Starting phenix.real_space_refine on Tue Jun 10 10:27:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rmg_19361/06_2025/8rmg_19361.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rmg_19361/06_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_19361/06_2025/8rmg_19361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rmg_19361/06_2025/8rmg_19361.map" model { file = "/net/cci-nas-00/data/ceres_data/8rmg_19361/06_2025/8rmg_19361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rmg_19361/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 12.40, per 1000 atoms: 1.05 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: 3.39 Conformation dependent library (CDL) restraints added in 3.4 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: 1.43 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: 3.46 Time building geometry restraints manager: 3.82 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 40.690 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:16.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.560 ------------------------------------------------------------------------------- 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 : 1.264 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: 2.0614 time to fit residues: 434.0268 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 : 1.292 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.116311 restraints weight = 55722.906| |-----------------------------------------------------------------------------| 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 : 4.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8776 (tt0) cc_final: 0.8520 (tm-30) REVERT: A 164 ARG cc_start: 0.7742 (mtm180) cc_final: 0.7363 (mtt180) REVERT: A 324 LYS cc_start: 0.8614 (tttp) cc_final: 0.8256 (ttpp) REVERT: A 364 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7069 (tm-30) REVERT: A 416 GLU cc_start: 0.8383 (tt0) cc_final: 0.8135 (tt0) REVERT: B 41 ARG cc_start: 0.8543 (mtt90) cc_final: 0.8310 (mtt90) REVERT: C 14 GLU cc_start: 0.6551 (mt-10) cc_final: 0.6349 (mp0) REVERT: C 54 GLU cc_start: 0.6500 (mm-30) cc_final: 0.5293 (tm-30) REVERT: D 37 LYS cc_start: 0.7344 (tttt) cc_final: 0.6875 (ttpt) REVERT: D 121 LYS cc_start: 0.7500 (mmmt) cc_final: 0.7072 (mppt) REVERT: I 102 VAL cc_start: 0.7199 (OUTLIER) cc_final: 0.6907 (p) REVERT: I 134 GLU cc_start: 0.7022 (tt0) cc_final: 0.6703 (tt0) REVERT: E 145 ARG cc_start: 0.8045 (mtp-110) cc_final: 0.7785 (mtm-85) REVERT: E 417 GLU cc_start: 0.8128 (tt0) cc_final: 0.7752 (mp0) REVERT: E 432 ARG cc_start: 0.7763 (ttm-80) cc_final: 0.7473 (ttm170) REVERT: E 441 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7194 (tt0) REVERT: F 58 LYS cc_start: 0.8008 (tptt) cc_final: 0.7496 (ttmt) REVERT: H 140 MET cc_start: 0.7245 (mtt) cc_final: 0.6770 (mmt) outliers start: 16 outliers final: 5 residues processed: 172 average time/residue: 2.9636 time to fit residues: 544.1006 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 : 3.185 ------------------------------------------------------------------------------- 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: 0.8980 chunk 57 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 97 optimal weight: 0.0170 chunk 5 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN G 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.177166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.114052 restraints weight = 58753.345| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.14 r_work: 0.3263 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 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 = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11788 Z= 0.105 Angle : 0.474 11.557 15923 Z= 0.245 Chirality : 0.041 0.143 1802 Planarity : 0.003 0.035 2061 Dihedral : 9.696 171.791 1683 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.19 % Allowed : 16.79 % Favored : 82.02 % 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: 1.77 (0.19), residues: 793 sheet: 0.80 (0.40), residues: 196 loop : 0.11 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 454 HIS 0.005 0.001 HIS F 71 PHE 0.010 0.001 PHE F 23 TYR 0.013 0.002 TYR H 43 ARG 0.003 0.000 ARG E 272 Details of bonding type rmsd hydrogen bonds : bond 0.04470 ( 614) hydrogen bonds : angle 4.34393 ( 1811) metal coordination : bond 0.01290 ( 4) metal coordination : angle 3.49536 ( 6) covalent geometry : bond 0.00216 (11782) covalent geometry : angle 0.46912 (15917) Misc. bond : bond 0.00031 ( 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 164 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8808 (tt0) cc_final: 0.8582 (tm-30) REVERT: A 164 ARG cc_start: 0.7784 (mtm180) cc_final: 0.7432 (mtt180) REVERT: A 324 LYS cc_start: 0.8606 (tttp) cc_final: 0.8271 (ttpp) REVERT: A 364 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7130 (tm-30) REVERT: A 372 ASP cc_start: 0.8509 (p0) cc_final: 0.8261 (p0) REVERT: A 416 GLU cc_start: 0.8427 (tt0) cc_final: 0.8195 (tt0) REVERT: B 41 ARG cc_start: 0.8555 (mtt90) cc_final: 0.8301 (mtt90) REVERT: C 14 GLU cc_start: 0.6465 (mt-10) cc_final: 0.6236 (mp0) REVERT: C 54 GLU cc_start: 0.6604 (mm-30) cc_final: 0.5235 (tm-30) REVERT: D 37 LYS cc_start: 0.7439 (tttt) cc_final: 0.6955 (ttpt) REVERT: D 121 LYS cc_start: 0.7519 (mmmt) cc_final: 0.7095 (mppt) REVERT: D 144 ASP cc_start: 0.8078 (m-30) cc_final: 0.7662 (m-30) REVERT: I 134 GLU cc_start: 0.7104 (tt0) cc_final: 0.6826 (tt0) REVERT: E 100 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: E 145 ARG cc_start: 0.8072 (mtp-110) cc_final: 0.7501 (mtm110) REVERT: E 327 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7386 (mt-10) REVERT: E 417 GLU cc_start: 0.8119 (tt0) cc_final: 0.7817 (mp0) REVERT: E 432 ARG cc_start: 0.7845 (ttm-80) cc_final: 0.7545 (ttm170) REVERT: F 58 LYS cc_start: 0.8097 (tptt) cc_final: 0.7612 (ttmt) REVERT: H 140 MET cc_start: 0.7287 (mtt) cc_final: 0.6841 (mmt) outliers start: 15 outliers final: 4 residues processed: 158 average time/residue: 1.7834 time to fit residues: 299.2130 Evaluate side-chains 146 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 1.473 ------------------------------------------------------------------------------- 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 C residue 42 GLU 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: 10.0000 chunk 107 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.173318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110725 restraints weight = 39830.158| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.69 r_work: 0.3190 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11788 Z= 0.143 Angle : 0.514 9.259 15923 Z= 0.269 Chirality : 0.043 0.155 1802 Planarity : 0.004 0.032 2061 Dihedral : 10.067 166.689 1682 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.27 % Allowed : 17.26 % 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: 1.60 (0.23), residues: 1462 helix: 1.78 (0.19), residues: 792 sheet: 0.75 (0.40), residues: 198 loop : 0.08 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 440 HIS 0.017 0.002 HIS B 71 PHE 0.009 0.002 PHE E 123 TYR 0.016 0.002 TYR H 43 ARG 0.004 0.001 ARG E 272 Details of bonding type rmsd hydrogen bonds : bond 0.05226 ( 614) hydrogen bonds : angle 4.45499 ( 1811) metal coordination : bond 0.01541 ( 4) metal coordination : angle 3.64801 ( 6) covalent geometry : bond 0.00324 (11782) covalent geometry : angle 0.50878 (15917) Misc. bond : bond 0.00026 ( 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 169 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.9009 (tt0) cc_final: 0.8791 (tm-30) REVERT: A 164 ARG cc_start: 0.8080 (mtm180) cc_final: 0.7600 (mtt180) REVERT: A 324 LYS cc_start: 0.8766 (tttp) cc_final: 0.8418 (ttpp) REVERT: A 364 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7358 (tm-30) REVERT: A 372 ASP cc_start: 0.8713 (p0) cc_final: 0.8502 (p0) REVERT: A 416 GLU cc_start: 0.8651 (tt0) cc_final: 0.8424 (tt0) REVERT: C 14 GLU cc_start: 0.6531 (mt-10) cc_final: 0.6223 (mp0) REVERT: C 54 GLU cc_start: 0.6628 (mm-30) cc_final: 0.5259 (tm-30) REVERT: D 37 LYS cc_start: 0.7376 (tttt) cc_final: 0.6857 (ttpt) REVERT: D 121 LYS cc_start: 0.7584 (mmmt) cc_final: 0.7119 (mppt) REVERT: I 134 GLU cc_start: 0.7331 (tt0) cc_final: 0.6945 (tt0) REVERT: E 145 ARG cc_start: 0.8053 (mtp-110) cc_final: 0.7556 (mtm110) REVERT: E 273 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7939 (tmt-80) REVERT: E 316 GLU cc_start: 0.8239 (tt0) cc_final: 0.7480 (mp0) REVERT: E 327 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7659 (mt-10) REVERT: E 364 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7723 (tm-30) REVERT: E 399 GLU cc_start: 0.4044 (OUTLIER) cc_final: 0.3495 (tm-30) REVERT: E 417 GLU cc_start: 0.8298 (tt0) cc_final: 0.7861 (mp0) REVERT: E 432 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7944 (ttm170) REVERT: F 58 LYS cc_start: 0.8248 (tptt) cc_final: 0.7716 (ttmt) REVERT: H 127 LYS cc_start: 0.6536 (mtmm) cc_final: 0.6317 (mtmt) outliers start: 16 outliers final: 5 residues processed: 163 average time/residue: 1.6125 time to fit residues: 280.3047 Evaluate side-chains 150 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain I residue 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: 4.9990 chunk 44 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 142 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 HIS E 93 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.169912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.106476 restraints weight = 54663.446| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.99 r_work: 0.3107 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 11788 Z= 0.237 Angle : 0.611 7.934 15923 Z= 0.323 Chirality : 0.048 0.169 1802 Planarity : 0.005 0.060 2061 Dihedral : 10.761 165.093 1682 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.91 % Allowed : 16.23 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.24 (0.22), residues: 1462 helix: 1.49 (0.19), residues: 790 sheet: 0.56 (0.39), residues: 198 loop : -0.07 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP E 454 HIS 0.024 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 0.06471 ( 614) hydrogen bonds : angle 4.74100 ( 1811) metal coordination : bond 0.02169 ( 4) metal coordination : angle 4.01418 ( 6) covalent geometry : bond 0.00568 (11782) covalent geometry : angle 0.60598 (15917) Misc. bond : bond 0.00068 ( 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 170 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8885 (tt0) cc_final: 0.8653 (tm-30) REVERT: A 164 ARG cc_start: 0.7944 (mtm180) cc_final: 0.7534 (mtt180) REVERT: A 316 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6613 (mp0) REVERT: A 324 LYS cc_start: 0.8726 (tttp) cc_final: 0.8378 (ttpp) REVERT: A 327 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7738 (mt-10) REVERT: A 364 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7207 (tm-30) REVERT: A 372 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8420 (p0) REVERT: A 416 GLU cc_start: 0.8513 (tt0) cc_final: 0.8256 (tt0) REVERT: D 37 LYS cc_start: 0.7440 (tttt) cc_final: 0.6901 (ttpt) REVERT: I 134 GLU cc_start: 0.7267 (tt0) cc_final: 0.6951 (tt0) REVERT: E 273 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7803 (tmt-80) REVERT: E 316 GLU cc_start: 0.8234 (tt0) cc_final: 0.7495 (mp0) REVERT: E 327 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7433 (mt-10) REVERT: E 364 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: E 399 GLU cc_start: 0.4458 (OUTLIER) cc_final: 0.3985 (tm-30) REVERT: E 417 GLU cc_start: 0.8245 (tt0) cc_final: 0.7828 (mp0) REVERT: F 58 LYS cc_start: 0.8196 (tptt) cc_final: 0.7673 (ttmt) REVERT: H 121 LYS cc_start: 0.7248 (mmtp) cc_final: 0.6847 (mmmt) outliers start: 24 outliers final: 6 residues processed: 155 average time/residue: 1.5379 time to fit residues: 255.0215 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 : 1.351 ------------------------------------------------------------------------------- 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 G residue 28 SER Chi-restraints excluded: chain H residue 122 ASN Chi-restraints excluded: chain H residue 147 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 53 optimal weight: 0.0070 chunk 21 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN B 71 HIS B 74 GLN F 8 GLN F 71 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.174561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.111839 restraints weight = 55090.378| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.04 r_work: 0.3226 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 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 = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2083 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= 0.106 Angle : 0.472 9.768 15923 Z= 0.246 Chirality : 0.041 0.174 1802 Planarity : 0.003 0.031 2061 Dihedral : 9.750 154.542 1682 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.35 % Allowed : 17.10 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.63 (0.23), residues: 1462 helix: 1.82 (0.19), residues: 790 sheet: 0.74 (0.40), residues: 198 loop : 0.08 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 454 HIS 0.017 0.001 HIS B 71 PHE 0.008 0.001 PHE H 90 TYR 0.016 0.002 TYR H 43 ARG 0.003 0.000 ARG E 143 Details of bonding type rmsd hydrogen bonds : bond 0.04507 ( 614) hydrogen bonds : angle 4.35828 ( 1811) metal coordination : bond 0.01429 ( 4) metal coordination : angle 4.08476 ( 6) covalent geometry : bond 0.00221 (11782) covalent geometry : angle 0.46491 (15917) Misc. bond : bond 0.00017 ( 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 168 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8798 (tt0) cc_final: 0.8592 (tm-30) REVERT: A 164 ARG cc_start: 0.7828 (mtm180) cc_final: 0.7413 (mtt180) REVERT: A 316 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6394 (mp0) REVERT: A 324 LYS cc_start: 0.8599 (tttp) cc_final: 0.8306 (ttpp) REVERT: A 364 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7273 (tm-30) REVERT: A 416 GLU cc_start: 0.8410 (tt0) cc_final: 0.8162 (tt0) REVERT: C 14 GLU cc_start: 0.6421 (mt-10) cc_final: 0.6079 (mp0) REVERT: C 54 GLU cc_start: 0.6586 (mm-30) cc_final: 0.5271 (tm-30) REVERT: D 37 LYS cc_start: 0.7359 (tttt) cc_final: 0.6828 (ttpt) REVERT: D 144 ASP cc_start: 0.8028 (m-30) cc_final: 0.7638 (m-30) REVERT: I 134 GLU cc_start: 0.7229 (tt0) cc_final: 0.6800 (tt0) REVERT: I 148 GLU cc_start: 0.7817 (pt0) cc_final: 0.7576 (pt0) REVERT: E 145 ARG cc_start: 0.7878 (mtp-110) cc_final: 0.7380 (mtm110) REVERT: E 273 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7747 (tpp-160) REVERT: E 316 GLU cc_start: 0.8028 (tt0) cc_final: 0.7358 (mp0) REVERT: E 327 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: E 364 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7496 (tm-30) REVERT: E 399 GLU cc_start: 0.4225 (OUTLIER) cc_final: 0.3846 (tt0) REVERT: E 417 GLU cc_start: 0.8057 (tt0) cc_final: 0.7755 (mp0) REVERT: F 42 GLU cc_start: 0.7600 (pt0) cc_final: 0.7155 (pt0) REVERT: F 58 LYS cc_start: 0.8140 (tptt) cc_final: 0.7657 (ttmt) REVERT: H 103 SER cc_start: 0.7486 (t) cc_final: 0.7222 (p) REVERT: H 127 LYS cc_start: 0.6584 (mtmm) cc_final: 0.6356 (mtmt) outliers start: 17 outliers final: 4 residues processed: 159 average time/residue: 1.5232 time to fit residues: 258.7071 Evaluate side-chains 149 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain G residue 28 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 79 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 HIS E 429 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.172867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.109758 restraints weight = 56688.286| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.06 r_work: 0.3157 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11788 Z= 0.133 Angle : 0.502 9.018 15923 Z= 0.262 Chirality : 0.042 0.153 1802 Planarity : 0.004 0.031 2061 Dihedral : 9.770 153.688 1682 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.03 % Allowed : 17.18 % Favored : 81.78 % 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: 1.63 (0.23), residues: 1462 helix: 1.81 (0.19), residues: 793 sheet: 0.69 (0.40), residues: 198 loop : 0.10 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 454 HIS 0.016 0.001 HIS B 71 PHE 0.007 0.001 PHE E 123 TYR 0.016 0.002 TYR H 43 ARG 0.003 0.000 ARG E 143 Details of bonding type rmsd hydrogen bonds : bond 0.05024 ( 614) hydrogen bonds : angle 4.39671 ( 1811) metal coordination : bond 0.01499 ( 4) metal coordination : angle 4.00384 ( 6) covalent geometry : bond 0.00302 (11782) covalent geometry : angle 0.49621 (15917) Misc. bond : bond 0.00017 ( 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 154 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 1.324 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8817 (tt0) cc_final: 0.8600 (tm-30) REVERT: A 164 ARG cc_start: 0.7845 (mtm180) cc_final: 0.7427 (mtt180) REVERT: A 316 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6474 (mp0) REVERT: A 324 LYS cc_start: 0.8683 (tttp) cc_final: 0.8347 (ttpp) REVERT: A 364 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7269 (tm-30) REVERT: A 416 GLU cc_start: 0.8459 (tt0) cc_final: 0.8213 (tt0) REVERT: D 37 LYS cc_start: 0.7380 (tttt) cc_final: 0.6838 (ttpt) REVERT: I 134 GLU cc_start: 0.7199 (tt0) cc_final: 0.6840 (tt0) REVERT: I 148 GLU cc_start: 0.7879 (pt0) cc_final: 0.7611 (pt0) REVERT: E 145 ARG cc_start: 0.7996 (mtp-110) cc_final: 0.7501 (mtm110) REVERT: E 226 LYS cc_start: 0.8533 (mtpp) cc_final: 0.8067 (mppt) REVERT: E 273 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7932 (tmt-80) REVERT: E 316 GLU cc_start: 0.8087 (tt0) cc_final: 0.7398 (mp0) REVERT: E 327 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7442 (mt-10) REVERT: E 364 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7507 (tm-30) REVERT: E 399 GLU cc_start: 0.4288 (OUTLIER) cc_final: 0.3900 (tt0) REVERT: E 417 GLU cc_start: 0.8086 (tt0) cc_final: 0.7770 (mp0) REVERT: E 441 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: F 58 LYS cc_start: 0.8148 (tptt) cc_final: 0.7669 (ttmt) REVERT: H 127 LYS cc_start: 0.6609 (mtmm) cc_final: 0.6396 (mtmt) outliers start: 13 outliers final: 3 residues processed: 148 average time/residue: 1.5443 time to fit residues: 245.0018 Evaluate side-chains 148 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 1.283 ------------------------------------------------------------------------------- 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 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 E residue 441 GLU Chi-restraints excluded: chain G residue 28 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.5116 > 50: distance: 18 - 47: 20.434 distance: 22 - 56: 30.463 distance: 26 - 56: 30.462 distance: 34 - 64: 26.026 distance: 38 - 47: 20.725 distance: 47 - 48: 11.814 distance: 48 - 49: 7.531 distance: 48 - 51: 33.081 distance: 49 - 50: 16.841 distance: 49 - 56: 41.735 distance: 51 - 52: 20.553 distance: 52 - 53: 13.716 distance: 56 - 57: 23.220 distance: 57 - 58: 25.737 distance: 57 - 60: 6.500 distance: 58 - 59: 19.727 distance: 58 - 64: 21.221 distance: 64 - 65: 15.572 distance: 65 - 66: 40.416 distance: 66 - 70: 18.875 distance: 67 - 99: 38.643 distance: 68 - 69: 17.000 distance: 70 - 71: 20.120 distance: 70 - 76: 45.498 distance: 72 - 73: 21.196 distance: 72 - 77: 23.029 distance: 73 - 108: 42.492 distance: 74 - 75: 40.525 distance: 77 - 78: 41.779 distance: 78 - 79: 30.664 distance: 78 - 81: 20.367 distance: 79 - 80: 21.612 distance: 79 - 85: 38.475 distance: 80 - 116: 44.449 distance: 81 - 82: 34.637 distance: 82 - 83: 20.018 distance: 82 - 84: 21.962 distance: 85 - 86: 27.798 distance: 86 - 87: 25.110 distance: 86 - 89: 12.081 distance: 87 - 88: 5.518 distance: 87 - 99: 43.140 distance: 88 - 123: 25.818 distance: 89 - 90: 14.225 distance: 92 - 94: 11.728 distance: 92 - 95: 10.054 distance: 93 - 94: 8.012 distance: 96 - 98: 9.686 distance: 97 - 98: 13.996 distance: 99 - 100: 23.704 distance: 100 - 101: 24.029 distance: 100 - 103: 4.582 distance: 101 - 102: 15.915 distance: 101 - 108: 16.107 distance: 102 - 132: 28.520 distance: 103 - 104: 23.199 distance: 104 - 105: 19.602 distance: 105 - 106: 11.318 distance: 105 - 107: 29.809 distance: 108 - 109: 19.160 distance: 109 - 110: 16.375 distance: 109 - 112: 34.516 distance: 112 - 113: 38.303 distance: 113 - 114: 29.078 distance: 114 - 115: 40.875 distance: 116 - 117: 4.124 distance: 117 - 118: 16.829 distance: 118 - 119: 9.623 distance: 118 - 123: 18.710 distance: 120 - 121: 10.534 distance: 120 - 122: 23.773 distance: 124 - 125: 7.429 distance: 124 - 127: 17.606 distance: 125 - 132: 31.274 distance: 129 - 130: 5.423 distance: 129 - 131: 3.999