Starting phenix.real_space_refine on Fri Jul 3 02:13:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rmg_19361/07_2026/8rmg_19361.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rmg_19361/07_2026/8rmg_19361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rmg_19361/07_2026/8rmg_19361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rmg_19361/07_2026/8rmg_19361.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rmg_19361/07_2026/8rmg_19361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rmg_19361/07_2026/8rmg_19361.map" } resolution = 2.46 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= 0.045 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 Fe 4 7.16 5 P 4 5.49 5 S 68 5.16 5 C 7257 2.51 5 N 2034 2.21 5 O 2388 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11755 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3170 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 402, 3145 Classifications: {'peptide': 402} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 382} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 402, 3145 Classifications: {'peptide': 402} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 382} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3176 Chain: "B" Number of atoms: 689 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 81, 678 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Conformer: "B" Number of residues, atoms: 81, 678 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} bond proxies already assigned to first conformer: 674 Chain: "C" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "D" Number of atoms: 948 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 124, 936 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Conformer: "D" Number of residues, atoms: 124, 936 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} bond proxies already assigned to first conformer: 936 Chain: "I" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 787 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "E" Number of atoms: 3140 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3126 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 380} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 400, 3126 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 380} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3168 Chain: "F" Number of atoms: 689 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 81, 678 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Conformer: "B" Number of residues, atoms: 81, 678 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} bond proxies already assigned to first conformer: 674 Chain: "G" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 948 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 124, 936 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Conformer: "B" Number of residues, atoms: 124, 936 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} bond proxies already assigned to first conformer: 936 Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {'FE2': 1} Chain breaks: 1 Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {'FE2': 1} Chain breaks: 1 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2537 SG CYS A 381 31.840 45.650 66.899 1.00102.82 S ATOM 4913 SG CYS D 95 32.751 42.816 64.266 1.00 59.35 S ATOM 5683 SG CYS I 108 48.786 38.012 81.353 1.00126.95 S ATOM 5722 SG CYS I 114 46.416 40.707 82.428 1.00107.81 S ATOM 5741 SG CYS I 117 50.625 41.943 85.459 1.00100.89 S ATOM 6038 SG CYS I 154 53.259 39.381 84.414 1.00100.88 S ATOM 8707 SG CYS E 381 71.650 98.544 66.847 1.00105.41 S ATOM 11053 SG CYS H 95 72.055 101.401 64.453 1.00 62.52 S Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N AASN A 83 " occ=0.42 ... (14 atoms not shown) pdb=" ND2BASN A 83 " occ=0.58 residue: pdb=" N ACYS A 426 " occ=0.27 ... (10 atoms not shown) pdb=" SG BCYS A 426 " occ=0.73 residue: pdb=" N AARG A 432 " occ=0.46 ... (20 atoms not shown) pdb=" NH2BARG A 432 " occ=0.54 residue: pdb=" N AARG B 14 " occ=0.34 ... (20 atoms not shown) pdb=" NH2BARG B 14 " occ=0.66 residue: pdb=" N BTYR D 35 " occ=0.40 ... (22 atoms not shown) pdb=" OH DTYR D 35 " occ=0.60 residue: pdb=" N AASN E 83 " occ=0.40 ... (14 atoms not shown) pdb=" ND2BASN E 83 " occ=0.60 residue: pdb=" N ACYS E 426 " occ=0.45 ... (10 atoms not shown) pdb=" SG BCYS E 426 " occ=0.55 residue: pdb=" N AARG F 14 " occ=0.38 ... (20 atoms not shown) pdb=" NH2BARG F 14 " occ=0.62 residue: pdb=" N ATYR H 35 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR H 35 " occ=0.50 Time building chain proxies: 4.29, per 1000 atoms: 0.36 Number of scatterers: 11755 At special positions: 0 Unit cell: (104.328, 145.728, 113.436, 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) Fe 4 26.01 S 68 16.00 P 4 15.00 O 2388 8.00 N 2034 7.00 C 7257 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 990.1 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES I 201 " pdb="FE1 FES I 201 " - pdb=" SG CYS I 114 " pdb="FE2 FES I 201 " - pdb=" SG CYS I 154 " pdb="FE1 FES I 201 " - pdb=" SG CYS I 108 " pdb="FE2 FES I 201 " - pdb=" SG CYS I 117 " Number of angles added : 6 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 9 sheets defined 54.5% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 70 through 83 Proline residue: A 79 - end of helix Processing helix chain 'A' and resid 93 through 115 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 126 through 142 Processing helix chain 'A' and resid 156 through 168 Processing helix chain 'A' and resid 185 through 192 Processing helix chain 'A' and resid 214 through 225 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 297 through 337 removed outlier: 5.283A pdb=" N GLU A 316 " --> pdb=" O GLN A 312 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TYR A 317 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 370 Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 398 through 403 removed outlier: 3.746A pdb=" N HIS A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 437 Processing helix chain 'A' and resid 437 through 445 Processing helix chain 'B' and resid 6 through 21 Processing helix chain 'B' and resid 25 through 43 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.631A pdb=" N ASN B 85 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 17 removed outlier: 3.560A pdb=" N LYS C 9 " --> pdb=" O GLU C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 51 Processing helix chain 'C' and resid 56 through 63 removed outlier: 3.569A pdb=" N LYS C 62 " --> pdb=" O GLU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 76 Processing helix chain 'D' and resid 36 through 45 Processing helix chain 'D' and resid 95 through 110 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.501A pdb=" N ILE D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 134 No H-bonds generated for 'chain 'D' and resid 132 through 134' Processing helix chain 'D' and resid 135 through 157 removed outlier: 4.215A pdb=" N SER D 139 " --> pdb=" O LYS D 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 99 removed outlier: 3.753A pdb=" N GLN I 98 " --> pdb=" O LEU I 94 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG I 99 " --> pdb=" O HIS I 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 94 through 99' Processing helix chain 'I' and resid 122 through 127 removed outlier: 4.242A pdb=" N ASP I 127 " --> pdb=" O GLU I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 143 removed outlier: 3.871A pdb=" N MET I 142 " --> pdb=" O ASP I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 156 No H-bonds generated for 'chain 'I' and resid 154 through 156' Processing helix chain 'I' and resid 159 through 163 Processing helix chain 'E' and resid 70 through 83 Proline residue: E 79 - end of helix Processing helix chain 'E' and resid 93 through 115 Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 126 through 142 Processing helix chain 'E' and resid 156 through 169 Processing helix chain 'E' and resid 185 through 193 Processing helix chain 'E' and resid 214 through 226 Processing helix chain 'E' and resid 257 through 259 No H-bonds generated for 'chain 'E' and resid 257 through 259' Processing helix chain 'E' and resid 287 through 291 Processing helix chain 'E' and resid 297 through 337 removed outlier: 5.803A pdb=" N GLU E 316 " --> pdb=" O GLN E 312 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N TYR E 317 " --> pdb=" O GLN E 313 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 349 removed outlier: 3.708A pdb=" N HIS E 348 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS E 349 " --> pdb=" O PRO E 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 345 through 349' Processing helix chain 'E' and resid 362 through 370 Processing helix chain 'E' and resid 389 through 395 Processing helix chain 'E' and resid 398 through 403 Processing helix chain 'E' and resid 415 through 437 Processing helix chain 'E' and resid 437 through 445 Processing helix chain 'F' and resid 6 through 21 Processing helix chain 'F' and resid 25 through 43 removed outlier: 3.577A pdb=" N TYR F 31 " --> pdb=" O ASN F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'G' and resid 4 through 17 Processing helix chain 'G' and resid 36 through 51 removed outlier: 3.561A pdb=" N GLU G 42 " --> pdb=" O LEU G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 63 Processing helix chain 'G' and resid 65 through 76 Processing helix chain 'H' and resid 36 through 45 Processing helix chain 'H' and resid 95 through 110 Processing helix chain 'H' and resid 113 through 118 Processing helix chain 'H' and resid 121 through 130 Processing helix chain 'H' and resid 132 through 134 No H-bonds generated for 'chain 'H' and resid 132 through 134' Processing helix chain 'H' and resid 135 through 158 removed outlier: 4.158A pdb=" N SER H 139 " --> pdb=" O LYS H 135 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.754A pdb=" N LEU A 59 " --> pdb=" O ALA A 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 124 removed outlier: 6.808A pdb=" N SER A 198 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N HIS A 230 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL A 200 " --> pdb=" O HIS A 230 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ASP A 232 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N HIS A 148 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 200 " --> pdb=" O HIS A 148 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A 150 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 149 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU A 176 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR A 151 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 340 through 342 removed outlier: 3.657A pdb=" N SER A 376 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 59 through 66 removed outlier: 3.783A pdb=" N ALA D 66 " --> pdb=" O ASP D 71 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP D 71 " --> pdb=" O ALA D 66 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP D 87 " --> pdb=" O GLN D 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 82 through 88 removed outlier: 8.570A pdb=" N PHE I 167 " --> pdb=" O ASN I 72 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL I 74 " --> pdb=" O PHE I 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.681A pdb=" N LEU E 59 " --> pdb=" O ALA E 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 121 through 124 removed outlier: 6.804A pdb=" N SER E 198 " --> pdb=" O TYR E 228 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N HIS E 230 " --> pdb=" O SER E 198 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL E 200 " --> pdb=" O HIS E 230 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASP E 232 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N HIS E 148 " --> pdb=" O SER E 198 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL E 200 " --> pdb=" O HIS E 148 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE E 150 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU E 149 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU E 176 " --> pdb=" O LEU E 149 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR E 151 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 340 through 342 removed outlier: 3.685A pdb=" N SER E 376 " --> pdb=" O ARG E 407 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 59 through 65 removed outlier: 3.841A pdb=" N ASP H 87 " --> pdb=" O GLN H 78 " (cutoff:3.500A) 614 hydrogen bonds defined for protein. 1811 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.40: 4615 1.40 - 1.60: 7055 1.60 - 1.80: 42 1.80 - 2.00: 66 2.00 - 2.20: 4 Bond restraints: 11782 Sorted by residual: bond pdb=" NZ LLP A 258 " pdb=" C4' LLP A 258 " ideal model delta sigma weight residual 1.273 1.430 -0.157 2.00e-02 2.50e+03 6.17e+01 bond pdb=" NZ LLP E 258 " pdb=" C4' LLP E 258 " ideal model delta sigma weight residual 1.273 1.430 -0.157 2.00e-02 2.50e+03 6.16e+01 bond pdb=" OP4 LLP A 258 " pdb=" P LLP A 258 " ideal model delta sigma weight residual 1.726 1.612 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" OP4 LLP E 258 " pdb=" P LLP E 258 " ideal model delta sigma weight residual 1.726 1.614 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" N PRO D 46 " pdb=" CD PRO D 46 " ideal model delta sigma weight residual 1.473 1.541 -0.068 1.40e-02 5.10e+03 2.33e+01 ... (remaining 11777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 15778 3.42 - 6.83: 127 6.83 - 10.25: 5 10.25 - 13.66: 6 13.66 - 17.08: 1 Bond angle restraints: 15917 Sorted by residual: angle pdb=" S1 FES I 201 " pdb="FE2 FES I 201 " pdb=" S2 FES I 201 " ideal model delta sigma weight residual 104.33 91.02 13.31 1.14e+00 7.69e-01 1.36e+02 angle pdb="FE1 FES I 201 " pdb=" S2 FES I 201 " pdb="FE2 FES I 201 " ideal model delta sigma weight residual 75.66 88.92 -13.26 1.14e+00 7.69e-01 1.35e+02 angle pdb=" S1 FES I 201 " pdb="FE1 FES I 201 " pdb=" S2 FES I 201 " ideal model delta sigma weight residual 104.33 91.03 13.30 1.20e+00 6.94e-01 1.23e+02 angle pdb="FE1 FES I 201 " pdb=" S1 FES I 201 " pdb="FE2 FES I 201 " ideal model delta sigma weight residual 75.66 88.89 -13.23 1.20e+00 6.94e-01 1.22e+02 angle pdb=" C PRO D 46 " pdb=" CA PRO D 46 " pdb=" CB PRO D 46 " ideal model delta sigma weight residual 111.21 119.25 -8.04 1.33e+00 5.65e-01 3.66e+01 ... (remaining 15912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.53: 6943 32.53 - 65.05: 276 65.05 - 97.58: 36 97.58 - 130.11: 3 130.11 - 162.64: 7 Dihedral angle restraints: 7265 sinusoidal: 2990 harmonic: 4275 Sorted by residual: dihedral pdb=" C37 8Q1 G 101 " pdb=" C38 8Q1 G 101 " pdb=" C39 8Q1 G 101 " pdb=" O40 8Q1 G 101 " ideal model delta sinusoidal sigma weight residual -114.72 47.92 -162.64 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C37 8Q1 G 101 " pdb=" C38 8Q1 G 101 " pdb=" C39 8Q1 G 101 " pdb=" N41 8Q1 G 101 " ideal model delta sinusoidal sigma weight residual 64.60 -133.74 -161.66 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C39 8Q1 G 101 " pdb=" C42 8Q1 G 101 " pdb=" N41 8Q1 G 101 " pdb=" C43 8Q1 G 101 " ideal model delta sinusoidal sigma weight residual 89.93 -67.51 157.44 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 7262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1524 0.065 - 0.129: 236 0.129 - 0.194: 27 0.194 - 0.258: 6 0.258 - 0.323: 9 Chirality restraints: 1802 Sorted by residual: chirality pdb=" CA LEU I 104 " pdb=" N LEU I 104 " pdb=" C LEU I 104 " pdb=" CB LEU I 104 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA ARG A 412 " pdb=" N ARG A 412 " pdb=" C ARG A 412 " pdb=" CB ARG A 412 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA ASN F 27 " pdb=" N ASN F 27 " pdb=" C ASN F 27 " pdb=" CB ASN F 27 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 1799 not shown) Planarity restraints: 2061 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 8Q1 G 101 " -0.052 2.00e-02 2.50e+03 5.44e-02 3.70e+01 pdb=" C39 8Q1 G 101 " 0.027 2.00e-02 2.50e+03 pdb=" C42 8Q1 G 101 " -0.066 2.00e-02 2.50e+03 pdb=" N41 8Q1 G 101 " 0.083 2.00e-02 2.50e+03 pdb=" O40 8Q1 G 101 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP A 258 " 0.058 2.00e-02 2.50e+03 5.76e-02 3.32e+01 pdb=" NZ LLP A 258 " -0.077 2.00e-02 2.50e+03 pdb=" C4 LLP A 258 " 0.052 2.00e-02 2.50e+03 pdb=" C4' LLP A 258 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BTYR D 35 " -0.027 2.00e-02 2.50e+03 5.52e-02 3.05e+01 pdb=" C BTYR D 35 " 0.096 2.00e-02 2.50e+03 pdb=" O BTYR D 35 " -0.036 2.00e-02 2.50e+03 pdb=" N HIS D 36 " -0.033 2.00e-02 2.50e+03 ... (remaining 2058 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 116 2.61 - 3.18: 10037 3.18 - 3.75: 19292 3.75 - 4.33: 27951 4.33 - 4.90: 44299 Nonbonded interactions: 101695 Sorted by model distance: nonbonded pdb=" OD2 ASP H 71 " pdb="FE FE2 H 201 " model vdw 2.034 3.000 nonbonded pdb=" OD2 ASP D 71 " pdb="FE FE2 D 201 " model vdw 2.058 3.000 nonbonded pdb=" O GLY E 344 " pdb=" O HOH E 601 " model vdw 2.097 3.040 nonbonded pdb=" NE2 HIS H 137 " pdb="FE FE2 H 201 " model vdw 2.143 3.080 nonbonded pdb=" OH TYR E 317 " pdb=" OD2 ASP F 38 " model vdw 2.149 3.040 ... (remaining 101690 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 56 through 82 or resid 84 through 425 or resid 427 through \ 431 or resid 433 through 455)) selection = (chain 'E' and (resid 56 through 82 or resid 84 through 425 or resid 427 through \ 431 or resid 433 through 455)) } ncs_group { reference = (chain 'B' and (resid 5 through 13 or resid 15 through 85)) selection = (chain 'F' and (resid 5 through 13 or resid 15 through 85)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 36 through 201) selection = (chain 'H' and resid 36 through 201) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.100 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 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 : 0.005 0.157 11788 Z= 0.310 Angle : 0.832 21.370 15923 Z= 0.516 Chirality : 0.052 0.323 1802 Planarity : 0.005 0.102 2061 Dihedral : 17.730 162.636 4511 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.75 % Allowed : 15.67 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.82 (0.22), residues: 1462 helix: 1.07 (0.19), residues: 777 sheet: 0.70 (0.39), residues: 198 loop : -0.24 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 432 TYR 0.016 0.002 TYR D 43 PHE 0.010 0.001 PHE H 90 TRP 0.036 0.002 TRP A 454 HIS 0.007 0.001 HIS F 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.31 (11782) covalent geometry : angle 0.80441 / 0.52 (15917) hydrogen bonds : bond 0.13914 / 9.29 ( 614) hydrogen bonds : angle 5.57835 / 4.03 ( 1811) metal coordination : bond 0.01754 / 0.87 ( 4) metal coordination : angle 10.88667 / 3.73 ( 6) Misc. bond : bond 0.00016 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.9004 (tt0) cc_final: 0.8679 (tt0) REVERT: A 164 ARG cc_start: 0.7624 (mtm180) cc_final: 0.7366 (mtt180) REVERT: A 190 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7487 (mt-10) REVERT: A 324 LYS cc_start: 0.8514 (tttp) cc_final: 0.8294 (ttpp) REVERT: C 14 GLU cc_start: 0.6372 (mp0) cc_final: 0.6162 (mp0) REVERT: C 54 GLU cc_start: 0.6609 (mm-30) cc_final: 0.5377 (tm-30) REVERT: D 37 LYS cc_start: 0.7243 (tttt) cc_final: 0.6620 (ttpt) REVERT: D 89 ARG cc_start: 0.8072 (mmm-85) cc_final: 0.7311 (mmt90) REVERT: D 121 LYS cc_start: 0.7446 (mmmt) cc_final: 0.7084 (mppt) REVERT: I 102 VAL cc_start: 0.7449 (OUTLIER) cc_final: 0.7104 (p) REVERT: I 134 GLU cc_start: 0.6881 (tt0) cc_final: 0.6481 (tt0) REVERT: E 100 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8260 (tm-30) REVERT: E 145 ARG cc_start: 0.7918 (mtp-110) cc_final: 0.7308 (mtm110) REVERT: E 316 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: E 417 GLU cc_start: 0.7676 (tt0) cc_final: 0.7455 (mp0) REVERT: E 432 ARG cc_start: 0.7308 (ttm-80) cc_final: 0.7057 (ttm170) REVERT: F 42 GLU cc_start: 0.6789 (pt0) cc_final: 0.6565 (pt0) REVERT: F 58 LYS cc_start: 0.7770 (tptt) cc_final: 0.7274 (ttmt) REVERT: H 121 LYS cc_start: 0.7088 (mmtp) cc_final: 0.6534 (mmtt) outliers start: 20 outliers final: 5 residues processed: 198 average time/residue: 0.7504 time to fit residues: 158.0494 Evaluate side-chains 157 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 GLN B 74 GLN D 48 ASN E 93 HIS E 429 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.171965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.108575 restraints weight = 58061.708| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.06 r_work: 0.3149 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11788 Z= 0.180 Angle : 0.584 7.856 15923 Z= 0.308 Chirality : 0.045 0.164 1802 Planarity : 0.005 0.043 2061 Dihedral : 11.800 178.790 1700 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.51 % Allowed : 16.23 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 1.13 (0.22), residues: 1462 helix: 1.38 (0.19), residues: 796 sheet: 0.63 (0.39), residues: 198 loop : -0.14 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 272 TYR 0.021 0.002 TYR F 31 PHE 0.013 0.002 PHE F 40 TRP 0.017 0.002 TRP A 454 HIS 0.015 0.002 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (11782) covalent geometry : angle 0.57752 / 0.31 (15917) hydrogen bonds : bond 0.05961 / 3.88 ( 614) hydrogen bonds : angle 4.75685 / 3.42 ( 1811) metal coordination : bond 0.01627 / 0.79 ( 4) metal coordination : angle 4.48916 / 1.73 ( 6) Misc. bond : bond 0.00033 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8877 (tt0) cc_final: 0.8651 (tm-30) REVERT: A 164 ARG cc_start: 0.7925 (mtm180) cc_final: 0.7548 (mtt180) REVERT: A 324 LYS cc_start: 0.8695 (tttp) cc_final: 0.8375 (ttpp) REVERT: A 364 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7154 (tm-30) REVERT: A 416 GLU cc_start: 0.8519 (tt0) cc_final: 0.8264 (tt0) REVERT: C 54 GLU cc_start: 0.6537 (mm-30) cc_final: 0.5292 (tm-30) REVERT: D 37 LYS cc_start: 0.7473 (tttt) cc_final: 0.6968 (ttpt) REVERT: D 121 LYS cc_start: 0.7537 (mmmt) cc_final: 0.7115 (mppt) REVERT: I 102 VAL cc_start: 0.7232 (OUTLIER) cc_final: 0.6958 (p) REVERT: I 134 GLU cc_start: 0.7201 (tt0) cc_final: 0.6896 (tt0) REVERT: E 145 ARG cc_start: 0.8054 (mtp-110) cc_final: 0.7575 (mtm110) REVERT: E 316 GLU cc_start: 0.8106 (tt0) cc_final: 0.7559 (mp0) REVERT: E 399 GLU cc_start: 0.4270 (OUTLIER) cc_final: 0.3792 (tt0) REVERT: E 417 GLU cc_start: 0.8241 (tt0) cc_final: 0.7881 (mp0) REVERT: E 432 ARG cc_start: 0.8000 (ttm-80) cc_final: 0.7798 (ttm170) REVERT: E 441 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7391 (tt0) REVERT: F 42 GLU cc_start: 0.7362 (pt0) cc_final: 0.7153 (pt0) REVERT: F 58 LYS cc_start: 0.8162 (tptt) cc_final: 0.7665 (ttmt) outliers start: 18 outliers final: 5 residues processed: 168 average time/residue: 0.7238 time to fit residues: 129.3061 Evaluate side-chains 156 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 441 GLU Chi-restraints excluded: chain G residue 28 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 101 optimal weight: 3.9990 chunk 116 optimal weight: 0.0060 chunk 100 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 58 optimal weight: 0.0270 chunk 36 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 overall best weight: 0.5054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN G 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.176062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.113166 restraints weight = 63448.908| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.19 r_work: 0.3245 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11788 Z= 0.101 Angle : 0.467 10.734 15923 Z= 0.244 Chirality : 0.041 0.142 1802 Planarity : 0.003 0.029 2061 Dihedral : 10.167 170.819 1683 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.11 % Allowed : 16.71 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 1.55 (0.23), residues: 1462 helix: 1.72 (0.19), residues: 793 sheet: 0.84 (0.40), residues: 196 loop : 0.02 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 61 TYR 0.014 0.001 TYR H 43 PHE 0.009 0.001 PHE H 90 TRP 0.013 0.001 TRP A 454 HIS 0.009 0.001 HIS F 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.10 (11782) covalent geometry : angle 0.46121 / 0.24 (15917) hydrogen bonds : bond 0.04430 / 2.85 ( 614) hydrogen bonds : angle 4.40374 / 3.14 ( 1811) metal coordination : bond 0.01281 / 0.63 ( 4) metal coordination : angle 3.78112 / 1.69 ( 6) Misc. bond : bond 0.00022 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8815 (tt0) cc_final: 0.8602 (tm-30) REVERT: A 164 ARG cc_start: 0.7805 (mtm180) cc_final: 0.7457 (mtt180) REVERT: A 324 LYS cc_start: 0.8608 (tttp) cc_final: 0.8278 (ttpp) REVERT: A 364 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7194 (tm-30) REVERT: A 416 GLU cc_start: 0.8442 (tt0) cc_final: 0.8224 (tt0) REVERT: B 41 ARG cc_start: 0.8578 (mtt90) cc_final: 0.8274 (mtt90) REVERT: B 42 GLU cc_start: 0.7791 (pt0) cc_final: 0.7426 (pt0) REVERT: C 54 GLU cc_start: 0.6476 (mm-30) cc_final: 0.5177 (tm-30) REVERT: D 37 LYS cc_start: 0.7424 (tttt) cc_final: 0.6921 (ttpt) REVERT: D 121 LYS cc_start: 0.7526 (mmmt) cc_final: 0.7093 (mppt) REVERT: I 102 VAL cc_start: 0.7162 (t) cc_final: 0.6893 (p) REVERT: I 134 GLU cc_start: 0.7154 (tt0) cc_final: 0.6853 (tt0) REVERT: E 145 ARG cc_start: 0.8003 (mtp-110) cc_final: 0.7518 (mtm110) REVERT: E 316 GLU cc_start: 0.7967 (tt0) cc_final: 0.7464 (mp0) REVERT: E 327 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7437 (mt-10) REVERT: E 364 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7592 (tm-30) REVERT: E 399 GLU cc_start: 0.4010 (OUTLIER) cc_final: 0.3605 (tt0) REVERT: E 417 GLU cc_start: 0.8108 (tt0) cc_final: 0.7761 (mp0) REVERT: F 58 LYS cc_start: 0.8121 (tptt) cc_final: 0.7628 (ttmt) REVERT: H 121 LYS cc_start: 0.7112 (mmtp) cc_final: 0.6696 (mmmt) REVERT: H 127 LYS cc_start: 0.6509 (mtmm) cc_final: 0.6306 (mtmt) REVERT: H 140 MET cc_start: 0.7320 (mtt) cc_final: 0.6842 (mmt) outliers start: 14 outliers final: 3 residues processed: 164 average time/residue: 0.7052 time to fit residues: 122.5778 Evaluate side-chains 150 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 143 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain G residue 28 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 123 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 GLN B 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.173275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.110203 restraints weight = 52290.699| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.97 r_work: 0.3169 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11788 Z= 0.134 Angle : 0.505 8.653 15923 Z= 0.265 Chirality : 0.042 0.149 1802 Planarity : 0.004 0.030 2061 Dihedral : 10.196 166.538 1682 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.35 % Allowed : 16.79 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 1.58 (0.23), residues: 1462 helix: 1.77 (0.19), residues: 791 sheet: 0.78 (0.40), residues: 198 loop : 0.03 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 143 TYR 0.015 0.002 TYR H 43 PHE 0.008 0.001 PHE E 123 TRP 0.011 0.001 TRP A 454 HIS 0.016 0.001 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (11782) covalent geometry : angle 0.49993 / 0.26 (15917) hydrogen bonds : bond 0.05092 / 3.29 ( 614) hydrogen bonds : angle 4.46717 / 3.20 ( 1811) metal coordination : bond 0.01496 / 0.73 ( 4) metal coordination : angle 3.87040 / 1.81 ( 6) Misc. bond : bond 0.00028 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8813 (tt0) cc_final: 0.8591 (tm-30) REVERT: A 164 ARG cc_start: 0.7880 (mtm180) cc_final: 0.7530 (mtt180) REVERT: A 324 LYS cc_start: 0.8659 (tttp) cc_final: 0.8339 (ttpp) REVERT: A 327 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: A 364 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: A 416 GLU cc_start: 0.8436 (tt0) cc_final: 0.8196 (tt0) REVERT: B 41 ARG cc_start: 0.8627 (mtt90) cc_final: 0.8301 (mtt90) REVERT: B 42 GLU cc_start: 0.7808 (pt0) cc_final: 0.7429 (pt0) REVERT: C 14 GLU cc_start: 0.6150 (mp0) cc_final: 0.5944 (mp0) REVERT: C 54 GLU cc_start: 0.6532 (mm-30) cc_final: 0.5236 (tm-30) REVERT: D 37 LYS cc_start: 0.7416 (tttt) cc_final: 0.6898 (ttpt) REVERT: D 121 LYS cc_start: 0.7606 (mmmt) cc_final: 0.7134 (mppt) REVERT: I 102 VAL cc_start: 0.7151 (OUTLIER) cc_final: 0.6869 (p) REVERT: I 134 GLU cc_start: 0.7149 (tt0) cc_final: 0.6805 (tt0) REVERT: E 145 ARG cc_start: 0.8019 (mtp-110) cc_final: 0.7518 (mtm110) REVERT: E 273 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7724 (tmt-80) REVERT: E 316 GLU cc_start: 0.8005 (tt0) cc_final: 0.7378 (mp0) REVERT: E 327 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: E 364 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: E 399 GLU cc_start: 0.4205 (OUTLIER) cc_final: 0.3787 (tt0) REVERT: E 417 GLU cc_start: 0.8138 (tt0) cc_final: 0.7779 (mp0) REVERT: F 58 LYS cc_start: 0.8141 (tptt) cc_final: 0.7630 (ttmt) REVERT: H 121 LYS cc_start: 0.7209 (mmtp) cc_final: 0.6777 (mmmt) REVERT: H 127 LYS cc_start: 0.6574 (mtmm) cc_final: 0.6359 (mtmt) outliers start: 17 outliers final: 6 residues processed: 166 average time/residue: 0.7223 time to fit residues: 127.4973 Evaluate side-chains 162 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 122 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 89 optimal weight: 0.4980 chunk 81 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.175347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.112674 restraints weight = 53700.517| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.01 r_work: 0.3245 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11788 Z= 0.105 Angle : 0.459 7.681 15923 Z= 0.240 Chirality : 0.041 0.139 1802 Planarity : 0.003 0.031 2061 Dihedral : 9.564 155.936 1682 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.43 % Allowed : 16.87 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 1.71 (0.23), residues: 1462 helix: 1.88 (0.19), residues: 790 sheet: 0.82 (0.40), residues: 198 loop : 0.11 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 143 TYR 0.014 0.001 TYR H 43 PHE 0.008 0.001 PHE F 23 TRP 0.011 0.001 TRP A 454 HIS 0.004 0.001 HIS F 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (11782) covalent geometry : angle 0.45197 / 0.24 (15917) hydrogen bonds : bond 0.04403 / 2.83 ( 614) hydrogen bonds : angle 4.31262 / 3.08 ( 1811) metal coordination : bond 0.01283 / 0.63 ( 4) metal coordination : angle 4.01002 / 1.97 ( 6) Misc. bond : bond 0.00015 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8793 (tt0) cc_final: 0.8561 (tm-30) REVERT: A 157 LYS cc_start: 0.8499 (mttp) cc_final: 0.8295 (tptt) REVERT: A 164 ARG cc_start: 0.7829 (mtm180) cc_final: 0.7597 (mtt180) REVERT: A 324 LYS cc_start: 0.8618 (tttp) cc_final: 0.8311 (ttpp) REVERT: A 327 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7705 (mt-10) REVERT: A 364 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7273 (tm-30) REVERT: A 416 GLU cc_start: 0.8400 (tt0) cc_final: 0.8164 (tt0) REVERT: B 42 GLU cc_start: 0.7817 (pt0) cc_final: 0.7406 (pt0) REVERT: B 44 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8083 (mtpp) REVERT: C 54 GLU cc_start: 0.6601 (mm-30) cc_final: 0.5259 (tm-30) REVERT: D 37 LYS cc_start: 0.7372 (tttt) cc_final: 0.6844 (ttpt) REVERT: D 121 LYS cc_start: 0.7610 (mmmt) cc_final: 0.7135 (mppt) REVERT: D 144 ASP cc_start: 0.8078 (m-30) cc_final: 0.7711 (m-30) REVERT: I 102 VAL cc_start: 0.7149 (OUTLIER) cc_final: 0.6885 (p) REVERT: I 134 GLU cc_start: 0.7161 (tt0) cc_final: 0.6877 (tt0) REVERT: E 145 ARG cc_start: 0.7957 (mtp-110) cc_final: 0.7466 (mtm110) REVERT: E 226 LYS cc_start: 0.8505 (mtpp) cc_final: 0.8060 (mppt) REVERT: E 316 GLU cc_start: 0.7945 (tt0) cc_final: 0.7394 (mp0) REVERT: E 327 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7478 (mt-10) REVERT: E 364 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7565 (tm-30) REVERT: E 399 GLU cc_start: 0.4093 (OUTLIER) cc_final: 0.3720 (tt0) REVERT: E 417 GLU cc_start: 0.8093 (tt0) cc_final: 0.7733 (mp0) REVERT: F 58 LYS cc_start: 0.8112 (tptt) cc_final: 0.7633 (ttmt) REVERT: H 121 LYS cc_start: 0.7112 (mmtp) cc_final: 0.6689 (mmmt) REVERT: H 127 LYS cc_start: 0.6525 (mtmm) cc_final: 0.6312 (mtmt) outliers start: 18 outliers final: 5 residues processed: 164 average time/residue: 0.7008 time to fit residues: 122.0399 Evaluate side-chains 148 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain G residue 28 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.174715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.111864 restraints weight = 54147.604| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.02 r_work: 0.3228 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11788 Z= 0.111 Angle : 0.471 8.405 15923 Z= 0.245 Chirality : 0.041 0.207 1802 Planarity : 0.003 0.030 2061 Dihedral : 9.431 153.059 1682 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.03 % Allowed : 17.10 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 1.76 (0.23), residues: 1462 helix: 1.92 (0.19), residues: 790 sheet: 0.80 (0.40), residues: 198 loop : 0.14 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 143 TYR 0.015 0.002 TYR H 43 PHE 0.008 0.001 PHE H 90 TRP 0.009 0.001 TRP A 454 HIS 0.015 0.001 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (11782) covalent geometry : angle 0.46476 / 0.24 (15917) hydrogen bonds : bond 0.04564 / 2.94 ( 614) hydrogen bonds : angle 4.32650 / 3.09 ( 1811) metal coordination : bond 0.01264 / 0.62 ( 4) metal coordination : angle 4.05586 / 2.04 ( 6) Misc. bond : bond 0.00009 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8797 (tt0) cc_final: 0.8563 (tm-30) REVERT: A 157 LYS cc_start: 0.8504 (mttp) cc_final: 0.8295 (tptt) REVERT: A 164 ARG cc_start: 0.7860 (mtm180) cc_final: 0.7656 (mtt180) REVERT: A 324 LYS cc_start: 0.8641 (tttp) cc_final: 0.8319 (ttpp) REVERT: A 327 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: A 364 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7285 (tm-30) REVERT: A 416 GLU cc_start: 0.8434 (tt0) cc_final: 0.8209 (tt0) REVERT: B 42 GLU cc_start: 0.7854 (pt0) cc_final: 0.7459 (pt0) REVERT: B 44 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8108 (mtpp) REVERT: D 37 LYS cc_start: 0.7373 (tttt) cc_final: 0.6840 (ttpt) REVERT: D 144 ASP cc_start: 0.8112 (m-30) cc_final: 0.7698 (m-30) REVERT: I 102 VAL cc_start: 0.7181 (OUTLIER) cc_final: 0.6911 (p) REVERT: I 134 GLU cc_start: 0.7168 (tt0) cc_final: 0.6820 (tt0) REVERT: E 145 ARG cc_start: 0.8014 (mtp-110) cc_final: 0.7520 (mtm110) REVERT: E 226 LYS cc_start: 0.8517 (mtpp) cc_final: 0.8070 (mppt) REVERT: E 273 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7891 (tmt-80) REVERT: E 316 GLU cc_start: 0.7957 (tt0) cc_final: 0.7355 (mp0) REVERT: E 327 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7440 (mt-10) REVERT: E 364 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7573 (tm-30) REVERT: E 399 GLU cc_start: 0.4147 (OUTLIER) cc_final: 0.3761 (tt0) REVERT: E 417 GLU cc_start: 0.8074 (tt0) cc_final: 0.7758 (mp0) REVERT: F 58 LYS cc_start: 0.8125 (tptt) cc_final: 0.7661 (ttmt) REVERT: F 60 LYS cc_start: 0.8504 (mttp) cc_final: 0.8287 (mttt) outliers start: 13 outliers final: 4 residues processed: 146 average time/residue: 0.7005 time to fit residues: 109.0197 Evaluate side-chains 150 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain G residue 28 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 111 optimal weight: 8.9990 chunk 3 optimal weight: 0.1980 chunk 116 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 23 optimal weight: 0.3980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 429 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.173596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.110971 restraints weight = 45090.397| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.80 r_work: 0.3192 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11788 Z= 0.126 Angle : 0.489 7.783 15923 Z= 0.254 Chirality : 0.042 0.174 1802 Planarity : 0.003 0.032 2061 Dihedral : 9.445 151.426 1682 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.27 % Allowed : 17.10 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 1.73 (0.23), residues: 1462 helix: 1.91 (0.19), residues: 790 sheet: 0.76 (0.40), residues: 198 loop : 0.13 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 143 TYR 0.016 0.002 TYR H 43 PHE 0.007 0.001 PHE H 90 TRP 0.009 0.001 TRP A 454 HIS 0.015 0.001 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (11782) covalent geometry : angle 0.48294 / 0.25 (15917) hydrogen bonds : bond 0.04847 / 3.12 ( 614) hydrogen bonds : angle 4.35994 / 3.11 ( 1811) metal coordination : bond 0.01425 / 0.70 ( 4) metal coordination : angle 4.06594 / 2.06 ( 6) Misc. bond : bond 0.00024 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.9005 (tt0) cc_final: 0.8785 (tm-30) REVERT: A 164 ARG cc_start: 0.8034 (mtm180) cc_final: 0.7540 (mtt180) REVERT: A 324 LYS cc_start: 0.8758 (tttp) cc_final: 0.8419 (ttpp) REVERT: A 327 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7938 (mt-10) REVERT: A 364 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7481 (tm-30) REVERT: A 416 GLU cc_start: 0.8665 (tt0) cc_final: 0.8435 (tt0) REVERT: B 42 GLU cc_start: 0.8101 (pt0) cc_final: 0.7625 (pt0) REVERT: B 44 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8111 (mtpp) REVERT: D 37 LYS cc_start: 0.7314 (tttt) cc_final: 0.6771 (ttpt) REVERT: I 102 VAL cc_start: 0.7172 (OUTLIER) cc_final: 0.6898 (p) REVERT: I 134 GLU cc_start: 0.7326 (tt0) cc_final: 0.6953 (tt0) REVERT: E 226 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8133 (mppt) REVERT: E 273 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8098 (tmt-80) REVERT: E 316 GLU cc_start: 0.8209 (tt0) cc_final: 0.7471 (mp0) REVERT: E 327 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7708 (mt-10) REVERT: E 364 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: E 399 GLU cc_start: 0.4195 (OUTLIER) cc_final: 0.3742 (tt0) REVERT: E 417 GLU cc_start: 0.8289 (tt0) cc_final: 0.7834 (mp0) REVERT: F 58 LYS cc_start: 0.8236 (tptt) cc_final: 0.7703 (ttmt) REVERT: F 60 LYS cc_start: 0.8618 (mttp) cc_final: 0.8399 (mttt) outliers start: 16 outliers final: 5 residues processed: 150 average time/residue: 0.7195 time to fit residues: 115.5985 Evaluate side-chains 151 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain G residue 28 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 HIS F 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.170773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.107619 restraints weight = 49637.909| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.91 r_work: 0.3131 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11788 Z= 0.193 Angle : 0.570 8.196 15923 Z= 0.300 Chirality : 0.045 0.171 1802 Planarity : 0.004 0.042 2061 Dihedral : 10.082 154.950 1682 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.19 % Allowed : 17.26 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 1.48 (0.23), residues: 1462 helix: 1.67 (0.19), residues: 792 sheet: 0.67 (0.39), residues: 198 loop : 0.05 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 145 TYR 0.017 0.002 TYR H 43 PHE 0.011 0.002 PHE E 141 TRP 0.015 0.002 TRP E 440 HIS 0.010 0.002 HIS F 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 (11782) covalent geometry : angle 0.56415 / 0.30 (15917) hydrogen bonds : bond 0.06007 / 3.89 ( 614) hydrogen bonds : angle 4.62625 / 3.31 ( 1811) metal coordination : bond 0.01840 / 0.89 ( 4) metal coordination : angle 4.14900 / 2.06 ( 6) Misc. bond : bond 0.00048 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.9054 (tt0) cc_final: 0.8838 (tm-30) REVERT: A 164 ARG cc_start: 0.8089 (mtm180) cc_final: 0.7566 (mtt180) REVERT: A 324 LYS cc_start: 0.8820 (tttp) cc_final: 0.8452 (ttpp) REVERT: A 327 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.8006 (mt-10) REVERT: A 364 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7431 (tm-30) REVERT: A 416 GLU cc_start: 0.8699 (tt0) cc_final: 0.8456 (tt0) REVERT: B 44 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8163 (mtpp) REVERT: D 37 LYS cc_start: 0.7469 (tttt) cc_final: 0.6951 (ttpt) REVERT: D 144 ASP cc_start: 0.8121 (m-30) cc_final: 0.7772 (m-30) REVERT: I 102 VAL cc_start: 0.7094 (OUTLIER) cc_final: 0.6807 (p) REVERT: I 134 GLU cc_start: 0.7426 (tt0) cc_final: 0.7043 (tt0) REVERT: E 273 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8150 (tmt-80) REVERT: E 316 GLU cc_start: 0.8360 (tt0) cc_final: 0.7521 (mp0) REVERT: E 327 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7724 (mt-10) REVERT: E 364 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: E 399 GLU cc_start: 0.4247 (OUTLIER) cc_final: 0.3733 (tm-30) REVERT: E 417 GLU cc_start: 0.8449 (tt0) cc_final: 0.7906 (mp0) REVERT: E 441 GLU cc_start: 0.8411 (tt0) cc_final: 0.8194 (tt0) REVERT: F 58 LYS cc_start: 0.8293 (tptt) cc_final: 0.7732 (ttmt) outliers start: 15 outliers final: 5 residues processed: 156 average time/residue: 0.6943 time to fit residues: 116.3496 Evaluate side-chains 160 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain G residue 28 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 23 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 125 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 74 GLN F 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.172005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.109062 restraints weight = 52227.434| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.95 r_work: 0.3152 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11788 Z= 0.150 Angle : 0.525 8.100 15923 Z= 0.276 Chirality : 0.043 0.172 1802 Planarity : 0.004 0.030 2061 Dihedral : 9.750 151.899 1682 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.27 % Allowed : 17.34 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 1.55 (0.23), residues: 1462 helix: 1.74 (0.19), residues: 791 sheet: 0.70 (0.39), residues: 198 loop : 0.08 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 145 TYR 0.017 0.002 TYR H 43 PHE 0.008 0.002 PHE E 141 TRP 0.011 0.002 TRP A 454 HIS 0.017 0.001 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (11782) covalent geometry : angle 0.51907 / 0.28 (15917) hydrogen bonds : bond 0.05317 / 3.43 ( 614) hydrogen bonds : angle 4.50059 / 3.22 ( 1811) metal coordination : bond 0.01656 / 0.81 ( 4) metal coordination : angle 4.18787 / 2.13 ( 6) Misc. bond : bond 0.00026 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8853 (tt0) cc_final: 0.8630 (tm-30) REVERT: A 164 ARG cc_start: 0.7845 (mtm180) cc_final: 0.7421 (mtt180) REVERT: A 324 LYS cc_start: 0.8648 (tttp) cc_final: 0.8320 (ttpp) REVERT: A 327 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7703 (mt-10) REVERT: A 364 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: A 416 GLU cc_start: 0.8457 (tt0) cc_final: 0.8196 (tt0) REVERT: B 44 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8066 (mtpp) REVERT: D 37 LYS cc_start: 0.7360 (tttt) cc_final: 0.6792 (ttpt) REVERT: D 144 ASP cc_start: 0.8055 (m-30) cc_final: 0.7681 (m-30) REVERT: I 102 VAL cc_start: 0.7066 (OUTLIER) cc_final: 0.6777 (p) REVERT: I 134 GLU cc_start: 0.7162 (tt0) cc_final: 0.6796 (tt0) REVERT: E 273 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7758 (tpp-160) REVERT: E 316 GLU cc_start: 0.8066 (tt0) cc_final: 0.7383 (mp0) REVERT: E 327 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7429 (mt-10) REVERT: E 364 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7618 (tm-30) REVERT: E 399 GLU cc_start: 0.4291 (OUTLIER) cc_final: 0.3764 (tm-30) REVERT: E 417 GLU cc_start: 0.8181 (tt0) cc_final: 0.7806 (mp0) REVERT: F 58 LYS cc_start: 0.8171 (tptt) cc_final: 0.7676 (ttmt) outliers start: 16 outliers final: 5 residues processed: 157 average time/residue: 0.6885 time to fit residues: 115.9785 Evaluate side-chains 161 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain G residue 28 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 74 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 24 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.174931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.112716 restraints weight = 47109.590| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.85 r_work: 0.3243 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11788 Z= 0.103 Angle : 0.464 8.831 15923 Z= 0.242 Chirality : 0.041 0.164 1802 Planarity : 0.003 0.031 2061 Dihedral : 9.008 144.128 1682 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.03 % Allowed : 17.50 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 1.81 (0.23), residues: 1462 helix: 1.95 (0.19), residues: 791 sheet: 0.84 (0.40), residues: 198 loop : 0.16 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 145 TYR 0.016 0.001 TYR H 43 PHE 0.008 0.001 PHE H 90 TRP 0.012 0.001 TRP A 454 HIS 0.014 0.001 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (11782) covalent geometry : angle 0.45656 / 0.24 (15917) hydrogen bonds : bond 0.04371 / 2.81 ( 614) hydrogen bonds : angle 4.29872 / 3.07 ( 1811) metal coordination : bond 0.01310 / 0.64 ( 4) metal coordination : angle 4.37573 / 2.28 ( 6) Misc. bond : bond 0.00009 / 0.00 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8784 (tt0) cc_final: 0.8550 (tm-30) REVERT: A 164 ARG cc_start: 0.7768 (mtm180) cc_final: 0.7376 (mtt180) REVERT: A 324 LYS cc_start: 0.8594 (tttp) cc_final: 0.8287 (ttpp) REVERT: A 364 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7269 (tm-30) REVERT: A 416 GLU cc_start: 0.8407 (tt0) cc_final: 0.8183 (tt0) REVERT: B 42 GLU cc_start: 0.7863 (pt0) cc_final: 0.7425 (pt0) REVERT: B 44 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7998 (mtpp) REVERT: D 37 LYS cc_start: 0.7282 (tttt) cc_final: 0.6722 (ttpt) REVERT: D 144 ASP cc_start: 0.7969 (m-30) cc_final: 0.7620 (m-30) REVERT: I 102 VAL cc_start: 0.7027 (OUTLIER) cc_final: 0.6745 (p) REVERT: I 134 GLU cc_start: 0.7144 (tt0) cc_final: 0.6789 (tt0) REVERT: E 145 ARG cc_start: 0.7865 (mtp-110) cc_final: 0.7648 (mtm-85) REVERT: E 226 LYS cc_start: 0.8500 (mtpp) cc_final: 0.8069 (mppt) REVERT: E 273 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7711 (tpp-160) REVERT: E 316 GLU cc_start: 0.7966 (tt0) cc_final: 0.7334 (mp0) REVERT: E 327 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7410 (mt-10) REVERT: E 364 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7524 (tm-30) REVERT: E 399 GLU cc_start: 0.4218 (OUTLIER) cc_final: 0.3811 (tt0) REVERT: E 417 GLU cc_start: 0.8017 (tt0) cc_final: 0.7713 (mp0) REVERT: F 58 LYS cc_start: 0.8129 (tptt) cc_final: 0.7664 (ttmt) outliers start: 13 outliers final: 5 residues processed: 148 average time/residue: 0.7361 time to fit residues: 116.5902 Evaluate side-chains 155 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain G residue 28 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 22 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 134 optimal weight: 0.0370 chunk 40 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 0.0670 chunk 110 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.176969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.114795 restraints weight = 57219.067| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.09 r_work: 0.3273 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11788 Z= 0.093 Angle : 0.451 9.035 15923 Z= 0.233 Chirality : 0.040 0.154 1802 Planarity : 0.003 0.031 2061 Dihedral : 8.227 131.194 1682 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.88 % Allowed : 17.98 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 1.94 (0.23), residues: 1462 helix: 2.05 (0.19), residues: 794 sheet: 0.94 (0.40), residues: 198 loop : 0.21 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 434 TYR 0.015 0.001 TYR H 43 PHE 0.008 0.001 PHE H 90 TRP 0.011 0.001 TRP A 454 HIS 0.013 0.001 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.09 (11782) covalent geometry : angle 0.44245 / 0.23 (15917) hydrogen bonds : bond 0.03954 / 2.54 ( 614) hydrogen bonds : angle 4.18480 / 2.99 ( 1811) metal coordination : bond 0.01132 / 0.56 ( 4) metal coordination : angle 4.47769 / 2.34 ( 6) Misc. bond : bond 0.00009 / 0.00 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5255.64 seconds wall clock time: 90 minutes 12.70 seconds (5412.70 seconds total)