonds : angle 4.74794 / 3.38 ( 4634) metal coordination : bond 0.15904 / 9.23 ( 8) metal coordination : angle 32.89883 / 20.47 ( 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: 0.2174 time to fit residues: 49.8742 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 : 0.876 ------------------------------------------------------------------------------- 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: 50.0000 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: 50.0000 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: 10.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 39 HIS e 108 ASN g 31 HIS g 73 ASN 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: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.069619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.049361 restraints weight = 517154.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.046606 restraints weight = 315353.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.045299 restraints weight = 231481.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.045182 restraints weight = 202309.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.044941 restraints weight = 191825.812| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 31550 Z= 0.267 Angle : 0.817 11.295 45034 Z= 0.449 Chirality : 0.049 0.257 5070 Planarity : 0.006 0.069 3698 Dihedral : 30.850 177.417 8810 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.88 % Allowed : 11.02 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.05 (0.17), residues: 2204 helix: 0.85 (0.13), residues: 1388 sheet: -0.89 (0.45), residues: 106 loop : -1.38 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 134 TYR 0.020 0.002 TYR H 40 PHE 0.030 0.002 PHE k 503 TRP 0.008 0.001 TRP k 343 HIS 0.008 0.002 HIS K 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.27 (31542) covalent geometry : angle 0.81567 / 0.45 (45028) hydrogen bonds : bond 0.07751 / 5.31 ( 1810) hydrogen bonds : angle 3.80606 / 2.71 ( 4634) metal coordination : bond 0.04154 / 2.37 ( 8) metal coordination : angle 3.74556 / 1.99 ( 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 79 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8852 (mt-10) REVERT: K 298 MET cc_start: 0.5051 (tmm) cc_final: 0.4807 (tmm) REVERT: b 84 MET cc_start: 0.9379 (ptp) cc_final: 0.9149 (ptt) outliers start: 17 outliers final: 10 residues processed: 76 average time/residue: 0.1828 time to fit residues: 23.4845 Evaluate side-chains 60 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 D residue 62 MET Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain h residue 90 THR 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: 50.0000 chunk 89 optimal weight: 40.0000 chunk 148 optimal weight: 9.9990 chunk 106 optimal weight: 30.0000 chunk 213 optimal weight: 50.0000 chunk 95 optimal weight: 50.0000 chunk 31 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 chunk 85 optimal weight: 50.0000 chunk 218 optimal weight: 50.0000 chunk 21 optimal weight: 5.9990 overall best weight: 11.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS E 113 HIS G 38 ASN a 68 GLN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 47 GLN ** d 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 82 HIS d 95 GLN g 38 ASN ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 482 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.067948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.047063 restraints weight = 424980.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.046912 restraints weight = 235034.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.045593 restraints weight = 179913.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.043967 restraints weight = 163467.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.044093 restraints weight = 174499.309| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 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 = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 31550 Z= 0.279 Angle : 0.785 10.911 45034 Z= 0.433 Chirality : 0.046 0.451 5070 Planarity : 0.005 0.061 3698 Dihedral : 31.130 179.576 8806 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.72 % Allowed : 13.93 % Favored : 84.36 % 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: 0.50 (0.18), residues: 2204 helix: 1.24 (0.13), residues: 1378 sheet: -0.94 (0.48), residues: 114 loop : -1.21 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 40 TYR 0.022 0.003 TYR k 358 PHE 0.029 0.003 PHE k 484 TRP 0.012 0.002 TRP k 343 HIS 0.009 0.002 HIS a 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.28 (31542) covalent geometry : angle 0.78298 / 0.43 (45028) hydrogen bonds : bond 0.07622 / 5.17 ( 1810) hydrogen bonds : angle 3.93387 / 2.79 ( 4634) metal coordination : bond 0.02101 / 1.28 ( 8) metal coordination : angle 5.01376 / 3.17 ( 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 87 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 54 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8786 (mt-10) REVERT: A 107 THR cc_start: 0.9720 (OUTLIER) cc_final: 0.9414 (p) REVERT: D 59 MET cc_start: 0.8961 (tpp) cc_final: 0.8693 (tpp) REVERT: a 90 MET cc_start: 0.8902 (mmp) cc_final: 0.8275 (ptt) REVERT: b 84 MET cc_start: 0.9434 (ptp) cc_final: 0.9220 (ptt) REVERT: d 47 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7636 (tm-30) outliers start: 33 outliers final: 19 residues processed: 83 average time/residue: 0.1789 time to fit residues: 25.6559 Evaluate side-chains 69 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 112 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 49 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 G residue 79 ILE Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain d residue 47 GLN Chi-restraints excluded: chain h residue 59 MET 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: 1.9990 chunk 110 optimal weight: 30.0000 chunk 53 optimal weight: 6.9990 chunk 71 optimal weight: 50.0000 chunk 138 optimal weight: 6.9990 chunk 234 optimal weight: 50.0000 chunk 221 optimal weight: 50.0000 chunk 86 optimal weight: 50.0000 chunk 98 optimal weight: 50.0000 chunk 113 optimal weight: 0.7980 chunk 212 optimal weight: 50.0000 overall best weight: 9.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 73 ASN ** 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 = 0.4045 r_free = 0.4045 target = 0.067828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.047727 restraints weight = 461774.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.046739 restraints weight = 279810.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.045952 restraints weight = 230311.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.045378 restraints weight = 184893.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.045027 restraints weight = 177872.375| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 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 = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31550 Z= 0.226 Angle : 0.711 9.981 45034 Z= 0.399 Chirality : 0.044 0.258 5070 Planarity : 0.005 0.070 3698 Dihedral : 31.110 173.737 8806 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.35 % Allowed : 15.38 % Favored : 83.26 % 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: 0.91 (0.18), residues: 2204 helix: 1.60 (0.13), residues: 1370 sheet: -0.94 (0.49), residues: 114 loop : -1.08 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 281 TYR 0.024 0.002 TYR k 248 PHE 0.022 0.002 PHE k 503 TRP 0.008 0.001 TRP K 375 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.23 (31542) covalent geometry : angle 0.71033 / 0.40 (45028) hydrogen bonds : bond 0.06901 / 4.73 ( 1810) hydrogen bonds : angle 3.71305 / 2.63 ( 4634) metal coordination : bond 0.01848 / 1.20 ( 8) metal coordination : angle 3.05814 / 2.00 ( 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 74 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 48 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8850 (mt-10) REVERT: f 84 MET cc_start: 0.7888 (ppp) cc_final: 0.7654 (pmm) outliers start: 26 outliers final: 16 residues processed: 71 average time/residue: 0.1920 time to fit residues: 23.1915 Evaluate side-chains 62 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 62 MET 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 G residue 16 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain e residue 121 PRO Chi-restraints excluded: chain h residue 90 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 103 optimal weight: 3.9990 chunk 221 optimal weight: 50.0000 chunk 242 optimal weight: 30.0000 chunk 125 optimal weight: 20.0000 chunk 215 optimal weight: 50.0000 chunk 57 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 231 optimal weight: 50.0000 chunk 244 optimal weight: 40.0000 chunk 182 optimal weight: 6.9990 chunk 99 optimal weight: 50.0000 overall best weight: 12.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** B 25 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** H 49 HIS b 27 GLN ** b 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 47 GLN g 24 GLN ** g 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.081637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.049585 restraints weight = 457984.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.049029 restraints weight = 269178.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.048127 restraints weight = 194326.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.047971 restraints weight = 181952.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.047844 restraints weight = 168813.258| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 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 = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 31550 Z= 0.282 Angle : 0.774 13.481 45034 Z= 0.425 Chirality : 0.046 0.261 5070 Planarity : 0.005 0.068 3698 Dihedral : 31.296 168.398 8806 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.13 % Allowed : 16.06 % Favored : 81.81 % 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: 1.37 (0.14), residues: 1372 sheet: -1.02 (0.50), residues: 114 loop : -1.15 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG e 116 TYR 0.022 0.002 TYR d 83 PHE 0.020 0.002 PHE k 503 TRP 0.025 0.002 TRP K 375 HIS 0.008 0.002 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.28 (31542) covalent geometry : angle 0.77266 / 0.43 (45028) hydrogen bonds : bond 0.08582 / 5.81 ( 1810) hydrogen bonds : angle 3.96793 / 2.81 ( 4634) metal coordination : bond 0.02082 / 1.34 ( 8) metal coordination : angle 3.34560 / 2.26 ( 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 88 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 47 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8857 (mt-10) REVERT: a 120 MET cc_start: 0.3649 (tpp) cc_final: 0.3410 (mmm) REVERT: d 47 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7660 (tm-30) outliers start: 41 outliers final: 23 residues processed: 84 average time/residue: 0.1747 time to fit residues: 25.5486 Evaluate side-chains 69 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 45 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 97 GLU 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 36 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 57 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain d residue 47 GLN Chi-restraints excluded: chain e residue 121 PRO Chi-restraints excluded: chain h residue 90 THR Chi-restraints excluded: chain k residue 395 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 119 optimal weight: 0.6980 chunk 222 optimal weight: 50.0000 chunk 232 optimal weight: 50.0000 chunk 3 optimal weight: 5.9990 chunk 214 optimal weight: 50.0000 chunk 229 optimal weight: 50.0000 chunk 180 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 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** ** b 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 73 ASN ** 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 = 0.4040 r_free = 0.4040 target = 0.067654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.047769 restraints weight = 488499.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.046366 restraints weight = 309706.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.045456 restraints weight = 248371.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.045233 restraints weight = 190798.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.045223 restraints weight = 172053.801| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 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 = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31550 Z= 0.173 Angle : 0.673 10.943 45034 Z= 0.381 Chirality : 0.044 0.280 5070 Planarity : 0.004 0.069 3698 Dihedral : 31.173 169.383 8806 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.35 % Allowed : 17.05 % 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: 1.11 (0.18), residues: 2204 helix: 1.78 (0.14), residues: 1368 sheet: -1.37 (0.48), residues: 112 loop : -0.94 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 236 TYR 0.021 0.002 TYR k 358 PHE 0.018 0.002 PHE A 67 TRP 0.015 0.002 TRP K 375 HIS 0.014 0.001 HIS K 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.17 (31542) covalent geometry : angle 0.67224 / 0.38 (45028) hydrogen bonds : bond 0.05809 / 4.02 ( 1810) hydrogen bonds : angle 3.61790 / 2.57 ( 4634) metal coordination : bond 0.01536 / 0.98 ( 8) metal coordination : angle 2.82885 / 1.92 ( 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 73 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 47 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8900 (tt0) REVERT: A 107 THR cc_start: 0.9683 (OUTLIER) cc_final: 0.9370 (p) REVERT: f 84 MET cc_start: 0.7883 (ppp) cc_final: 0.7585 (pmm) outliers start: 26 outliers final: 17 residues processed: 70 average time/residue: 0.1734 time to fit residues: 21.6430 Evaluate side-chains 63 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 82 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 48 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 54 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain g residue 16 THR Chi-restraints excluded: chain h residue 90 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 213 optimal weight: 50.0000 chunk 66 optimal weight: 8.9990 chunk 243 optimal weight: 40.0000 chunk 28 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 85 optimal weight: 50.0000 chunk 56 optimal weight: 2.9990 chunk 199 optimal weight: 30.0000 chunk 138 optimal weight: 6.9990 chunk 162 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 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** a 55 GLN ** b 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.067820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.047898 restraints weight = 559945.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.047065 restraints weight = 311124.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.045504 restraints weight = 270520.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.044023 restraints weight = 204018.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.043882 restraints weight = 187883.125| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 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 = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31550 Z= 0.157 Angle : 0.644 13.687 45034 Z= 0.367 Chirality : 0.042 0.293 5070 Planarity : 0.004 0.057 3698 Dihedral : 30.875 169.236 8806 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.25 % Allowed : 17.46 % Favored : 81.29 % 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: 1.50 (0.18), residues: 2204 helix: 2.10 (0.14), residues: 1366 sheet: -1.56 (0.47), residues: 112 loop : -0.73 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 236 TYR 0.022 0.001 TYR k 358 PHE 0.017 0.002 PHE k 503 TRP 0.025 0.002 TRP K 375 HIS 0.013 0.001 HIS K 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.16 (31542) covalent geometry : angle 0.64369 / 0.37 (45028) hydrogen bonds : bond 0.05299 / 3.68 ( 1810) hydrogen bonds : angle 3.44887 / 2.44 ( 4634) metal coordination : bond 0.01465 / 0.93 ( 8) metal coordination : angle 2.61220 / 1.79 ( 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 70 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 46 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 94 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8097 (tp30) REVERT: a 90 MET cc_start: 0.8523 (mmp) cc_final: 0.7829 (ptt) REVERT: f 84 MET cc_start: 0.7787 (ppp) cc_final: 0.7568 (pmm) outliers start: 24 outliers final: 12 residues processed: 68 average time/residue: 0.1740 time to fit residues: 20.6363 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 : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain D residue 36 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 H residue 90 THR Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain g residue 16 THR 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: 4.9990 chunk 229 optimal weight: 50.0000 chunk 227 optimal weight: 50.0000 chunk 165 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 121 optimal weight: 20.0000 chunk 168 optimal weight: 6.9990 chunk 263 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 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** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 73 ASN ** 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 = 0.4030 r_free = 0.4030 target = 0.067312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.046536 restraints weight = 358278.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.046601 restraints weight = 202494.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.044378 restraints weight = 158493.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.043513 restraints weight = 148961.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.043367 restraints weight = 143958.963| |-----------------------------------------------------------------------------| 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: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31550 Z= 0.180 Angle : 0.658 11.772 45034 Z= 0.371 Chirality : 0.042 0.280 5070 Planarity : 0.004 0.068 3698 Dihedral : 30.874 169.878 8806 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.46 % Allowed : 17.46 % Favored : 81.08 % 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: 1.40 (0.18), residues: 2204 helix: 2.01 (0.14), residues: 1368 sheet: -1.64 (0.46), residues: 112 loop : -0.74 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 300 TYR 0.022 0.002 TYR k 358 PHE 0.016 0.002 PHE k 503 TRP 0.028 0.002 TRP K 375 HIS 0.013 0.001 HIS K 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.18 (31542) covalent geometry : angle 0.65750 / 0.37 (45028) hydrogen bonds : bond 0.06037 / 4.14 ( 1810) hydrogen bonds : angle 3.51063 / 2.49 ( 4634) metal coordination : bond 0.01633 / 1.06 ( 8) metal coordination : angle 2.68854 / 1.91 ( 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: 28 poor density : 45 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8923 (tt0) REVERT: A 107 THR cc_start: 0.9680 (OUTLIER) cc_final: 0.9353 (p) REVERT: A 120 MET cc_start: 0.8467 (mmp) cc_final: 0.7938 (mmm) REVERT: C 84 GLN cc_start: 0.9506 (OUTLIER) cc_final: 0.8946 (tp-100) REVERT: b 20 LYS cc_start: 0.2175 (OUTLIER) cc_final: 0.1969 (ptpt) REVERT: f 84 MET cc_start: 0.8201 (ppp) cc_final: 0.7931 (pmm) outliers start: 28 outliers final: 18 residues processed: 71 average time/residue: 0.1774 time to fit residues: 22.3406 Evaluate side-chains 64 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 82 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 41 VAL 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 Chi-restraints excluded: chain h residue 90 THR Chi-restraints excluded: chain k residue 395 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 258 optimal weight: 50.0000 chunk 189 optimal weight: 10.0000 chunk 83 optimal weight: 50.0000 chunk 249 optimal weight: 7.9990 chunk 78 optimal weight: 50.0000 chunk 14 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 74 optimal weight: 50.0000 chunk 114 optimal weight: 20.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 47 GLN ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.067261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.047633 restraints weight = 513826.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.044880 restraints weight = 314148.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.043554 restraints weight = 221987.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.043381 restraints weight = 185340.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.043337 restraints weight = 185733.660| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 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 = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 31550 Z= 0.177 Angle : 0.651 11.411 45034 Z= 0.369 Chirality : 0.042 0.296 5070 Planarity : 0.004 0.062 3698 Dihedral : 30.861 170.052 8806 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.30 % Allowed : 17.78 % Favored : 80.93 % 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: 1.46 (0.18), residues: 2204 helix: 2.03 (0.14), residues: 1368 sheet: -1.35 (0.48), residues: 104 loop : -0.72 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG b 55 TYR 0.021 0.002 TYR k 358 PHE 0.015 0.002 PHE A 67 TRP 0.032 0.002 TRP K 375 HIS 0.012 0.001 HIS K 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.18 (31542) covalent geometry : angle 0.65004 / 0.37 (45028) hydrogen bonds : bond 0.05659 / 3.90 ( 1810) hydrogen bonds : angle 3.49868 / 2.48 ( 4634) metal coordination : bond 0.01724 / 1.12 ( 8) metal coordination : angle 2.79838 / 2.00 ( 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 69 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 44 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8947 (tt0) REVERT: A 107 THR cc_start: 0.9686 (OUTLIER) cc_final: 0.9393 (p) REVERT: A 120 MET cc_start: 0.8442 (mmp) cc_final: 0.8052 (mmm) REVERT: C 84 GLN cc_start: 0.9498 (OUTLIER) cc_final: 0.8921 (tp-100) REVERT: a 90 MET cc_start: 0.8539 (mmp) cc_final: 0.7791 (ptt) REVERT: d 47 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.8007 (tm-30) outliers start: 25 outliers final: 17 residues processed: 67 average time/residue: 0.1748 time to fit residues: 20.8263 Evaluate side-chains 64 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 86 VAL Chi-restraints excluded: chain C residue 84 GLN 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 E residue 130 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain d residue 47 GLN Chi-restraints excluded: chain g residue 16 THR Chi-restraints excluded: chain h residue 90 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: 0.2980 chunk 97 optimal weight: 50.0000 chunk 53 optimal weight: 1.9990 chunk 194 optimal weight: 20.0000 chunk 232 optimal weight: 50.0000 chunk 15 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 54 optimal weight: 0.0060 chunk 193 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 overall best weight: 2.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.067825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.048332 restraints weight = 516778.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.045110 restraints weight = 310600.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.043988 restraints weight = 226308.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.043808 restraints weight = 198048.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.043769 restraints weight = 176520.330| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 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 = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 31550 Z= 0.131 Angle : 0.618 10.957 45034 Z= 0.355 Chirality : 0.042 0.287 5070 Planarity : 0.004 0.065 3698 Dihedral : 30.697 170.777 8806 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.62 % Allowed : 18.40 % Favored : 80.98 % 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: 1.69 (0.18), residues: 2204 helix: 2.20 (0.14), residues: 1378 sheet: -1.40 (0.47), residues: 104 loop : -0.62 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 35 TYR 0.021 0.001 TYR k 358 PHE 0.016 0.001 PHE K 357 TRP 0.026 0.002 TRP K 375 HIS 0.012 0.001 HIS K 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.13 (31542) covalent geometry : angle 0.61733 / 0.35 (45028) hydrogen bonds : bond 0.04716 / 3.31 ( 1810) hydrogen bonds : angle 3.31369 / 2.35 ( 4634) metal coordination : bond 0.01380 / 0.89 ( 8) metal coordination : angle 2.62231 / 1.84 ( 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 59 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8351 (mmp) cc_final: 0.8012 (mmm) REVERT: C 84 GLN cc_start: 0.9498 (OUTLIER) cc_final: 0.9179 (tm-30) REVERT: E 94 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7988 (tp30) REVERT: a 90 MET cc_start: 0.8585 (mmp) cc_final: 0.7819 (ptt) REVERT: f 84 MET cc_start: 0.9123 (pmm) cc_final: 0.8726 (pmm) REVERT: k 298 MET cc_start: 0.6655 (ttm) cc_final: 0.6272 (tpt) outliers start: 12 outliers final: 6 residues processed: 57 average time/residue: 0.1873 time to fit residues: 18.7044 Evaluate side-chains 52 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain K residue 395 THR 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: 8.9990 chunk 213 optimal weight: 50.0000 chunk 230 optimal weight: 50.0000 chunk 81 optimal weight: 40.0000 chunk 90 optimal weight: 50.0000 chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 116 optimal weight: 40.0000 chunk 216 optimal weight: 50.0000 chunk 205 optimal weight: 7.9990 chunk 100 optimal weight: 0.3980 overall best weight: 6.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 ASN k 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.067178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.047449 restraints weight = 526697.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.045535 restraints weight = 303585.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.044691 restraints weight = 253540.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.044485 restraints weight = 197283.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.044404 restraints weight = 180982.227| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4696 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= 0.172 Angle : 0.649 12.473 45034 Z= 0.365 Chirality : 0.041 0.285 5070 Planarity : 0.004 0.063 3698 Dihedral : 30.704 170.342 8806 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.57 % Allowed : 18.71 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.61 (0.18), residues: 2204 helix: 2.12 (0.14), residues: 1376 sheet: -1.38 (0.47), residues: 104 loop : -0.61 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 35 TYR 0.021 0.002 TYR k 358 PHE 0.016 0.001 PHE k 503 TRP 0.025 0.002 TRP K 375 HIS 0.012 0.001 HIS K 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.17 (31542) covalent geometry : angle 0.64817 / 0.36 (45028) hydrogen bonds : bond 0.05724 / 3.94 ( 1810) hydrogen bonds : angle 3.42992 / 2.43 ( 4634) metal coordination : bond 0.01688 / 1.10 ( 8) metal coordination : angle 2.71980 / 1.96 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8693.25 seconds wall clock time: 149 minutes 1.52 seconds (8941.52 seconds total)