Starting phenix.real_space_refine on Wed May 14 08:15:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rmg_19361/05_2025/8rmg_19361.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rmg_19361/05_2025/8rmg_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8rmg_19361/05_2025/8rmg_19361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rmg_19361/05_2025/8rmg_19361.map" model { file = "/net/cci-nas-00/data/ceres_data/8rmg_19361/05_2025/8rmg_19361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rmg_19361/05_2025/8rmg_19361.cif" } resolution = 2.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.045 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 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, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 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: 10.99, per 1000 atoms: 0.93 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: 3.03 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 1.27 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: 3.94 Time building geometry restraints manager: 3.45 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 158 or resid 201)) selection = (chain 'H' and (resid 36 through 158 or resid 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 37.470 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.036 0.002 TRP A 454 HIS 0.007 0.001 HIS F 71 PHE 0.010 0.001 PHE H 90 TYR 0.016 0.002 TYR D 43 ARG 0.011 0.001 ARG E 432 Details of bonding type rmsd hydrogen bonds : bond 0.13914 ( 614) hydrogen bonds : angle 5.57835 ( 1811) metal coordination : bond 0.01754 ( 4) metal coordination : angle 10.88667 ( 6) covalent geometry : bond 0.00514 (11782) covalent geometry : angle 0.80441 (15917) Misc. bond : bond 0.00016 ( 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 : 1.194 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: 0.7454 (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: 1.6059 time to fit residues: 338.1874 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 : 1.323 ------------------------------------------------------------------------------- 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 121 optimal weight: 0.4980 chunk 109 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 58 optimal weight: 0.0370 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN B 74 GLN D 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.179396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.116305 restraints weight = 55722.895| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.12 r_work: 0.3272 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 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 = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11788 Z= 0.109 Angle : 0.490 5.762 15923 Z= 0.258 Chirality : 0.041 0.142 1802 Planarity : 0.004 0.037 2061 Dihedral : 11.100 179.929 1700 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.35 % Allowed : 15.99 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.23), residues: 1462 helix: 1.58 (0.19), residues: 794 sheet: 0.80 (0.39), residues: 196 loop : -0.09 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 454 HIS 0.013 0.001 HIS B 71 PHE 0.010 0.001 PHE D 93 TYR 0.015 0.002 TYR D 43 ARG 0.004 0.000 ARG A 289 Details of bonding type rmsd hydrogen bonds : bond 0.04580 ( 614) hydrogen bonds : angle 4.52107 ( 1811) metal coordination : bond 0.01860 ( 4) metal coordination : angle 3.75042 ( 6) covalent geometry : bond 0.00222 (11782) covalent geometry : angle 0.48420 (15917) Misc. bond : bond 0.00008 ( 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 178 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8776 (tt0) cc_final: 0.8521 (tm-30) REVERT: A 164 ARG cc_start: 0.7746 (mtm180) cc_final: 0.7364 (mtt180) REVERT: A 324 LYS cc_start: 0.8613 (tttp) cc_final: 0.8254 (ttpp) REVERT: A 364 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7069 (tm-30) REVERT: A 416 GLU cc_start: 0.8388 (tt0) cc_final: 0.8140 (tt0) REVERT: B 41 ARG cc_start: 0.8544 (mtt90) cc_final: 0.8311 (mtt90) REVERT: C 14 GLU cc_start: 0.6551 (mt-10) cc_final: 0.6348 (mp0) REVERT: C 54 GLU cc_start: 0.6499 (mm-30) cc_final: 0.5292 (tm-30) REVERT: D 37 LYS cc_start: 0.7349 (tttt) cc_final: 0.6880 (ttpt) REVERT: D 121 LYS cc_start: 0.7501 (mmmt) cc_final: 0.7074 (mppt) REVERT: I 102 VAL cc_start: 0.7198 (OUTLIER) cc_final: 0.6906 (p) REVERT: I 134 GLU cc_start: 0.7024 (tt0) cc_final: 0.6705 (tt0) REVERT: E 145 ARG cc_start: 0.8045 (mtp-110) cc_final: 0.7784 (mtm-85) REVERT: E 417 GLU cc_start: 0.8125 (tt0) cc_final: 0.7750 (mp0) REVERT: E 432 ARG cc_start: 0.7767 (ttm-80) cc_final: 0.7476 (ttm170) REVERT: E 441 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7197 (tt0) REVERT: F 58 LYS cc_start: 0.8009 (tptt) cc_final: 0.7496 (ttmt) REVERT: H 140 MET cc_start: 0.7248 (mtt) cc_final: 0.6772 (mmt) outliers start: 16 outliers final: 5 residues processed: 172 average time/residue: 1.6614 time to fit residues: 303.7348 Evaluate side-chains 155 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU 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 327 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 46 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 97 optimal weight: 0.0470 chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.177643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.114647 restraints weight = 59168.311| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.15 r_work: 0.3275 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 11788 Z= 0.103 Angle : 0.466 11.171 15923 Z= 0.242 Chirality : 0.041 0.141 1802 Planarity : 0.003 0.037 2061 Dihedral : 9.649 171.889 1683 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.27 % Allowed : 16.79 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.23), residues: 1462 helix: 1.78 (0.19), residues: 793 sheet: 0.80 (0.40), residues: 196 loop : 0.10 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 454 HIS 0.008 0.001 HIS F 71 PHE 0.009 0.001 PHE F 23 TYR 0.013 0.001 TYR H 43 ARG 0.002 0.000 ARG E 272 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 614) hydrogen bonds : angle 4.32949 ( 1811) metal coordination : bond 0.01192 ( 4) metal coordination : angle 3.51993 ( 6) covalent geometry : bond 0.00206 (11782) covalent geometry : angle 0.46098 (15917) Misc. bond : bond 0.00002 ( 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 163 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8802 (tt0) cc_final: 0.8571 (tm-30) REVERT: A 164 ARG cc_start: 0.7749 (mtm180) cc_final: 0.7410 (mtt180) REVERT: A 324 LYS cc_start: 0.8633 (tttp) cc_final: 0.8298 (ttpp) REVERT: A 364 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7114 (tm-30) REVERT: A 372 ASP cc_start: 0.8486 (p0) cc_final: 0.8240 (p0) REVERT: A 416 GLU cc_start: 0.8399 (tt0) cc_final: 0.8172 (tt0) REVERT: C 14 GLU cc_start: 0.6458 (mt-10) cc_final: 0.6213 (mp0) REVERT: C 54 GLU cc_start: 0.6601 (mm-30) cc_final: 0.5261 (tm-30) REVERT: D 37 LYS cc_start: 0.7393 (tttt) cc_final: 0.6947 (ttpt) REVERT: D 121 LYS cc_start: 0.7515 (mmmt) cc_final: 0.7091 (mppt) REVERT: D 144 ASP cc_start: 0.8112 (m-30) cc_final: 0.7699 (m-30) REVERT: I 134 GLU cc_start: 0.7095 (tt0) cc_final: 0.6822 (tt0) REVERT: E 100 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8224 (tt0) REVERT: E 145 ARG cc_start: 0.8068 (mtp-110) cc_final: 0.7500 (mtm110) REVERT: E 327 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: E 417 GLU cc_start: 0.8103 (tt0) cc_final: 0.7807 (mp0) REVERT: E 432 ARG cc_start: 0.7812 (ttm-80) cc_final: 0.7514 (ttm170) REVERT: F 58 LYS cc_start: 0.8102 (tptt) cc_final: 0.7616 (ttmt) REVERT: H 140 MET cc_start: 0.7282 (mtt) cc_final: 0.6845 (mmt) outliers start: 16 outliers final: 3 residues processed: 157 average time/residue: 1.7129 time to fit residues: 286.0570 Evaluate side-chains 145 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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 100 GLU Chi-restraints excluded: chain E residue 327 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 105 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 429 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.172804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.110256 restraints weight = 39634.535| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.67 r_work: 0.3212 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11788 Z= 0.155 Angle : 0.528 9.620 15923 Z= 0.277 Chirality : 0.043 0.158 1802 Planarity : 0.004 0.036 2061 Dihedral : 10.210 168.205 1682 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.59 % Allowed : 16.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.23), residues: 1462 helix: 1.74 (0.19), residues: 792 sheet: 0.74 (0.40), residues: 198 loop : 0.06 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 440 HIS 0.017 0.002 HIS B 71 PHE 0.009 0.002 PHE E 141 TYR 0.016 0.002 TYR H 43 ARG 0.004 0.001 ARG E 272 Details of bonding type rmsd hydrogen bonds : bond 0.05424 ( 614) hydrogen bonds : angle 4.49901 ( 1811) metal coordination : bond 0.01608 ( 4) metal coordination : angle 3.67957 ( 6) covalent geometry : bond 0.00354 (11782) covalent geometry : angle 0.52366 (15917) Misc. bond : bond 0.00037 ( 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 168 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.9004 (tt0) cc_final: 0.8786 (tm-30) REVERT: A 164 ARG cc_start: 0.8077 (mtm180) cc_final: 0.7599 (mtt180) REVERT: A 316 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6725 (mp0) REVERT: A 324 LYS cc_start: 0.8763 (tttp) cc_final: 0.8418 (ttpp) REVERT: A 364 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7367 (tm-30) REVERT: A 372 ASP cc_start: 0.8708 (p0) cc_final: 0.8489 (p0) REVERT: A 416 GLU cc_start: 0.8677 (tt0) cc_final: 0.8439 (tt0) REVERT: D 37 LYS cc_start: 0.7376 (tttt) cc_final: 0.6833 (ttpp) REVERT: D 121 LYS cc_start: 0.7591 (mmmt) cc_final: 0.7126 (mppt) REVERT: I 134 GLU cc_start: 0.7329 (tt0) cc_final: 0.6948 (tt0) REVERT: E 273 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7900 (tmt-80) REVERT: E 316 GLU cc_start: 0.8259 (tt0) cc_final: 0.7490 (mp0) REVERT: E 327 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7644 (mt-10) REVERT: E 364 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: E 399 GLU cc_start: 0.4037 (OUTLIER) cc_final: 0.3569 (tt0) REVERT: E 417 GLU cc_start: 0.8296 (tt0) cc_final: 0.7846 (mp0) REVERT: E 432 ARG cc_start: 0.8163 (ttm-80) cc_final: 0.7957 (ttm170) REVERT: F 58 LYS cc_start: 0.8262 (tptt) cc_final: 0.7723 (ttmt) REVERT: H 127 LYS cc_start: 0.6558 (mtmm) cc_final: 0.6343 (mtmt) outliers start: 20 outliers final: 6 residues processed: 158 average time/residue: 1.5300 time to fit residues: 258.1814 Evaluate side-chains 152 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 42 GLU 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 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 16 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 118 optimal weight: 0.0670 chunk 8 optimal weight: 0.0060 chunk 142 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 overall best weight: 1.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 74 GLN ** 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 = 0.4080 r_free = 0.4080 target = 0.173924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110634 restraints weight = 55959.800| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.05 r_work: 0.3206 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11788 Z= 0.130 Angle : 0.486 8.074 15923 Z= 0.255 Chirality : 0.042 0.150 1802 Planarity : 0.004 0.032 2061 Dihedral : 9.819 159.641 1682 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.19 % Allowed : 17.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.23), residues: 1462 helix: 1.79 (0.19), residues: 791 sheet: 0.73 (0.40), residues: 198 loop : 0.07 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 454 HIS 0.008 0.001 HIS F 71 PHE 0.009 0.001 PHE F 23 TYR 0.016 0.002 TYR H 43 ARG 0.004 0.000 ARG E 145 Details of bonding type rmsd hydrogen bonds : bond 0.04937 ( 614) hydrogen bonds : angle 4.41809 ( 1811) metal coordination : bond 0.01499 ( 4) metal coordination : angle 3.65327 ( 6) covalent geometry : bond 0.00288 (11782) covalent geometry : angle 0.48057 (15917) Misc. bond : bond 0.00027 ( 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 164 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8841 (tt0) cc_final: 0.8625 (tm-30) REVERT: A 164 ARG cc_start: 0.7907 (mtm180) cc_final: 0.7503 (mtt180) REVERT: A 324 LYS cc_start: 0.8645 (tttp) cc_final: 0.8350 (ttpp) REVERT: A 364 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7227 (tm-30) REVERT: A 372 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8399 (p0) REVERT: A 416 GLU cc_start: 0.8423 (tt0) cc_final: 0.8185 (tt0) REVERT: C 14 GLU cc_start: 0.6442 (mt-10) cc_final: 0.6135 (mp0) REVERT: C 54 GLU cc_start: 0.6620 (mm-30) cc_final: 0.5270 (tm-30) REVERT: D 37 LYS cc_start: 0.7372 (tttt) cc_final: 0.6844 (ttpt) REVERT: D 121 LYS cc_start: 0.7615 (mmmt) cc_final: 0.7140 (mppt) REVERT: D 144 ASP cc_start: 0.8039 (m-30) cc_final: 0.7642 (m-30) REVERT: I 134 GLU cc_start: 0.7229 (tt0) cc_final: 0.6949 (tt0) REVERT: E 100 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8164 (tm-30) REVERT: E 316 GLU cc_start: 0.8084 (tt0) cc_final: 0.7406 (mp0) REVERT: E 327 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7425 (mt-10) REVERT: E 364 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7498 (tm-30) REVERT: E 399 GLU cc_start: 0.4157 (OUTLIER) cc_final: 0.3763 (tt0) REVERT: E 417 GLU cc_start: 0.8067 (tt0) cc_final: 0.7773 (mp0) REVERT: E 441 GLU cc_start: 0.8368 (tt0) cc_final: 0.8114 (tt0) REVERT: F 58 LYS cc_start: 0.8166 (tptt) cc_final: 0.7679 (ttmt) REVERT: H 127 LYS cc_start: 0.6552 (mtmm) cc_final: 0.6330 (mtmt) outliers start: 15 outliers final: 6 residues processed: 157 average time/residue: 1.5726 time to fit residues: 263.2438 Evaluate side-chains 147 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain B residue 21 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 F residue 42 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 53 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 HIS D 42 HIS E 93 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.169829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.106444 restraints weight = 54337.278| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.00 r_work: 0.3106 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 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 = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 11788 Z= 0.233 Angle : 0.609 8.666 15923 Z= 0.321 Chirality : 0.047 0.192 1802 Planarity : 0.005 0.052 2061 Dihedral : 10.666 162.793 1682 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.91 % Allowed : 16.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.22), residues: 1462 helix: 1.52 (0.19), residues: 790 sheet: 0.56 (0.39), residues: 198 loop : -0.03 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP E 440 HIS 0.021 0.002 HIS B 71 PHE 0.013 0.002 PHE E 141 TYR 0.020 0.003 TYR E 80 ARG 0.005 0.001 ARG F 34 Details of bonding type rmsd hydrogen bonds : bond 0.06430 ( 614) hydrogen bonds : angle 4.72587 ( 1811) metal coordination : bond 0.02139 ( 4) metal coordination : angle 4.04520 ( 6) covalent geometry : bond 0.00560 (11782) covalent geometry : angle 0.60371 (15917) Misc. bond : bond 0.00056 ( 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 172 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8898 (tt0) cc_final: 0.8668 (tm-30) REVERT: A 164 ARG cc_start: 0.7947 (mtm180) cc_final: 0.7514 (mtt180) REVERT: A 316 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6634 (mp0) REVERT: A 324 LYS cc_start: 0.8721 (tttp) cc_final: 0.8369 (ttpp) REVERT: A 327 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7749 (mt-10) REVERT: A 364 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7232 (tm-30) REVERT: A 372 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8408 (p0) REVERT: A 416 GLU cc_start: 0.8504 (tt0) cc_final: 0.8224 (tt0) REVERT: D 37 LYS cc_start: 0.7517 (tttt) cc_final: 0.7003 (ttpt) REVERT: I 134 GLU cc_start: 0.7259 (tt0) cc_final: 0.6945 (tt0) REVERT: E 273 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7874 (tmt-80) REVERT: E 316 GLU cc_start: 0.8254 (tt0) cc_final: 0.7508 (mp0) REVERT: E 327 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7423 (mt-10) REVERT: E 364 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7566 (tm-30) REVERT: E 399 GLU cc_start: 0.4488 (OUTLIER) cc_final: 0.4033 (tm-30) REVERT: E 417 GLU cc_start: 0.8248 (tt0) cc_final: 0.7831 (mp0) REVERT: E 441 GLU cc_start: 0.8312 (tt0) cc_final: 0.8080 (tt0) REVERT: F 58 LYS cc_start: 0.8230 (tptt) cc_final: 0.7707 (ttmt) outliers start: 24 outliers final: 6 residues processed: 157 average time/residue: 1.4698 time to fit residues: 247.3932 Evaluate side-chains 155 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 372 ASP 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 F residue 42 GLU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 147 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 79 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 38 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN E 429 HIS F 8 GLN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.173714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.110819 restraints weight = 56472.904| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.06 r_work: 0.3210 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 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 = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2135 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= 0.113 Angle : 0.486 8.184 15923 Z= 0.254 Chirality : 0.041 0.203 1802 Planarity : 0.003 0.031 2061 Dihedral : 9.789 155.356 1682 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.95 % Allowed : 17.82 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.23), residues: 1462 helix: 1.78 (0.19), residues: 793 sheet: 0.66 (0.40), residues: 198 loop : 0.09 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 454 HIS 0.019 0.001 HIS B 71 PHE 0.007 0.001 PHE H 90 TYR 0.017 0.002 TYR H 43 ARG 0.004 0.000 ARG E 143 Details of bonding type rmsd hydrogen bonds : bond 0.04732 ( 614) hydrogen bonds : angle 4.40165 ( 1811) metal coordination : bond 0.01518 ( 4) metal coordination : angle 4.09646 ( 6) covalent geometry : bond 0.00241 (11782) covalent geometry : angle 0.47948 (15917) Misc. bond : bond 0.00012 ( 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 155 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8824 (tt0) cc_final: 0.8615 (tm-30) REVERT: A 164 ARG cc_start: 0.7805 (mtm180) cc_final: 0.7395 (mtt180) REVERT: A 324 LYS cc_start: 0.8621 (tttp) cc_final: 0.8299 (ttpp) REVERT: A 327 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7753 (mt-10) REVERT: A 364 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7283 (tm-30) REVERT: A 416 GLU cc_start: 0.8407 (tt0) cc_final: 0.8154 (tt0) REVERT: C 14 GLU cc_start: 0.6441 (mt-10) cc_final: 0.6097 (mp0) REVERT: D 37 LYS cc_start: 0.7326 (tttt) cc_final: 0.6755 (ttpt) REVERT: I 134 GLU cc_start: 0.7243 (tt0) cc_final: 0.6820 (tt0) REVERT: I 148 GLU cc_start: 0.7722 (pt0) cc_final: 0.7410 (pt0) REVERT: E 145 ARG cc_start: 0.7849 (mtp-110) cc_final: 0.7614 (mtm110) REVERT: E 273 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7758 (tpp-160) REVERT: E 316 GLU cc_start: 0.8054 (tt0) cc_final: 0.7369 (mp0) REVERT: E 327 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: E 364 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7506 (tm-30) REVERT: E 399 GLU cc_start: 0.4279 (OUTLIER) cc_final: 0.3847 (tm-30) REVERT: E 417 GLU cc_start: 0.8082 (tt0) cc_final: 0.7788 (mp0) REVERT: F 58 LYS cc_start: 0.8153 (tptt) cc_final: 0.7668 (ttmt) REVERT: H 103 SER cc_start: 0.7466 (t) cc_final: 0.7154 (p) REVERT: H 127 LYS cc_start: 0.6620 (mtmm) cc_final: 0.6395 (mtmt) outliers start: 12 outliers final: 4 residues processed: 149 average time/residue: 1.4566 time to fit residues: 233.1163 Evaluate side-chains 146 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 37 SER 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 F residue 42 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 78 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** 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 = 0.4055 r_free = 0.4055 target = 0.171636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.108431 restraints weight = 55268.142| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.03 r_work: 0.3135 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 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 = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11788 Z= 0.161 Angle : 0.532 8.065 15923 Z= 0.280 Chirality : 0.044 0.194 1802 Planarity : 0.004 0.031 2061 Dihedral : 9.996 154.688 1682 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.23), residues: 1462 helix: 1.72 (0.19), residues: 793 sheet: 0.65 (0.40), residues: 198 loop : 0.07 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 454 HIS 0.017 0.001 HIS B 71 PHE 0.008 0.002 PHE E 141 TYR 0.017 0.002 TYR H 43 ARG 0.003 0.000 ARG E 143 Details of bonding type rmsd hydrogen bonds : bond 0.05490 ( 614) hydrogen bonds : angle 4.52203 ( 1811) metal coordination : bond 0.01722 ( 4) metal coordination : angle 4.05894 ( 6) covalent geometry : bond 0.00375 (11782) covalent geometry : angle 0.52642 (15917) Misc. bond : bond 0.00031 ( 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 158 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8861 (tt0) cc_final: 0.8637 (tm-30) REVERT: A 164 ARG cc_start: 0.7870 (mtm180) cc_final: 0.7437 (mtt180) REVERT: A 324 LYS cc_start: 0.8687 (tttp) cc_final: 0.8365 (ttpp) REVERT: A 327 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7775 (mt-10) REVERT: A 364 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7270 (tm-30) REVERT: A 416 GLU cc_start: 0.8454 (tt0) cc_final: 0.8187 (tt0) REVERT: C 14 GLU cc_start: 0.6513 (mt-10) cc_final: 0.6163 (mp0) REVERT: D 37 LYS cc_start: 0.7363 (tttt) cc_final: 0.6802 (ttpt) REVERT: D 144 ASP cc_start: 0.8046 (m-30) cc_final: 0.7701 (m-30) REVERT: I 134 GLU cc_start: 0.7211 (tt0) cc_final: 0.6834 (tt0) REVERT: E 273 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7787 (tpp-160) REVERT: E 316 GLU cc_start: 0.8133 (tt0) cc_final: 0.7399 (mp0) REVERT: E 327 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7442 (mt-10) REVERT: E 364 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7494 (tm-30) REVERT: E 399 GLU cc_start: 0.4322 (OUTLIER) cc_final: 0.3854 (tm-30) REVERT: E 417 GLU cc_start: 0.8092 (tt0) cc_final: 0.7762 (mp0) REVERT: F 58 LYS cc_start: 0.8190 (tptt) cc_final: 0.7683 (ttmt) REVERT: H 127 LYS cc_start: 0.6569 (mtmm) cc_final: 0.6359 (mtmt) outliers start: 16 outliers final: 5 residues processed: 150 average time/residue: 1.4491 time to fit residues: 233.2938 Evaluate side-chains 152 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain I residue 129 LEU 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 F residue 42 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 101 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 90 optimal weight: 0.0370 chunk 69 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.174084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111191 restraints weight = 53364.609| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.01 r_work: 0.3187 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 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 = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2232 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= 0.112 Angle : 0.476 8.764 15923 Z= 0.249 Chirality : 0.041 0.185 1802 Planarity : 0.003 0.031 2061 Dihedral : 9.343 148.356 1682 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.23), residues: 1462 helix: 1.86 (0.19), residues: 792 sheet: 0.74 (0.40), residues: 198 loop : 0.14 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 454 HIS 0.015 0.001 HIS B 71 PHE 0.007 0.001 PHE H 90 TYR 0.016 0.002 TYR H 43 ARG 0.005 0.000 ARG E 145 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 614) hydrogen bonds : angle 4.32366 ( 1811) metal coordination : bond 0.01382 ( 4) metal coordination : angle 4.29672 ( 6) covalent geometry : bond 0.00243 (11782) covalent geometry : angle 0.46897 (15917) Misc. bond : bond 0.00015 ( 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 152 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8808 (tt0) cc_final: 0.8586 (tm-30) REVERT: A 164 ARG cc_start: 0.7806 (mtm180) cc_final: 0.7392 (mtt180) REVERT: A 324 LYS cc_start: 0.8627 (tttp) cc_final: 0.8293 (ttpp) REVERT: A 364 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7283 (tm-30) REVERT: A 416 GLU cc_start: 0.8435 (tt0) cc_final: 0.8189 (tt0) REVERT: D 37 LYS cc_start: 0.7311 (tttt) cc_final: 0.6736 (ttpt) REVERT: D 144 ASP cc_start: 0.8041 (m-30) cc_final: 0.7704 (m-30) REVERT: I 134 GLU cc_start: 0.7216 (tt0) cc_final: 0.6823 (tt0) REVERT: E 226 LYS cc_start: 0.8519 (mtpp) cc_final: 0.8074 (mppt) REVERT: E 273 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7745 (tpp-160) REVERT: E 316 GLU cc_start: 0.8021 (tt0) cc_final: 0.7355 (mp0) REVERT: E 327 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7450 (mt-10) REVERT: E 364 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7514 (tm-30) REVERT: E 399 GLU cc_start: 0.4207 (OUTLIER) cc_final: 0.3849 (tt0) REVERT: E 417 GLU cc_start: 0.8052 (tt0) cc_final: 0.7752 (mp0) REVERT: F 58 LYS cc_start: 0.8141 (tptt) cc_final: 0.7670 (ttmt) REVERT: H 103 SER cc_start: 0.7444 (t) cc_final: 0.7151 (p) REVERT: H 127 LYS cc_start: 0.6603 (mtmm) cc_final: 0.6394 (mtmt) outliers start: 11 outliers final: 4 residues processed: 146 average time/residue: 1.4511 time to fit residues: 227.2457 Evaluate side-chains 146 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain D residue 86 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 136 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 71 optimal weight: 0.0670 chunk 108 optimal weight: 0.0870 overall best weight: 0.9498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.174251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.111569 restraints weight = 51555.639| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.96 r_work: 0.3226 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 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 = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11788 Z= 0.112 Angle : 0.478 8.818 15923 Z= 0.249 Chirality : 0.041 0.177 1802 Planarity : 0.003 0.031 2061 Dihedral : 9.086 142.034 1682 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.80 % Allowed : 17.98 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.23), residues: 1462 helix: 1.89 (0.19), residues: 792 sheet: 0.77 (0.40), residues: 198 loop : 0.18 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 454 HIS 0.016 0.001 HIS B 71 PHE 0.007 0.001 PHE C 51 TYR 0.016 0.002 TYR H 43 ARG 0.005 0.000 ARG E 145 Details of bonding type rmsd hydrogen bonds : bond 0.04597 ( 614) hydrogen bonds : angle 4.30120 ( 1811) metal coordination : bond 0.01336 ( 4) metal coordination : angle 4.25814 ( 6) covalent geometry : bond 0.00241 (11782) covalent geometry : angle 0.47135 (15917) Misc. bond : bond 0.00012 ( 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 152 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8800 (tt0) cc_final: 0.8571 (tm-30) REVERT: A 164 ARG cc_start: 0.7805 (mtm180) cc_final: 0.7398 (mtt180) REVERT: A 324 LYS cc_start: 0.8628 (tttp) cc_final: 0.8316 (ttpp) REVERT: A 364 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7260 (tm-30) REVERT: A 416 GLU cc_start: 0.8429 (tt0) cc_final: 0.8195 (tt0) REVERT: D 37 LYS cc_start: 0.7317 (tttt) cc_final: 0.6773 (ttpt) REVERT: I 134 GLU cc_start: 0.7169 (tt0) cc_final: 0.6818 (tt0) REVERT: E 273 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7738 (tpp-160) REVERT: E 316 GLU cc_start: 0.7994 (tt0) cc_final: 0.7344 (mp0) REVERT: E 327 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: E 364 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7491 (tm-30) REVERT: E 399 GLU cc_start: 0.4245 (OUTLIER) cc_final: 0.3884 (tt0) REVERT: E 417 GLU cc_start: 0.8032 (tt0) cc_final: 0.7732 (mp0) REVERT: F 58 LYS cc_start: 0.8149 (tptt) cc_final: 0.7688 (ttmt) outliers start: 10 outliers final: 5 residues processed: 147 average time/residue: 1.4656 time to fit residues: 231.2036 Evaluate side-chains 147 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 86 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 95 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 79 optimal weight: 0.2980 chunk 100 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4094 r_free = 0.4094 target = 0.175194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.113166 restraints weight = 47585.196| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.88 r_work: 0.3229 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2349 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 : 0.467 9.020 15923 Z= 0.243 Chirality : 0.041 0.175 1802 Planarity : 0.003 0.031 2061 Dihedral : 8.685 135.634 1682 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.88 % Allowed : 17.82 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.23), residues: 1462 helix: 1.95 (0.19), residues: 792 sheet: 0.78 (0.40), residues: 198 loop : 0.22 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 454 HIS 0.015 0.001 HIS B 71 PHE 0.007 0.001 PHE H 90 TYR 0.016 0.001 TYR H 43 ARG 0.003 0.000 ARG E 143 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 614) hydrogen bonds : angle 4.23863 ( 1811) metal coordination : bond 0.01265 ( 4) metal coordination : angle 4.35101 ( 6) covalent geometry : bond 0.00216 (11782) covalent geometry : angle 0.45917 (15917) Misc. bond : bond 0.00009 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10560.92 seconds wall clock time: 181 minutes 59.45 seconds (10919.45 seconds total)