Starting phenix.real_space_refine on Fri Sep 19 08:43:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t22_25609/09_2025/7t22_25609.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t22_25609/09_2025/7t22_25609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t22_25609/09_2025/7t22_25609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t22_25609/09_2025/7t22_25609.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t22_25609/09_2025/7t22_25609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t22_25609/09_2025/7t22_25609.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 8 Type Number sf(0) Gaussians Al 5 5.89 5 P 23 5.49 5 Mg 5 5.21 5 S 99 5.16 5 C 15138 2.51 5 N 4323 2.21 5 O 4923 1.98 5 F 20 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24536 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "B" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "C" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "D" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "E" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "F" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "G" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "H" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "I" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "M" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 260 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.17, per 1000 atoms: 0.25 Number of scatterers: 24536 At special positions: 0 Unit cell: (161.68, 155.1, 152.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 99 16.00 P 23 15.00 Al 5 13.00 Mg 5 11.99 F 20 9.00 O 4923 8.00 N 4323 7.00 C 15138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS G 568 " distance=2.04 Simple disulfide: pdb=" SG CYS D 103 " - pdb=" SG CYS H 568 " distance=2.04 Simple disulfide: pdb=" SG CYS F 103 " - pdb=" SG CYS I 568 " distance=2.04 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5790 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 7 sheets defined 66.3% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 30 through 44 Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.540A pdb=" N ARG A 54 " --> pdb=" O ASP A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 79 Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 97 through 100 Processing helix chain 'A' and resid 101 through 113 removed outlier: 3.586A pdb=" N THR A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 Processing helix chain 'A' and resid 153 through 172 removed outlier: 3.528A pdb=" N LEU A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG A 172 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 199 removed outlier: 3.561A pdb=" N GLN A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 219 Processing helix chain 'A' and resid 236 through 251 removed outlier: 3.725A pdb=" N ALA A 241 " --> pdb=" O LYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 290 through 308 Processing helix chain 'A' and resid 319 through 335 Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 356 through 376 Processing helix chain 'A' and resid 386 through 392 removed outlier: 3.504A pdb=" N LEU A 389 " --> pdb=" O ASN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 420 through 425 removed outlier: 3.776A pdb=" N TYR A 424 " --> pdb=" O ARG A 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 44 Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.705A pdb=" N ARG B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 78 Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'B' and resid 96 through 101 Processing helix chain 'B' and resid 101 through 113 removed outlier: 3.596A pdb=" N TYR B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 148 Processing helix chain 'B' and resid 153 through 177 removed outlier: 3.585A pdb=" N ILE B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU B 170 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP B 176 " --> pdb=" O ARG B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 199 Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 236 through 251 Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 280 through 287 Processing helix chain 'B' and resid 290 through 308 Processing helix chain 'B' and resid 319 through 335 Processing helix chain 'B' and resid 344 through 348 Processing helix chain 'B' and resid 350 through 354 Processing helix chain 'B' and resid 356 through 376 Processing helix chain 'B' and resid 386 through 392 Processing helix chain 'B' and resid 398 through 402 Processing helix chain 'B' and resid 404 through 412 removed outlier: 4.700A pdb=" N ILE B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU B 409 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN B 410 " --> pdb=" O GLY B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 425 removed outlier: 3.735A pdb=" N TYR B 424 " --> pdb=" O ARG B 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 79 Processing helix chain 'C' and resid 83 through 94 Processing helix chain 'C' and resid 96 through 101 removed outlier: 3.580A pdb=" N GLY C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 113 removed outlier: 3.691A pdb=" N TYR C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 148 Processing helix chain 'C' and resid 153 through 172 Processing helix chain 'C' and resid 182 through 199 removed outlier: 3.702A pdb=" N GLN C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 Processing helix chain 'C' and resid 236 through 251 Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 280 through 287 Processing helix chain 'C' and resid 290 through 308 Processing helix chain 'C' and resid 319 through 334 Processing helix chain 'C' and resid 344 through 348 Processing helix chain 'C' and resid 350 through 354 Processing helix chain 'C' and resid 356 through 376 Processing helix chain 'C' and resid 386 through 392 Processing helix chain 'C' and resid 398 through 402 removed outlier: 3.638A pdb=" N LEU C 402 " --> pdb=" O ASN C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 412 removed outlier: 4.576A pdb=" N ILE C 408 " --> pdb=" O GLU C 404 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU C 409 " --> pdb=" O SER C 405 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLN C 410 " --> pdb=" O GLY C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 425 removed outlier: 3.704A pdb=" N TYR C 424 " --> pdb=" O ARG C 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 44 Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 78 Processing helix chain 'D' and resid 83 through 94 Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 101 through 113 removed outlier: 3.935A pdb=" N THR D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 148 Processing helix chain 'D' and resid 153 through 172 removed outlier: 3.810A pdb=" N ARG D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 182 through 199 Processing helix chain 'D' and resid 211 through 219 Processing helix chain 'D' and resid 236 through 251 Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 280 through 287 Processing helix chain 'D' and resid 290 through 308 Processing helix chain 'D' and resid 319 through 335 Processing helix chain 'D' and resid 344 through 348 Processing helix chain 'D' and resid 350 through 354 Processing helix chain 'D' and resid 356 through 376 Processing helix chain 'D' and resid 386 through 392 Processing helix chain 'D' and resid 398 through 402 removed outlier: 3.557A pdb=" N LEU D 402 " --> pdb=" O ASN D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 412 removed outlier: 4.324A pdb=" N ILE D 408 " --> pdb=" O GLU D 404 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN D 410 " --> pdb=" O GLY D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 425 removed outlier: 3.912A pdb=" N TYR D 424 " --> pdb=" O ARG D 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 44 Processing helix chain 'E' and resid 47 through 53 Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 78 Processing helix chain 'E' and resid 83 through 94 Processing helix chain 'E' and resid 97 through 100 Processing helix chain 'E' and resid 101 through 113 removed outlier: 3.622A pdb=" N TYR E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 148 Processing helix chain 'E' and resid 153 through 172 removed outlier: 3.646A pdb=" N ARG E 172 " --> pdb=" O ILE E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 199 removed outlier: 4.182A pdb=" N VAL E 185 " --> pdb=" O ASN E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 219 Processing helix chain 'E' and resid 236 through 252 Processing helix chain 'E' and resid 264 through 278 Processing helix chain 'E' and resid 280 through 287 Processing helix chain 'E' and resid 290 through 308 Processing helix chain 'E' and resid 319 through 335 Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 350 through 354 Processing helix chain 'E' and resid 356 through 376 Processing helix chain 'E' and resid 387 through 392 Processing helix chain 'E' and resid 398 through 402 removed outlier: 3.697A pdb=" N LEU E 402 " --> pdb=" O ASN E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 412 removed outlier: 4.377A pdb=" N ILE E 408 " --> pdb=" O GLU E 404 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN E 410 " --> pdb=" O GLY E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 425 removed outlier: 3.895A pdb=" N TYR E 424 " --> pdb=" O ARG E 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 44 Processing helix chain 'F' and resid 47 through 55 removed outlier: 3.926A pdb=" N ARG F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 62 through 79 Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'F' and resid 96 through 101 Processing helix chain 'F' and resid 101 through 112 removed outlier: 3.689A pdb=" N TYR F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 117 No H-bonds generated for 'chain 'F' and resid 115 through 117' Processing helix chain 'F' and resid 118 through 148 Processing helix chain 'F' and resid 153 through 169 removed outlier: 3.968A pdb=" N ILE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 172 No H-bonds generated for 'chain 'F' and resid 170 through 172' Processing helix chain 'F' and resid 182 through 198 removed outlier: 4.310A pdb=" N PHE F 197 " --> pdb=" O ILE F 193 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 219 Processing helix chain 'F' and resid 236 through 251 Processing helix chain 'F' and resid 264 through 278 Processing helix chain 'F' and resid 280 through 287 Processing helix chain 'F' and resid 290 through 308 Processing helix chain 'F' and resid 319 through 335 Processing helix chain 'F' and resid 344 through 348 Processing helix chain 'F' and resid 350 through 354 Processing helix chain 'F' and resid 356 through 376 Processing helix chain 'F' and resid 387 through 392 removed outlier: 3.706A pdb=" N GLN F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG F 392 " --> pdb=" O SER F 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 387 through 392' Processing helix chain 'F' and resid 398 through 402 Processing helix chain 'F' and resid 404 through 412 removed outlier: 3.645A pdb=" N ILE F 408 " --> pdb=" O GLU F 404 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLN F 410 " --> pdb=" O GLY F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 425 removed outlier: 3.737A pdb=" N TYR F 424 " --> pdb=" O ARG F 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 461 Processing helix chain 'G' and resid 462 through 468 removed outlier: 3.603A pdb=" N THR G 466 " --> pdb=" O GLU G 463 " (cutoff:3.500A) Processing helix chain 'G' and resid 482 through 495 removed outlier: 3.780A pdb=" N GLN G 495 " --> pdb=" O THR G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 499 through 505 Processing helix chain 'G' and resid 506 through 511 removed outlier: 4.599A pdb=" N GLY G 509 " --> pdb=" O HIS G 506 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ASN G 511 " --> pdb=" O ARG G 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 512 through 522 removed outlier: 3.646A pdb=" N MET G 521 " --> pdb=" O GLU G 517 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP G 522 " --> pdb=" O LYS G 518 " (cutoff:3.500A) Processing helix chain 'G' and resid 528 through 559 removed outlier: 3.601A pdb=" N GLU G 532 " --> pdb=" O LYS G 528 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN G 533 " --> pdb=" O ASN G 529 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR G 534 " --> pdb=" O ILE G 530 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU G 553 " --> pdb=" O LEU G 549 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU G 558 " --> pdb=" O LEU G 554 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG G 559 " --> pdb=" O ILE G 555 " (cutoff:3.500A) Processing helix chain 'G' and resid 564 through 580 removed outlier: 3.587A pdb=" N LEU G 574 " --> pdb=" O GLU G 570 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN G 575 " --> pdb=" O LEU G 571 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN G 576 " --> pdb=" O TRP G 572 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU G 577 " --> pdb=" O THR G 573 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU G 578 " --> pdb=" O LEU G 574 " (cutoff:3.500A) Processing helix chain 'H' and resid 450 through 461 Processing helix chain 'H' and resid 462 through 468 removed outlier: 3.821A pdb=" N THR H 466 " --> pdb=" O GLU H 463 " (cutoff:3.500A) Processing helix chain 'H' and resid 481 through 493 removed outlier: 4.381A pdb=" N PHE H 485 " --> pdb=" O GLY H 481 " (cutoff:3.500A) Processing helix chain 'H' and resid 499 through 505 Processing helix chain 'H' and resid 506 through 508 No H-bonds generated for 'chain 'H' and resid 506 through 508' Processing helix chain 'H' and resid 512 through 522 removed outlier: 3.759A pdb=" N MET H 521 " --> pdb=" O GLU H 517 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP H 522 " --> pdb=" O LYS H 518 " (cutoff:3.500A) Processing helix chain 'H' and resid 530 through 562 removed outlier: 3.815A pdb=" N THR H 534 " --> pdb=" O ILE H 530 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU H 546 " --> pdb=" O MET H 542 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU H 547 " --> pdb=" O PHE H 543 " (cutoff:3.500A) Processing helix chain 'H' and resid 564 through 580 removed outlier: 3.589A pdb=" N LEU H 578 " --> pdb=" O LEU H 574 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS H 580 " --> pdb=" O GLN H 576 " (cutoff:3.500A) Processing helix chain 'I' and resid 450 through 461 Processing helix chain 'I' and resid 462 through 468 Processing helix chain 'I' and resid 481 through 495 removed outlier: 4.395A pdb=" N PHE I 485 " --> pdb=" O GLY I 481 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN I 495 " --> pdb=" O THR I 491 " (cutoff:3.500A) Processing helix chain 'I' and resid 499 through 505 Processing helix chain 'I' and resid 506 through 511 removed outlier: 4.575A pdb=" N GLY I 509 " --> pdb=" O HIS I 506 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ASN I 511 " --> pdb=" O ARG I 508 " (cutoff:3.500A) Processing helix chain 'I' and resid 512 through 522 removed outlier: 3.632A pdb=" N MET I 521 " --> pdb=" O GLU I 517 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TRP I 522 " --> pdb=" O LYS I 518 " (cutoff:3.500A) Processing helix chain 'I' and resid 528 through 562 removed outlier: 3.850A pdb=" N GLU I 532 " --> pdb=" O LYS I 528 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN I 533 " --> pdb=" O ASN I 529 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR I 534 " --> pdb=" O ILE I 530 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER I 545 " --> pdb=" O HIS I 541 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU I 546 " --> pdb=" O MET I 542 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU I 547 " --> pdb=" O PHE I 543 " (cutoff:3.500A) Processing helix chain 'I' and resid 564 through 580 removed outlier: 3.642A pdb=" N GLU I 577 " --> pdb=" O THR I 573 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU I 578 " --> pdb=" O LEU I 574 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA I 579 " --> pdb=" O ASN I 575 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS I 580 " --> pdb=" O GLN I 576 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 181 removed outlier: 6.420A pdb=" N LEU B 257 " --> pdb=" O MET B 341 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASP B 343 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE B 259 " --> pdb=" O ASP B 343 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE B 340 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LEU B 382 " --> pdb=" O ILE B 340 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE B 342 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N GLN B 384 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE B 227 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N SER B 383 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL B 229 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE B 415 " --> pdb=" O GLY B 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 459 through 462 removed outlier: 6.059A pdb=" N ILE A 415 " --> pdb=" O GLY A 439 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU A 414 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE A 227 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N SER A 383 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL A 229 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE A 340 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LEU A 382 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE A 342 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N GLN A 384 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A 256 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ASP A 313 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A 258 " --> pdb=" O ASP A 313 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 180 through 181 removed outlier: 6.358A pdb=" N VAL C 256 " --> pdb=" O TYR C 311 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ASP C 313 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE C 258 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU C 257 " --> pdb=" O MET C 341 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ASP C 343 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE C 259 " --> pdb=" O ASP C 343 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE C 340 " --> pdb=" O VAL C 380 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU C 382 " --> pdb=" O ILE C 340 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE C 342 " --> pdb=" O LEU C 382 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE C 227 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N SER C 383 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL C 229 " --> pdb=" O SER C 383 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU C 226 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N MET C 416 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE C 228 " --> pdb=" O MET C 416 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE C 418 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA C 230 " --> pdb=" O ILE C 418 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE C 415 " --> pdb=" O GLY C 439 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 180 through 181 removed outlier: 6.599A pdb=" N LEU D 257 " --> pdb=" O MET D 341 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ASP D 343 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE D 259 " --> pdb=" O ASP D 343 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE D 340 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU D 382 " --> pdb=" O ILE D 340 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE D 342 " --> pdb=" O LEU D 382 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE D 227 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER D 383 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL D 229 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE D 415 " --> pdb=" O GLY D 439 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 180 through 181 removed outlier: 6.246A pdb=" N VAL E 256 " --> pdb=" O TYR E 311 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ASP E 313 " --> pdb=" O VAL E 256 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE E 258 " --> pdb=" O ASP E 313 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU E 257 " --> pdb=" O MET E 341 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ASP E 343 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE E 259 " --> pdb=" O ASP E 343 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE E 340 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE E 227 " --> pdb=" O ALA E 381 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N SER E 383 " --> pdb=" O ILE E 227 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL E 229 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 180 through 181 removed outlier: 6.246A pdb=" N VAL E 256 " --> pdb=" O TYR E 311 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ASP E 313 " --> pdb=" O VAL E 256 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE E 258 " --> pdb=" O ASP E 313 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU E 257 " --> pdb=" O MET E 341 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ASP E 343 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE E 259 " --> pdb=" O ASP E 343 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE E 340 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE E 227 " --> pdb=" O ALA E 381 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU E 226 " --> pdb=" O LEU E 414 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N MET E 416 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE E 228 " --> pdb=" O MET E 416 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE E 418 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA E 230 " --> pdb=" O ILE E 418 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE E 415 " --> pdb=" O GLY E 439 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 310 through 313 removed outlier: 6.418A pdb=" N VAL F 256 " --> pdb=" O TYR F 311 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ASP F 313 " --> pdb=" O VAL F 256 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE F 258 " --> pdb=" O ASP F 313 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE F 340 " --> pdb=" O VAL F 380 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU F 382 " --> pdb=" O ILE F 340 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE F 342 " --> pdb=" O LEU F 382 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL F 229 " --> pdb=" O ALA F 381 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA F 231 " --> pdb=" O SER F 383 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE F 415 " --> pdb=" O GLY F 439 " (cutoff:3.500A) 1468 hydrogen bonds defined for protein. 4128 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: 3.60 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8476 1.34 - 1.46: 4408 1.46 - 1.58: 11770 1.58 - 1.70: 40 1.70 - 1.82: 206 Bond restraints: 24900 Sorted by residual: bond pdb=" F1 ALF F1002 " pdb="AL ALF F1002 " ideal model delta sigma weight residual 1.684 1.805 -0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" F1 ALF D1002 " pdb="AL ALF D1002 " ideal model delta sigma weight residual 1.684 1.803 -0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" F1 ALF B1002 " pdb="AL ALF B1002 " ideal model delta sigma weight residual 1.684 1.803 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" F1 ALF E1002 " pdb="AL ALF E1002 " ideal model delta sigma weight residual 1.684 1.803 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" F4 ALF C1002 " pdb="AL ALF C1002 " ideal model delta sigma weight residual 1.686 1.804 -0.118 2.00e-02 2.50e+03 3.50e+01 ... (remaining 24895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.09: 33747 14.09 - 28.19: 20 28.19 - 42.28: 0 42.28 - 56.37: 0 56.37 - 70.46: 10 Bond angle restraints: 33777 Sorted by residual: angle pdb=" F1 ALF E1002 " pdb="AL ALF E1002 " pdb=" F2 ALF E1002 " ideal model delta sigma weight residual 108.68 179.14 -70.46 3.00e+00 1.11e-01 5.52e+02 angle pdb=" F1 ALF C1002 " pdb="AL ALF C1002 " pdb=" F2 ALF C1002 " ideal model delta sigma weight residual 108.68 179.11 -70.43 3.00e+00 1.11e-01 5.51e+02 angle pdb=" F1 ALF D1002 " pdb="AL ALF D1002 " pdb=" F2 ALF D1002 " ideal model delta sigma weight residual 108.68 179.08 -70.40 3.00e+00 1.11e-01 5.51e+02 angle pdb=" F1 ALF B1002 " pdb="AL ALF B1002 " pdb=" F2 ALF B1002 " ideal model delta sigma weight residual 108.68 179.03 -70.35 3.00e+00 1.11e-01 5.50e+02 angle pdb=" F1 ALF F1002 " pdb="AL ALF F1002 " pdb=" F2 ALF F1002 " ideal model delta sigma weight residual 108.68 178.95 -70.27 3.00e+00 1.11e-01 5.49e+02 ... (remaining 33772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.03: 15164 30.03 - 60.06: 166 60.06 - 90.09: 6 90.09 - 120.12: 7 120.12 - 150.15: 1 Dihedral angle restraints: 15344 sinusoidal: 6416 harmonic: 8928 Sorted by residual: dihedral pdb=" CA GLU D 404 " pdb=" C GLU D 404 " pdb=" N SER D 405 " pdb=" CA SER D 405 " ideal model delta harmonic sigma weight residual 180.00 -142.98 -37.02 0 5.00e+00 4.00e-02 5.48e+01 dihedral pdb=" O1B ADP F1001 " pdb=" O3A ADP F1001 " pdb=" PB ADP F1001 " pdb=" PA ADP F1001 " ideal model delta sinusoidal sigma weight residual -60.00 90.15 -150.15 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" CA GLU E 404 " pdb=" C GLU E 404 " pdb=" N SER E 405 " pdb=" CA SER E 405 " ideal model delta harmonic sigma weight residual -180.00 -147.90 -32.10 0 5.00e+00 4.00e-02 4.12e+01 ... (remaining 15341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2718 0.029 - 0.058: 718 0.058 - 0.088: 219 0.088 - 0.117: 147 0.117 - 0.146: 50 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CA VAL C 449 " pdb=" N VAL C 449 " pdb=" C VAL C 449 " pdb=" CB VAL C 449 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA VAL E 449 " pdb=" N VAL E 449 " pdb=" C VAL E 449 " pdb=" CB VAL E 449 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA VAL D 449 " pdb=" N VAL D 449 " pdb=" C VAL D 449 " pdb=" CB VAL D 449 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 3849 not shown) Planarity restraints: 4422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN F 199 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO F 200 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO F 200 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 200 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 199 " -0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO B 200 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 200 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 200 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 468 " 0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO G 469 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO G 469 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO G 469 " 0.015 5.00e-02 4.00e+02 ... (remaining 4419 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 327 2.57 - 3.15: 21509 3.15 - 3.74: 40104 3.74 - 4.32: 53707 4.32 - 4.90: 90437 Nonbonded interactions: 206084 Sorted by model distance: nonbonded pdb=" F4 ALF F1002 " pdb="MG MG F1003 " model vdw 1.992 2.120 nonbonded pdb=" F4 ALF B1002 " pdb="MG MG B1003 " model vdw 1.993 2.120 nonbonded pdb=" F1 ALF B1002 " pdb="MG MG B1003 " model vdw 1.993 2.120 nonbonded pdb=" F4 ALF D1002 " pdb="MG MG D1003 " model vdw 1.993 2.120 nonbonded pdb=" F1 ALF F1002 " pdb="MG MG F1003 " model vdw 1.994 2.120 ... (remaining 206079 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' selection = (chain 'B' and resid 24 through 471) selection = (chain 'C' and resid 24 through 471) selection = (chain 'D' and resid 24 through 471) selection = (chain 'E' and resid 24 through 471) selection = (chain 'F' and resid 24 through 471) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 21.650 Find NCS groups from input model: 0.540 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: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 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 0.255 24908 Z= 0.416 Angle : 1.412 70.464 33783 Z= 0.532 Chirality : 0.037 0.146 3852 Planarity : 0.003 0.038 4422 Dihedral : 10.318 150.151 9545 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.18 % Allowed : 3.45 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.51 (0.16), residues: 3066 helix: 2.89 (0.13), residues: 1717 sheet: -0.92 (0.26), residues: 319 loop : 0.48 (0.21), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 387 TYR 0.008 0.001 TYR B 344 PHE 0.006 0.001 PHE D 166 TRP 0.006 0.001 TRP B 48 HIS 0.003 0.001 HIS E 334 Details of bonding type rmsd covalent geometry : bond 0.00415 (24900) covalent geometry : angle 1.41161 (33777) SS BOND : bond 0.00543 ( 3) SS BOND : angle 1.24451 ( 6) hydrogen bonds : bond 0.15030 ( 1466) hydrogen bonds : angle 4.78735 ( 4128) Misc. bond : bond 0.25360 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 659 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8368 (tt0) cc_final: 0.8072 (pp20) REVERT: A 58 ASP cc_start: 0.9083 (m-30) cc_final: 0.8654 (p0) REVERT: A 135 MET cc_start: 0.9057 (ttm) cc_final: 0.8515 (ppp) REVERT: A 291 ASP cc_start: 0.8674 (m-30) cc_final: 0.8095 (p0) REVERT: A 345 LEU cc_start: 0.8307 (mt) cc_final: 0.7830 (mt) REVERT: B 72 MET cc_start: 0.8897 (mtt) cc_final: 0.8637 (mtt) REVERT: B 226 LEU cc_start: 0.8288 (tp) cc_final: 0.7775 (mm) REVERT: B 240 PHE cc_start: 0.9322 (t80) cc_final: 0.9079 (t80) REVERT: B 263 MET cc_start: 0.6032 (mtp) cc_final: 0.5786 (mtt) REVERT: B 269 MET cc_start: 0.8878 (tpp) cc_final: 0.8591 (tpp) REVERT: B 291 ASP cc_start: 0.8979 (m-30) cc_final: 0.8735 (p0) REVERT: B 324 ARG cc_start: 0.9166 (ttm170) cc_final: 0.8898 (ttm-80) REVERT: B 348 MET cc_start: 0.7184 (mtp) cc_final: 0.6966 (ttm) REVERT: B 414 LEU cc_start: 0.9277 (tp) cc_final: 0.8938 (tp) REVERT: C 60 PHE cc_start: 0.9225 (m-80) cc_final: 0.8922 (m-10) REVERT: C 61 TYR cc_start: 0.8669 (t80) cc_final: 0.8430 (t80) REVERT: C 240 PHE cc_start: 0.8919 (t80) cc_final: 0.8480 (t80) REVERT: C 259 PHE cc_start: 0.9023 (m-80) cc_final: 0.8749 (m-80) REVERT: C 263 MET cc_start: 0.7866 (mtp) cc_final: 0.7514 (ttm) REVERT: C 269 MET cc_start: 0.8870 (tpp) cc_final: 0.8559 (ttt) REVERT: C 270 MET cc_start: 0.9052 (mtm) cc_final: 0.8236 (mtp) REVERT: C 382 LEU cc_start: 0.8828 (mt) cc_final: 0.8326 (mt) REVERT: D 50 ASP cc_start: 0.8181 (m-30) cc_final: 0.7810 (p0) REVERT: D 58 ASP cc_start: 0.9006 (m-30) cc_final: 0.8762 (p0) REVERT: D 87 LEU cc_start: 0.8533 (tp) cc_final: 0.7932 (pp) REVERT: D 118 ASN cc_start: 0.9391 (m-40) cc_final: 0.9089 (m-40) REVERT: D 160 LEU cc_start: 0.9159 (tp) cc_final: 0.8873 (tt) REVERT: D 228 ILE cc_start: 0.8273 (mm) cc_final: 0.8045 (mm) REVERT: D 237 LYS cc_start: 0.8552 (ttpt) cc_final: 0.8189 (ptpt) REVERT: D 263 MET cc_start: 0.8062 (mtp) cc_final: 0.7790 (mtt) REVERT: D 337 ILE cc_start: 0.8701 (mt) cc_final: 0.8411 (mm) REVERT: D 341 MET cc_start: 0.7657 (tmt) cc_final: 0.7042 (tmm) REVERT: D 363 GLU cc_start: 0.7849 (tp30) cc_final: 0.7256 (tm-30) REVERT: D 426 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7601 (tp30) REVERT: E 60 PHE cc_start: 0.8983 (m-80) cc_final: 0.8285 (m-80) REVERT: E 92 GLU cc_start: 0.8879 (tt0) cc_final: 0.8484 (tm-30) REVERT: E 135 MET cc_start: 0.9300 (ttm) cc_final: 0.8934 (tmm) REVERT: E 235 MET cc_start: 0.8937 (mmt) cc_final: 0.8143 (mmm) REVERT: E 270 MET cc_start: 0.8963 (mtm) cc_final: 0.8354 (ppp) REVERT: E 301 MET cc_start: 0.9056 (mtp) cc_final: 0.8105 (tpp) REVERT: E 310 ILE cc_start: 0.9285 (mt) cc_final: 0.8954 (mm) REVERT: E 320 PRO cc_start: 0.8637 (Cg_exo) cc_final: 0.7891 (Cg_endo) REVERT: E 363 GLU cc_start: 0.9103 (tp30) cc_final: 0.8898 (tp30) REVERT: E 443 ASN cc_start: 0.8521 (m-40) cc_final: 0.7423 (t0) REVERT: F 282 THR cc_start: 0.9096 (m) cc_final: 0.8803 (p) REVERT: F 361 ILE cc_start: 0.9135 (mm) cc_final: 0.8910 (mm) REVERT: F 414 LEU cc_start: 0.9094 (tp) cc_final: 0.8892 (tp) REVERT: G 471 LEU cc_start: 0.7256 (pp) cc_final: 0.6464 (mp) REVERT: G 521 MET cc_start: 0.9210 (ppp) cc_final: 0.9009 (ppp) REVERT: G 553 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8743 (pm20) REVERT: G 568 CYS cc_start: 0.8504 (m) cc_final: 0.8111 (t) REVERT: H 498 LEU cc_start: 0.0378 (pt) cc_final: -0.0328 (pt) REVERT: H 550 ARG cc_start: 0.8960 (mmp80) cc_final: 0.8648 (mmm160) REVERT: I 530 ILE cc_start: 0.8998 (tt) cc_final: 0.8670 (pt) outliers start: 31 outliers final: 4 residues processed: 683 average time/residue: 0.1936 time to fit residues: 196.3863 Evaluate side-chains 377 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 372 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 0.0770 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 4.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 76 GLN A 96 GLN A 410 GLN A 441 GLN B 45 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN E 181 ASN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 ASN F 441 GLN G 541 HIS I 502 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.077758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.060534 restraints weight = 164817.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.062024 restraints weight = 117979.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.063100 restraints weight = 90858.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.063818 restraints weight = 74039.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.064415 restraints weight = 63603.094| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 24908 Z= 0.183 Angle : 1.053 30.718 33783 Z= 0.430 Chirality : 0.043 0.230 3852 Planarity : 0.005 0.096 4422 Dihedral : 7.587 123.244 3554 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.34 % Allowed : 2.13 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.15), residues: 3066 helix: 2.18 (0.12), residues: 1783 sheet: -0.59 (0.27), residues: 322 loop : 0.38 (0.21), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 387 TYR 0.025 0.002 TYR F 122 PHE 0.026 0.002 PHE F 240 TRP 0.019 0.002 TRP A 48 HIS 0.008 0.002 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00399 (24900) covalent geometry : angle 1.05271 (33777) SS BOND : bond 0.00795 ( 3) SS BOND : angle 1.78631 ( 6) hydrogen bonds : bond 0.04258 ( 1466) hydrogen bonds : angle 4.41565 ( 4128) Misc. bond : bond 0.00277 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 447 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.9101 (m-30) cc_final: 0.8635 (p0) REVERT: A 194 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8956 (tp30) REVERT: A 291 ASP cc_start: 0.8826 (m-30) cc_final: 0.8271 (p0) REVERT: A 345 LEU cc_start: 0.8084 (mt) cc_final: 0.7800 (mt) REVERT: B 72 MET cc_start: 0.8663 (mtt) cc_final: 0.8416 (mtt) REVERT: B 226 LEU cc_start: 0.8405 (tp) cc_final: 0.8204 (mm) REVERT: B 235 MET cc_start: 0.8837 (mmt) cc_final: 0.8539 (mmm) REVERT: B 240 PHE cc_start: 0.9163 (t80) cc_final: 0.8912 (t80) REVERT: B 269 MET cc_start: 0.8947 (tpp) cc_final: 0.8516 (tpp) REVERT: B 291 ASP cc_start: 0.8939 (m-30) cc_final: 0.8691 (p0) REVERT: B 297 ILE cc_start: 0.9466 (mm) cc_final: 0.9223 (pt) REVERT: B 301 MET cc_start: 0.8941 (tmm) cc_final: 0.8703 (tmm) REVERT: B 324 ARG cc_start: 0.9188 (ttm170) cc_final: 0.8711 (ttt180) REVERT: B 348 MET cc_start: 0.7265 (mtp) cc_final: 0.6745 (mpp) REVERT: C 235 MET cc_start: 0.9097 (mmp) cc_final: 0.8793 (mmm) REVERT: C 259 PHE cc_start: 0.9203 (m-80) cc_final: 0.8801 (m-80) REVERT: C 263 MET cc_start: 0.8306 (mtp) cc_final: 0.8074 (ttm) REVERT: C 312 ILE cc_start: 0.9430 (mp) cc_final: 0.9022 (tt) REVERT: C 382 LEU cc_start: 0.8848 (mt) cc_final: 0.8612 (mt) REVERT: C 427 ASN cc_start: 0.8090 (p0) cc_final: 0.7746 (p0) REVERT: D 34 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8729 (mt-10) REVERT: D 58 ASP cc_start: 0.9031 (m-30) cc_final: 0.8785 (p0) REVERT: D 118 ASN cc_start: 0.9471 (m-40) cc_final: 0.9171 (m-40) REVERT: D 160 LEU cc_start: 0.9201 (tp) cc_final: 0.8905 (tt) REVERT: D 237 LYS cc_start: 0.8687 (ttpt) cc_final: 0.8355 (ptpt) REVERT: D 269 MET cc_start: 0.8521 (ttm) cc_final: 0.8271 (ttm) REVERT: D 301 MET cc_start: 0.8881 (mtm) cc_final: 0.8556 (mtt) REVERT: D 337 ILE cc_start: 0.8678 (mt) cc_final: 0.8449 (mm) REVERT: E 60 PHE cc_start: 0.9105 (m-80) cc_final: 0.8882 (m-80) REVERT: E 85 ILE cc_start: 0.9507 (pt) cc_final: 0.9271 (mp) REVERT: E 92 GLU cc_start: 0.8810 (tt0) cc_final: 0.8553 (tm-30) REVERT: E 135 MET cc_start: 0.9261 (ttm) cc_final: 0.9040 (tmm) REVERT: E 235 MET cc_start: 0.8870 (mmt) cc_final: 0.8277 (mmm) REVERT: E 267 GLN cc_start: 0.9169 (mp10) cc_final: 0.8915 (mp10) REVERT: E 363 GLU cc_start: 0.9170 (tp30) cc_final: 0.8871 (tp30) REVERT: F 98 ASP cc_start: 0.7804 (t0) cc_final: 0.7585 (p0) REVERT: F 235 MET cc_start: 0.7352 (mtt) cc_final: 0.6475 (mtp) REVERT: F 263 MET cc_start: 0.6981 (mpp) cc_final: 0.6697 (mpp) REVERT: F 270 MET cc_start: 0.8548 (ttt) cc_final: 0.8344 (ttt) REVERT: F 282 THR cc_start: 0.9223 (m) cc_final: 0.8916 (p) REVERT: F 318 LEU cc_start: 0.8379 (mp) cc_final: 0.8098 (mp) REVERT: G 468 VAL cc_start: 0.6647 (t) cc_final: 0.6316 (t) REVERT: G 568 CYS cc_start: 0.8145 (m) cc_final: 0.7749 (t) REVERT: H 550 ARG cc_start: 0.8965 (mmp80) cc_final: 0.8700 (mmm160) REVERT: I 489 VAL cc_start: 0.4207 (t) cc_final: 0.3953 (t) REVERT: I 530 ILE cc_start: 0.8873 (tt) cc_final: 0.8663 (pt) outliers start: 9 outliers final: 2 residues processed: 452 average time/residue: 0.1740 time to fit residues: 119.9811 Evaluate side-chains 323 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 321 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 12 optimal weight: 20.0000 chunk 116 optimal weight: 5.9990 chunk 84 optimal weight: 0.0000 chunk 89 optimal weight: 20.0000 chunk 130 optimal weight: 4.9990 chunk 246 optimal weight: 8.9990 chunk 110 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 overall best weight: 5.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 ASN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 HIS F 96 GLN G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.075543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.058584 restraints weight = 171560.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.060025 restraints weight = 122284.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.061047 restraints weight = 94156.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.061799 restraints weight = 76991.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.062360 restraints weight = 66000.035| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24908 Z= 0.198 Angle : 1.042 30.837 33783 Z= 0.426 Chirality : 0.041 0.170 3852 Planarity : 0.005 0.086 4422 Dihedral : 7.470 127.630 3554 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.04 % Allowed : 2.47 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.15), residues: 3066 helix: 1.83 (0.12), residues: 1787 sheet: -0.56 (0.27), residues: 310 loop : 0.33 (0.22), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 278 TYR 0.025 0.002 TYR D 122 PHE 0.019 0.002 PHE F 240 TRP 0.027 0.002 TRP E 48 HIS 0.010 0.002 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00418 (24900) covalent geometry : angle 1.04216 (33777) SS BOND : bond 0.02025 ( 3) SS BOND : angle 1.86287 ( 6) hydrogen bonds : bond 0.03763 ( 1466) hydrogen bonds : angle 4.44251 ( 4128) Misc. bond : bond 0.00206 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 413 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.9143 (m-30) cc_final: 0.8682 (p0) REVERT: A 72 MET cc_start: 0.8444 (mmp) cc_final: 0.8238 (mmp) REVERT: A 135 MET cc_start: 0.9107 (mmm) cc_final: 0.8882 (mmm) REVERT: A 194 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8993 (tp30) REVERT: A 242 MET cc_start: 0.8895 (ppp) cc_final: 0.8626 (ppp) REVERT: A 291 ASP cc_start: 0.8780 (m-30) cc_final: 0.8198 (p0) REVERT: A 345 LEU cc_start: 0.7908 (mt) cc_final: 0.7565 (mt) REVERT: A 348 MET cc_start: 0.9167 (ttm) cc_final: 0.8635 (ttm) REVERT: A 416 MET cc_start: 0.8624 (mmt) cc_final: 0.8147 (mmm) REVERT: A 438 ILE cc_start: 0.8288 (mp) cc_final: 0.7635 (mp) REVERT: B 72 MET cc_start: 0.8695 (mtt) cc_final: 0.8467 (mtt) REVERT: B 226 LEU cc_start: 0.8422 (tp) cc_final: 0.7622 (mm) REVERT: B 240 PHE cc_start: 0.9096 (t80) cc_final: 0.8855 (t80) REVERT: B 269 MET cc_start: 0.8986 (tpp) cc_final: 0.8584 (tpp) REVERT: B 291 ASP cc_start: 0.8959 (m-30) cc_final: 0.8711 (p0) REVERT: B 297 ILE cc_start: 0.9443 (mm) cc_final: 0.9203 (pt) REVERT: B 301 MET cc_start: 0.9038 (tmm) cc_final: 0.8767 (tmm) REVERT: B 324 ARG cc_start: 0.9179 (ttm170) cc_final: 0.8647 (ttt180) REVERT: B 348 MET cc_start: 0.7507 (mtp) cc_final: 0.7132 (ttm) REVERT: B 369 LYS cc_start: 0.9097 (tptt) cc_final: 0.8865 (tptp) REVERT: C 235 MET cc_start: 0.9047 (mmp) cc_final: 0.8752 (mmm) REVERT: C 259 PHE cc_start: 0.9140 (m-80) cc_final: 0.8913 (m-80) REVERT: C 263 MET cc_start: 0.8490 (mtp) cc_final: 0.8217 (ttm) REVERT: C 322 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8144 (mt-10) REVERT: C 382 LEU cc_start: 0.8868 (mt) cc_final: 0.8571 (mt) REVERT: C 427 ASN cc_start: 0.8181 (p0) cc_final: 0.7897 (p0) REVERT: D 58 ASP cc_start: 0.9040 (m-30) cc_final: 0.8811 (p0) REVERT: D 118 ASN cc_start: 0.9503 (m-40) cc_final: 0.9275 (m-40) REVERT: D 160 LEU cc_start: 0.9243 (tp) cc_final: 0.8942 (tt) REVERT: D 235 MET cc_start: 0.9091 (mmp) cc_final: 0.8834 (mmp) REVERT: D 301 MET cc_start: 0.8920 (mtm) cc_final: 0.8584 (mtt) REVERT: D 337 ILE cc_start: 0.8719 (mt) cc_final: 0.8500 (mm) REVERT: E 85 ILE cc_start: 0.9561 (pt) cc_final: 0.9235 (mp) REVERT: E 92 GLU cc_start: 0.8817 (tt0) cc_final: 0.8503 (tp30) REVERT: E 135 MET cc_start: 0.9300 (ttm) cc_final: 0.9014 (tmm) REVERT: E 235 MET cc_start: 0.8919 (mmt) cc_final: 0.8357 (mmm) REVERT: E 363 GLU cc_start: 0.9163 (tp30) cc_final: 0.8845 (tp30) REVERT: E 443 ASN cc_start: 0.8328 (m-40) cc_final: 0.7294 (t0) REVERT: F 98 ASP cc_start: 0.7803 (t0) cc_final: 0.7549 (p0) REVERT: F 282 THR cc_start: 0.9284 (m) cc_final: 0.9010 (p) REVERT: F 391 GLN cc_start: 0.9390 (mt0) cc_final: 0.9156 (mt0) REVERT: G 537 ASP cc_start: 0.8795 (t0) cc_final: 0.8468 (t0) REVERT: G 568 CYS cc_start: 0.8063 (m) cc_final: 0.7698 (t) REVERT: H 550 ARG cc_start: 0.8978 (mmp80) cc_final: 0.8697 (mmm160) REVERT: I 489 VAL cc_start: 0.4072 (t) cc_final: 0.3849 (t) REVERT: I 530 ILE cc_start: 0.8948 (tt) cc_final: 0.8719 (pt) outliers start: 1 outliers final: 1 residues processed: 414 average time/residue: 0.1707 time to fit residues: 109.1081 Evaluate side-chains 307 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 306 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 28 optimal weight: 0.9990 chunk 296 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 160 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 118 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 284 optimal weight: 0.4980 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 441 GLN B 281 GLN C 195 GLN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 HIS ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.077175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.060333 restraints weight = 166723.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.061716 restraints weight = 120266.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.062718 restraints weight = 93379.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.063453 restraints weight = 76866.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.064007 restraints weight = 66274.221| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24908 Z= 0.125 Angle : 1.008 30.173 33783 Z= 0.401 Chirality : 0.041 0.182 3852 Planarity : 0.004 0.071 4422 Dihedral : 7.171 127.132 3554 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.04 % Allowed : 2.05 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.15), residues: 3066 helix: 1.85 (0.12), residues: 1789 sheet: -0.61 (0.27), residues: 328 loop : 0.39 (0.22), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 285 TYR 0.033 0.001 TYR B 122 PHE 0.018 0.002 PHE F 240 TRP 0.022 0.001 TRP A 48 HIS 0.006 0.001 HIS G 541 Details of bonding type rmsd covalent geometry : bond 0.00273 (24900) covalent geometry : angle 1.00752 (33777) SS BOND : bond 0.00893 ( 3) SS BOND : angle 1.59266 ( 6) hydrogen bonds : bond 0.03452 ( 1466) hydrogen bonds : angle 4.28232 ( 4128) Misc. bond : bond 0.00116 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 407 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.9192 (m-30) cc_final: 0.8688 (p0) REVERT: A 194 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8968 (tp30) REVERT: A 242 MET cc_start: 0.8897 (ppp) cc_final: 0.8607 (ppp) REVERT: A 291 ASP cc_start: 0.8795 (m-30) cc_final: 0.8234 (p0) REVERT: A 345 LEU cc_start: 0.8001 (mt) cc_final: 0.7579 (mt) REVERT: A 416 MET cc_start: 0.8737 (mmt) cc_final: 0.8259 (mmm) REVERT: A 438 ILE cc_start: 0.8199 (mp) cc_final: 0.7559 (mp) REVERT: B 72 MET cc_start: 0.8730 (mtt) cc_final: 0.8497 (mtt) REVERT: B 187 ASP cc_start: 0.9065 (m-30) cc_final: 0.8859 (m-30) REVERT: B 226 LEU cc_start: 0.8376 (tp) cc_final: 0.7584 (mm) REVERT: B 240 PHE cc_start: 0.9129 (t80) cc_final: 0.8870 (t80) REVERT: B 269 MET cc_start: 0.9028 (tpp) cc_final: 0.8645 (tpp) REVERT: B 291 ASP cc_start: 0.8931 (m-30) cc_final: 0.8684 (p0) REVERT: B 301 MET cc_start: 0.9046 (tmm) cc_final: 0.8560 (ppp) REVERT: B 324 ARG cc_start: 0.9123 (ttm170) cc_final: 0.8643 (ttt180) REVERT: B 348 MET cc_start: 0.7363 (mtp) cc_final: 0.7074 (ttm) REVERT: B 414 LEU cc_start: 0.9127 (tp) cc_final: 0.8752 (tp) REVERT: C 235 MET cc_start: 0.8972 (mmp) cc_final: 0.8667 (mmm) REVERT: C 259 PHE cc_start: 0.9017 (m-80) cc_final: 0.8746 (m-80) REVERT: C 270 MET cc_start: 0.8674 (mtp) cc_final: 0.8325 (ttt) REVERT: C 322 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8117 (mt-10) REVERT: C 382 LEU cc_start: 0.8877 (mt) cc_final: 0.8428 (mt) REVERT: C 419 TYR cc_start: 0.7755 (t80) cc_final: 0.7383 (t80) REVERT: C 427 ASN cc_start: 0.8160 (p0) cc_final: 0.7890 (p0) REVERT: D 42 MET cc_start: 0.7353 (mtp) cc_final: 0.7103 (mtp) REVERT: D 58 ASP cc_start: 0.9058 (m-30) cc_final: 0.8785 (p0) REVERT: D 118 ASN cc_start: 0.9452 (m-40) cc_final: 0.9109 (m-40) REVERT: D 160 LEU cc_start: 0.9271 (tp) cc_final: 0.8977 (tt) REVERT: D 235 MET cc_start: 0.8881 (mmp) cc_final: 0.8658 (mmp) REVERT: D 269 MET cc_start: 0.8743 (mtp) cc_final: 0.8467 (ttm) REVERT: D 301 MET cc_start: 0.8924 (mtm) cc_final: 0.8561 (mtt) REVERT: D 399 ASN cc_start: 0.8754 (m-40) cc_final: 0.8054 (p0) REVERT: E 92 GLU cc_start: 0.8926 (tt0) cc_final: 0.8514 (tp30) REVERT: E 135 MET cc_start: 0.9231 (ttm) cc_final: 0.8959 (tmm) REVERT: E 235 MET cc_start: 0.8788 (mmt) cc_final: 0.7953 (mmm) REVERT: E 301 MET cc_start: 0.9094 (mtm) cc_final: 0.8765 (mtt) REVERT: E 344 TYR cc_start: 0.7837 (p90) cc_final: 0.7380 (p90) REVERT: E 363 GLU cc_start: 0.9178 (tp30) cc_final: 0.8886 (tp30) REVERT: E 443 ASN cc_start: 0.8257 (m-40) cc_final: 0.7124 (t0) REVERT: F 98 ASP cc_start: 0.7813 (t0) cc_final: 0.7576 (p0) REVERT: F 235 MET cc_start: 0.7389 (mtt) cc_final: 0.6531 (mtp) REVERT: F 263 MET cc_start: 0.6843 (mpp) cc_final: 0.6614 (mpp) REVERT: F 282 THR cc_start: 0.9223 (m) cc_final: 0.8934 (p) REVERT: F 391 GLN cc_start: 0.9388 (mt0) cc_final: 0.9156 (mt0) REVERT: F 414 LEU cc_start: 0.9130 (tp) cc_final: 0.8775 (tp) REVERT: G 512 ASN cc_start: 0.7673 (t0) cc_final: 0.6614 (m110) REVERT: G 537 ASP cc_start: 0.8708 (t0) cc_final: 0.8382 (t0) REVERT: G 568 CYS cc_start: 0.8030 (m) cc_final: 0.7622 (t) REVERT: H 550 ARG cc_start: 0.9001 (mmp80) cc_final: 0.8712 (mmm160) REVERT: I 489 VAL cc_start: 0.4192 (t) cc_final: 0.3991 (t) REVERT: I 530 ILE cc_start: 0.8902 (tt) cc_final: 0.8678 (pt) outliers start: 1 outliers final: 0 residues processed: 408 average time/residue: 0.1741 time to fit residues: 109.0672 Evaluate side-chains 298 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 221 optimal weight: 20.0000 chunk 179 optimal weight: 0.5980 chunk 282 optimal weight: 30.0000 chunk 299 optimal weight: 5.9990 chunk 291 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 283 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 chunk 153 optimal weight: 2.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN C 281 GLN D 45 ASN D 198 GLN F 252 GLN G 541 HIS H 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 575 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.075621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.058922 restraints weight = 169508.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.060280 restraints weight = 122195.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.061261 restraints weight = 94990.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.061971 restraints weight = 78344.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.062515 restraints weight = 67530.564| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24908 Z= 0.155 Angle : 1.018 30.679 33783 Z= 0.409 Chirality : 0.041 0.172 3852 Planarity : 0.004 0.058 4422 Dihedral : 7.066 129.241 3554 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.04 % Allowed : 2.13 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.15), residues: 3066 helix: 1.80 (0.12), residues: 1787 sheet: -0.68 (0.27), residues: 330 loop : 0.38 (0.22), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 129 TYR 0.023 0.001 TYR D 122 PHE 0.017 0.002 PHE B 60 TRP 0.023 0.002 TRP A 48 HIS 0.006 0.001 HIS G 541 Details of bonding type rmsd covalent geometry : bond 0.00335 (24900) covalent geometry : angle 1.01765 (33777) SS BOND : bond 0.01074 ( 3) SS BOND : angle 1.94358 ( 6) hydrogen bonds : bond 0.03320 ( 1466) hydrogen bonds : angle 4.29263 ( 4128) Misc. bond : bond 0.00164 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 389 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.9202 (m-30) cc_final: 0.8703 (p0) REVERT: A 135 MET cc_start: 0.9127 (mmm) cc_final: 0.8892 (mmm) REVERT: A 194 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8961 (tp30) REVERT: A 291 ASP cc_start: 0.8821 (m-30) cc_final: 0.8229 (p0) REVERT: A 345 LEU cc_start: 0.7978 (mt) cc_final: 0.7652 (mt) REVERT: A 416 MET cc_start: 0.8728 (mmt) cc_final: 0.8183 (mmm) REVERT: A 438 ILE cc_start: 0.8120 (mp) cc_final: 0.7457 (mp) REVERT: A 440 LYS cc_start: 0.8911 (pttp) cc_final: 0.8710 (pttm) REVERT: B 187 ASP cc_start: 0.9015 (m-30) cc_final: 0.8810 (m-30) REVERT: B 235 MET cc_start: 0.8395 (mmp) cc_final: 0.8110 (mmm) REVERT: B 240 PHE cc_start: 0.9092 (t80) cc_final: 0.8780 (t80) REVERT: B 269 MET cc_start: 0.9017 (tpp) cc_final: 0.8639 (tpp) REVERT: B 291 ASP cc_start: 0.8937 (m-30) cc_final: 0.8641 (p0) REVERT: B 301 MET cc_start: 0.9092 (tmm) cc_final: 0.8748 (tmm) REVERT: B 348 MET cc_start: 0.7566 (mtp) cc_final: 0.7151 (ttm) REVERT: C 235 MET cc_start: 0.9019 (mmp) cc_final: 0.8706 (mmm) REVERT: C 250 MET cc_start: 0.8699 (tmm) cc_final: 0.8470 (tmm) REVERT: C 259 PHE cc_start: 0.9131 (m-80) cc_final: 0.8835 (m-80) REVERT: C 270 MET cc_start: 0.8738 (mtp) cc_final: 0.8466 (ttt) REVERT: C 322 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8109 (mt-10) REVERT: C 382 LEU cc_start: 0.8951 (mt) cc_final: 0.8481 (mt) REVERT: C 419 TYR cc_start: 0.7721 (t80) cc_final: 0.7228 (t80) REVERT: C 427 ASN cc_start: 0.8173 (p0) cc_final: 0.7924 (p0) REVERT: D 118 ASN cc_start: 0.9470 (m-40) cc_final: 0.9103 (m-40) REVERT: D 160 LEU cc_start: 0.9271 (tp) cc_final: 0.8969 (tt) REVERT: D 235 MET cc_start: 0.8933 (mmp) cc_final: 0.8710 (mmp) REVERT: D 269 MET cc_start: 0.8815 (mtp) cc_final: 0.8571 (ttm) REVERT: D 301 MET cc_start: 0.8925 (mtm) cc_final: 0.8569 (mtt) REVERT: E 42 MET cc_start: 0.8395 (ptp) cc_final: 0.7507 (ppp) REVERT: E 92 GLU cc_start: 0.8920 (tt0) cc_final: 0.8532 (tm-30) REVERT: E 135 MET cc_start: 0.9233 (ttm) cc_final: 0.8978 (tmm) REVERT: E 235 MET cc_start: 0.8805 (mmt) cc_final: 0.8543 (mmm) REVERT: E 301 MET cc_start: 0.9090 (mtm) cc_final: 0.8574 (mtp) REVERT: E 363 GLU cc_start: 0.9161 (tp30) cc_final: 0.8857 (tp30) REVERT: E 443 ASN cc_start: 0.8270 (m-40) cc_final: 0.7066 (t0) REVERT: F 98 ASP cc_start: 0.7789 (t0) cc_final: 0.7547 (p0) REVERT: F 235 MET cc_start: 0.7426 (mtt) cc_final: 0.6521 (mtp) REVERT: F 391 GLN cc_start: 0.9393 (mt0) cc_final: 0.9091 (mt0) REVERT: F 414 LEU cc_start: 0.9077 (tp) cc_final: 0.8859 (tp) REVERT: G 537 ASP cc_start: 0.8744 (t0) cc_final: 0.8400 (t0) REVERT: G 568 CYS cc_start: 0.8079 (m) cc_final: 0.7680 (t) REVERT: H 550 ARG cc_start: 0.9007 (mmp80) cc_final: 0.8732 (mmm160) REVERT: I 489 VAL cc_start: 0.3958 (t) cc_final: 0.3726 (t) REVERT: I 530 ILE cc_start: 0.8905 (tt) cc_final: 0.8687 (pt) outliers start: 1 outliers final: 0 residues processed: 390 average time/residue: 0.1689 time to fit residues: 101.9268 Evaluate side-chains 286 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 92 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 235 optimal weight: 0.0060 chunk 268 optimal weight: 50.0000 chunk 5 optimal weight: 2.9990 chunk 289 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 302 optimal weight: 20.0000 chunk 278 optimal weight: 8.9990 chunk 296 optimal weight: 7.9990 overall best weight: 5.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 GLN F 45 ASN ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS ** H 551 GLN ** 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 = 0.4023 r_free = 0.4023 target = 0.073952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.057203 restraints weight = 174159.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.058626 restraints weight = 123069.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.059622 restraints weight = 94285.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.060385 restraints weight = 77004.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.060923 restraints weight = 65978.810| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24908 Z= 0.192 Angle : 1.047 31.657 33783 Z= 0.427 Chirality : 0.041 0.240 3852 Planarity : 0.004 0.055 4422 Dihedral : 7.108 132.064 3554 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.15), residues: 3066 helix: 1.63 (0.12), residues: 1787 sheet: -0.67 (0.27), residues: 309 loop : 0.31 (0.21), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 324 TYR 0.027 0.002 TYR D 122 PHE 0.041 0.002 PHE C 166 TRP 0.022 0.002 TRP A 48 HIS 0.007 0.002 HIS H 541 Details of bonding type rmsd covalent geometry : bond 0.00408 (24900) covalent geometry : angle 1.04718 (33777) SS BOND : bond 0.00956 ( 3) SS BOND : angle 1.86539 ( 6) hydrogen bonds : bond 0.03441 ( 1466) hydrogen bonds : angle 4.47042 ( 4128) Misc. bond : bond 0.00184 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.9159 (m-30) cc_final: 0.8631 (p0) REVERT: A 135 MET cc_start: 0.9120 (mmm) cc_final: 0.8912 (mmm) REVERT: A 194 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8972 (tp30) REVERT: A 291 ASP cc_start: 0.8840 (m-30) cc_final: 0.8222 (p0) REVERT: A 416 MET cc_start: 0.8719 (mmt) cc_final: 0.8454 (mmp) REVERT: A 438 ILE cc_start: 0.8152 (mp) cc_final: 0.7892 (mp) REVERT: A 440 LYS cc_start: 0.9031 (pttp) cc_final: 0.8790 (pttm) REVERT: B 72 MET cc_start: 0.8806 (mtt) cc_final: 0.8242 (mtp) REVERT: B 187 ASP cc_start: 0.9069 (m-30) cc_final: 0.8851 (m-30) REVERT: B 235 MET cc_start: 0.8626 (mmp) cc_final: 0.8275 (mmm) REVERT: B 269 MET cc_start: 0.8970 (tpp) cc_final: 0.8569 (tpp) REVERT: B 291 ASP cc_start: 0.8959 (m-30) cc_final: 0.8691 (p0) REVERT: B 297 ILE cc_start: 0.9431 (mm) cc_final: 0.9193 (pt) REVERT: B 301 MET cc_start: 0.9125 (tmm) cc_final: 0.8787 (tmm) REVERT: B 348 MET cc_start: 0.7748 (mtp) cc_final: 0.7240 (ttm) REVERT: B 414 LEU cc_start: 0.9213 (tp) cc_final: 0.8681 (tt) REVERT: C 160 LEU cc_start: 0.9579 (tt) cc_final: 0.8965 (pp) REVERT: C 235 MET cc_start: 0.9018 (mmp) cc_final: 0.8739 (mmm) REVERT: C 250 MET cc_start: 0.8768 (tmm) cc_final: 0.8546 (tmm) REVERT: C 322 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8051 (mt-10) REVERT: C 382 LEU cc_start: 0.8979 (mt) cc_final: 0.8727 (mt) REVERT: C 419 TYR cc_start: 0.7670 (t80) cc_final: 0.7157 (t80) REVERT: C 427 ASN cc_start: 0.8276 (p0) cc_final: 0.8048 (p0) REVERT: D 50 ASP cc_start: 0.8527 (m-30) cc_final: 0.7876 (p0) REVERT: D 118 ASN cc_start: 0.9506 (m-40) cc_final: 0.9179 (m-40) REVERT: D 160 LEU cc_start: 0.9265 (tp) cc_final: 0.8965 (tt) REVERT: D 301 MET cc_start: 0.8975 (mtm) cc_final: 0.8554 (mtt) REVERT: D 348 MET cc_start: 0.8674 (tpp) cc_final: 0.8403 (tpp) REVERT: E 42 MET cc_start: 0.8336 (ptp) cc_final: 0.7584 (ppp) REVERT: E 92 GLU cc_start: 0.8930 (tt0) cc_final: 0.8506 (tm-30) REVERT: E 135 MET cc_start: 0.9198 (ttm) cc_final: 0.8929 (tmm) REVERT: E 263 MET cc_start: 0.8508 (mtp) cc_final: 0.8016 (mpp) REVERT: E 301 MET cc_start: 0.9080 (mtm) cc_final: 0.8774 (mtp) REVERT: E 363 GLU cc_start: 0.9114 (tp30) cc_final: 0.8853 (tp30) REVERT: F 72 MET cc_start: 0.8784 (ptt) cc_final: 0.8504 (ptt) REVERT: F 98 ASP cc_start: 0.7830 (t0) cc_final: 0.7561 (p0) REVERT: F 235 MET cc_start: 0.7407 (mtt) cc_final: 0.6496 (mtp) REVERT: F 263 MET cc_start: 0.7113 (mpp) cc_final: 0.6902 (mpp) REVERT: F 341 MET cc_start: 0.8821 (tpt) cc_final: 0.8523 (tpp) REVERT: F 391 GLN cc_start: 0.9393 (mt0) cc_final: 0.9042 (mt0) REVERT: G 537 ASP cc_start: 0.8774 (t0) cc_final: 0.8430 (t0) REVERT: G 568 CYS cc_start: 0.8124 (m) cc_final: 0.7746 (t) REVERT: H 541 HIS cc_start: 0.8984 (m-70) cc_final: 0.8781 (m-70) REVERT: H 550 ARG cc_start: 0.9013 (mmp80) cc_final: 0.8730 (mmm160) REVERT: I 489 VAL cc_start: 0.3880 (t) cc_final: 0.3479 (t) REVERT: I 530 ILE cc_start: 0.8876 (tt) cc_final: 0.8647 (pt) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.1652 time to fit residues: 94.7888 Evaluate side-chains 278 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 52 optimal weight: 7.9990 chunk 270 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 269 optimal weight: 20.0000 chunk 106 optimal weight: 0.1980 chunk 211 optimal weight: 0.2980 chunk 112 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN F 252 GLN G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 461 ASN ** 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 = 0.4049 r_free = 0.4049 target = 0.075029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.058178 restraints weight = 171691.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.059600 restraints weight = 121511.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.060637 restraints weight = 93592.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.061398 restraints weight = 76384.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.061928 restraints weight = 65483.809| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24908 Z= 0.145 Angle : 1.030 30.373 33783 Z= 0.414 Chirality : 0.042 0.252 3852 Planarity : 0.004 0.101 4422 Dihedral : 6.971 130.072 3554 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.15), residues: 3066 helix: 1.59 (0.12), residues: 1801 sheet: -0.72 (0.27), residues: 313 loop : 0.27 (0.22), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 326 TYR 0.025 0.001 TYR D 122 PHE 0.017 0.002 PHE B 240 TRP 0.041 0.002 TRP F 457 HIS 0.006 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00322 (24900) covalent geometry : angle 1.03011 (33777) SS BOND : bond 0.00843 ( 3) SS BOND : angle 1.52772 ( 6) hydrogen bonds : bond 0.03281 ( 1466) hydrogen bonds : angle 4.41252 ( 4128) Misc. bond : bond 0.00127 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.9207 (m-30) cc_final: 0.8661 (p0) REVERT: A 135 MET cc_start: 0.9229 (mmt) cc_final: 0.8956 (mmm) REVERT: A 160 LEU cc_start: 0.9272 (tp) cc_final: 0.9069 (tp) REVERT: A 167 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8571 (mttt) REVERT: A 194 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8980 (tp30) REVERT: A 291 ASP cc_start: 0.8872 (m-30) cc_final: 0.8256 (p0) REVERT: A 416 MET cc_start: 0.8732 (mmt) cc_final: 0.8327 (mmm) REVERT: A 451 LEU cc_start: 0.8942 (mt) cc_final: 0.8704 (mt) REVERT: B 187 ASP cc_start: 0.9036 (m-30) cc_final: 0.8824 (m-30) REVERT: B 228 ILE cc_start: 0.9101 (mp) cc_final: 0.8889 (mm) REVERT: B 235 MET cc_start: 0.8479 (mmp) cc_final: 0.8101 (mmm) REVERT: B 269 MET cc_start: 0.8948 (tpp) cc_final: 0.8557 (tpp) REVERT: B 291 ASP cc_start: 0.8937 (m-30) cc_final: 0.8678 (p0) REVERT: B 297 ILE cc_start: 0.9438 (mm) cc_final: 0.9209 (pt) REVERT: B 301 MET cc_start: 0.9129 (tmm) cc_final: 0.8801 (tmm) REVERT: B 348 MET cc_start: 0.7636 (mtp) cc_final: 0.7199 (ttm) REVERT: B 414 LEU cc_start: 0.9149 (tp) cc_final: 0.8616 (tt) REVERT: C 235 MET cc_start: 0.8937 (mmp) cc_final: 0.8656 (mmm) REVERT: C 250 MET cc_start: 0.8812 (tmm) cc_final: 0.8595 (tmm) REVERT: C 322 GLU cc_start: 0.8509 (mt-10) cc_final: 0.7995 (mt-10) REVERT: C 382 LEU cc_start: 0.8949 (mt) cc_final: 0.8741 (mt) REVERT: C 419 TYR cc_start: 0.7553 (t80) cc_final: 0.7135 (t80) REVERT: C 427 ASN cc_start: 0.8320 (p0) cc_final: 0.8084 (p0) REVERT: D 50 ASP cc_start: 0.8530 (m-30) cc_final: 0.7884 (p0) REVERT: D 118 ASN cc_start: 0.9490 (m-40) cc_final: 0.9129 (m-40) REVERT: D 160 LEU cc_start: 0.9258 (tp) cc_final: 0.8956 (tt) REVERT: D 301 MET cc_start: 0.8917 (mtm) cc_final: 0.8557 (mtt) REVERT: E 42 MET cc_start: 0.8334 (ptp) cc_final: 0.7611 (ppp) REVERT: E 92 GLU cc_start: 0.8908 (tt0) cc_final: 0.8467 (tm-30) REVERT: E 135 MET cc_start: 0.9195 (ttm) cc_final: 0.8955 (tmm) REVERT: E 235 MET cc_start: 0.8836 (mmm) cc_final: 0.8625 (mmm) REVERT: E 263 MET cc_start: 0.8486 (mtp) cc_final: 0.7989 (mpp) REVERT: E 301 MET cc_start: 0.9019 (mtm) cc_final: 0.8728 (mtp) REVERT: E 348 MET cc_start: 0.8577 (tpt) cc_final: 0.8200 (tpt) REVERT: E 363 GLU cc_start: 0.9100 (tp30) cc_final: 0.8835 (tp30) REVERT: E 373 LYS cc_start: 0.9565 (mmmt) cc_final: 0.9361 (mmmm) REVERT: F 72 MET cc_start: 0.8795 (ptt) cc_final: 0.8525 (ptt) REVERT: F 98 ASP cc_start: 0.7906 (t0) cc_final: 0.7653 (p0) REVERT: F 235 MET cc_start: 0.7350 (mtt) cc_final: 0.6477 (mtp) REVERT: F 341 MET cc_start: 0.8660 (tpt) cc_final: 0.8279 (tpp) REVERT: F 391 GLN cc_start: 0.9380 (mt0) cc_final: 0.9000 (mt0) REVERT: F 414 LEU cc_start: 0.9009 (tp) cc_final: 0.8767 (tp) REVERT: G 537 ASP cc_start: 0.8781 (t0) cc_final: 0.8452 (t0) REVERT: G 568 CYS cc_start: 0.8147 (m) cc_final: 0.7735 (t) REVERT: H 541 HIS cc_start: 0.8997 (m-70) cc_final: 0.8739 (m-70) REVERT: H 550 ARG cc_start: 0.9036 (mmp80) cc_final: 0.8741 (mmm160) REVERT: I 489 VAL cc_start: 0.3809 (t) cc_final: 0.3479 (t) REVERT: I 530 ILE cc_start: 0.8857 (tt) cc_final: 0.8631 (pt) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.1594 time to fit residues: 91.8905 Evaluate side-chains 281 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 33 optimal weight: 5.9990 chunk 258 optimal weight: 10.0000 chunk 257 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 30.0000 chunk 201 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 GLN ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.072508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.055965 restraints weight = 177360.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.057325 restraints weight = 125583.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.058271 restraints weight = 96918.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.059006 restraints weight = 79592.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.059527 restraints weight = 68542.881| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 24908 Z= 0.213 Angle : 1.073 31.753 33783 Z= 0.442 Chirality : 0.043 0.292 3852 Planarity : 0.005 0.055 4422 Dihedral : 7.168 133.121 3554 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.15), residues: 3066 helix: 1.39 (0.12), residues: 1804 sheet: -0.72 (0.28), residues: 301 loop : 0.02 (0.21), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 164 TYR 0.030 0.002 TYR D 122 PHE 0.020 0.002 PHE C 69 TRP 0.022 0.002 TRP F 457 HIS 0.008 0.002 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00454 (24900) covalent geometry : angle 1.07260 (33777) SS BOND : bond 0.00898 ( 3) SS BOND : angle 1.50022 ( 6) hydrogen bonds : bond 0.03513 ( 1466) hydrogen bonds : angle 4.58979 ( 4128) Misc. bond : bond 0.00191 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.9198 (m-30) cc_final: 0.8641 (p0) REVERT: A 84 LEU cc_start: 0.9332 (pp) cc_final: 0.8992 (mp) REVERT: A 135 MET cc_start: 0.9258 (mmt) cc_final: 0.9029 (mmm) REVERT: A 194 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8968 (tp30) REVERT: A 416 MET cc_start: 0.8769 (mmt) cc_final: 0.8449 (mmp) REVERT: A 451 LEU cc_start: 0.8992 (mt) cc_final: 0.8758 (mt) REVERT: B 187 ASP cc_start: 0.9028 (m-30) cc_final: 0.8801 (m-30) REVERT: B 235 MET cc_start: 0.8657 (mmp) cc_final: 0.8126 (mmm) REVERT: B 269 MET cc_start: 0.8983 (tpp) cc_final: 0.8547 (tpp) REVERT: B 291 ASP cc_start: 0.8951 (m-30) cc_final: 0.8675 (p0) REVERT: B 297 ILE cc_start: 0.9443 (mm) cc_final: 0.9211 (pt) REVERT: B 301 MET cc_start: 0.9140 (tmm) cc_final: 0.8790 (tmm) REVERT: C 235 MET cc_start: 0.8995 (mmp) cc_final: 0.8735 (mmm) REVERT: C 250 MET cc_start: 0.8835 (tmm) cc_final: 0.8615 (tmm) REVERT: C 312 ILE cc_start: 0.9619 (mt) cc_final: 0.9400 (tt) REVERT: C 322 GLU cc_start: 0.8482 (mt-10) cc_final: 0.7946 (mt-10) REVERT: C 382 LEU cc_start: 0.9058 (mt) cc_final: 0.8811 (mt) REVERT: C 419 TYR cc_start: 0.7519 (t80) cc_final: 0.6945 (t80) REVERT: D 38 LEU cc_start: 0.8942 (mt) cc_final: 0.8711 (mt) REVERT: D 50 ASP cc_start: 0.8458 (m-30) cc_final: 0.7802 (p0) REVERT: D 118 ASN cc_start: 0.9585 (m-40) cc_final: 0.9286 (m-40) REVERT: D 135 MET cc_start: 0.8951 (ppp) cc_final: 0.8497 (ppp) REVERT: D 160 LEU cc_start: 0.9252 (tp) cc_final: 0.8978 (tt) REVERT: D 270 MET cc_start: 0.9096 (ttm) cc_final: 0.8326 (tmm) REVERT: D 301 MET cc_start: 0.8951 (mtm) cc_final: 0.8620 (mtp) REVERT: D 348 MET cc_start: 0.8567 (tpp) cc_final: 0.8190 (tpp) REVERT: E 42 MET cc_start: 0.8375 (ptp) cc_final: 0.7610 (ppp) REVERT: E 92 GLU cc_start: 0.8915 (tt0) cc_final: 0.8493 (tm-30) REVERT: E 363 GLU cc_start: 0.9166 (tp30) cc_final: 0.8946 (tp30) REVERT: F 72 MET cc_start: 0.8799 (ptt) cc_final: 0.8482 (ptt) REVERT: F 235 MET cc_start: 0.7439 (mtt) cc_final: 0.6562 (mtt) REVERT: F 269 MET cc_start: 0.8800 (ttp) cc_final: 0.8578 (ttm) REVERT: F 341 MET cc_start: 0.8628 (tpt) cc_final: 0.8371 (tpp) REVERT: F 391 GLN cc_start: 0.9380 (mt0) cc_final: 0.8992 (mt0) REVERT: F 418 ILE cc_start: 0.8225 (mp) cc_final: 0.7818 (mp) REVERT: G 537 ASP cc_start: 0.8776 (t0) cc_final: 0.8447 (t0) REVERT: G 568 CYS cc_start: 0.8259 (m) cc_final: 0.7870 (t) REVERT: H 541 HIS cc_start: 0.9020 (m-70) cc_final: 0.8751 (m-70) REVERT: I 530 ILE cc_start: 0.8837 (tt) cc_final: 0.8600 (pt) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.1731 time to fit residues: 94.7153 Evaluate side-chains 264 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 60 optimal weight: 5.9990 chunk 295 optimal weight: 30.0000 chunk 61 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 136 optimal weight: 3.9990 chunk 245 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 ASN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 461 ASN ** 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 = 0.4009 r_free = 0.4009 target = 0.073065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.056456 restraints weight = 175613.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.057852 restraints weight = 124202.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.058838 restraints weight = 95353.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.059595 restraints weight = 77991.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.060088 restraints weight = 66861.700| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 24908 Z= 0.176 Angle : 1.058 30.914 33783 Z= 0.433 Chirality : 0.043 0.241 3852 Planarity : 0.004 0.053 4422 Dihedral : 7.175 132.629 3554 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.15), residues: 3066 helix: 1.37 (0.12), residues: 1803 sheet: -0.84 (0.28), residues: 313 loop : 0.00 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 164 TYR 0.031 0.002 TYR F 105 PHE 0.026 0.002 PHE B 240 TRP 0.035 0.002 TRP D 457 HIS 0.006 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00384 (24900) covalent geometry : angle 1.05757 (33777) SS BOND : bond 0.00950 ( 3) SS BOND : angle 2.55931 ( 6) hydrogen bonds : bond 0.03433 ( 1466) hydrogen bonds : angle 4.57642 ( 4128) Misc. bond : bond 0.00153 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.9182 (m-30) cc_final: 0.8577 (p0) REVERT: A 135 MET cc_start: 0.9243 (mmt) cc_final: 0.8976 (mmm) REVERT: A 194 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8949 (tp30) REVERT: A 451 LEU cc_start: 0.8984 (mt) cc_final: 0.8737 (mt) REVERT: B 72 MET cc_start: 0.8795 (mtt) cc_final: 0.8270 (mtp) REVERT: B 82 ILE cc_start: 0.8541 (mt) cc_final: 0.8295 (mt) REVERT: B 187 ASP cc_start: 0.9030 (m-30) cc_final: 0.8798 (m-30) REVERT: B 225 ASP cc_start: 0.7400 (m-30) cc_final: 0.7185 (m-30) REVERT: B 235 MET cc_start: 0.8630 (mmp) cc_final: 0.8104 (mmm) REVERT: B 269 MET cc_start: 0.8946 (tpp) cc_final: 0.8537 (tpp) REVERT: B 291 ASP cc_start: 0.8889 (m-30) cc_final: 0.8628 (p0) REVERT: B 297 ILE cc_start: 0.9448 (mm) cc_final: 0.9217 (pt) REVERT: B 301 MET cc_start: 0.9135 (tmm) cc_final: 0.8820 (tmm) REVERT: C 235 MET cc_start: 0.8907 (mmp) cc_final: 0.8653 (mmm) REVERT: C 250 MET cc_start: 0.8800 (tmm) cc_final: 0.8573 (tmm) REVERT: C 312 ILE cc_start: 0.9614 (mt) cc_final: 0.9384 (tt) REVERT: C 322 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7917 (mt-10) REVERT: C 337 ILE cc_start: 0.8791 (tt) cc_final: 0.8235 (mt) REVERT: C 382 LEU cc_start: 0.9055 (mt) cc_final: 0.8822 (mt) REVERT: C 419 TYR cc_start: 0.7525 (t80) cc_final: 0.6957 (t80) REVERT: C 427 ASN cc_start: 0.8388 (p0) cc_final: 0.8094 (p0) REVERT: D 50 ASP cc_start: 0.8463 (m-30) cc_final: 0.7758 (p0) REVERT: D 118 ASN cc_start: 0.9563 (m-40) cc_final: 0.9236 (m-40) REVERT: D 135 MET cc_start: 0.8966 (ppp) cc_final: 0.8539 (ppp) REVERT: D 301 MET cc_start: 0.8950 (mtm) cc_final: 0.8547 (mtt) REVERT: D 341 MET cc_start: 0.7764 (ttm) cc_final: 0.7554 (ttm) REVERT: D 348 MET cc_start: 0.8503 (tpp) cc_final: 0.8202 (tpp) REVERT: E 42 MET cc_start: 0.8471 (ptp) cc_final: 0.7654 (ppp) REVERT: E 92 GLU cc_start: 0.8908 (tt0) cc_final: 0.8497 (tm-30) REVERT: E 348 MET cc_start: 0.8817 (tpt) cc_final: 0.8329 (tpt) REVERT: E 363 GLU cc_start: 0.9158 (tp30) cc_final: 0.8900 (tp30) REVERT: F 72 MET cc_start: 0.8881 (ptt) cc_final: 0.8586 (ptt) REVERT: F 98 ASP cc_start: 0.7927 (t0) cc_final: 0.7631 (p0) REVERT: F 235 MET cc_start: 0.7381 (mtt) cc_final: 0.6510 (mtt) REVERT: F 263 MET cc_start: 0.7077 (mpp) cc_final: 0.6831 (mpp) REVERT: F 391 GLN cc_start: 0.9365 (mt0) cc_final: 0.8975 (mt0) REVERT: F 418 ILE cc_start: 0.8169 (mp) cc_final: 0.7741 (mp) REVERT: G 537 ASP cc_start: 0.8739 (t0) cc_final: 0.8409 (t0) REVERT: G 568 CYS cc_start: 0.8110 (m) cc_final: 0.7774 (t) REVERT: H 541 HIS cc_start: 0.9056 (m-70) cc_final: 0.8796 (m-70) REVERT: H 550 ARG cc_start: 0.9051 (mmp80) cc_final: 0.8711 (mmm160) REVERT: I 530 ILE cc_start: 0.8808 (tt) cc_final: 0.8583 (pt) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.1629 time to fit residues: 87.6991 Evaluate side-chains 265 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 145 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 170 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 267 optimal weight: 20.0000 chunk 244 optimal weight: 0.9990 chunk 299 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN G 512 ASN G 541 HIS ** I 461 ASN ** 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 = 0.4004 r_free = 0.4004 target = 0.072899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.056378 restraints weight = 175449.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.057740 restraints weight = 124676.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.058729 restraints weight = 96211.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.059457 restraints weight = 78799.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.059995 restraints weight = 67535.573| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 24908 Z= 0.179 Angle : 1.068 31.100 33783 Z= 0.439 Chirality : 0.043 0.305 3852 Planarity : 0.004 0.052 4422 Dihedral : 7.186 132.993 3554 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.15), residues: 3066 helix: 1.35 (0.12), residues: 1801 sheet: -0.92 (0.27), residues: 312 loop : 0.04 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 392 TYR 0.026 0.002 TYR D 122 PHE 0.016 0.002 PHE C 69 TRP 0.046 0.002 TRP E 48 HIS 0.005 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00396 (24900) covalent geometry : angle 1.06739 (33777) SS BOND : bond 0.01134 ( 3) SS BOND : angle 2.52847 ( 6) hydrogen bonds : bond 0.03438 ( 1466) hydrogen bonds : angle 4.60667 ( 4128) Misc. bond : bond 0.00136 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.9201 (m-30) cc_final: 0.8564 (p0) REVERT: A 84 LEU cc_start: 0.9394 (pp) cc_final: 0.9156 (mm) REVERT: A 135 MET cc_start: 0.9227 (mmt) cc_final: 0.8979 (mmm) REVERT: A 194 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8947 (tp30) REVERT: A 240 PHE cc_start: 0.9345 (t80) cc_final: 0.9132 (t80) REVERT: A 402 LEU cc_start: 0.9158 (mt) cc_final: 0.8615 (mt) REVERT: A 416 MET cc_start: 0.8987 (mmt) cc_final: 0.8628 (mmp) REVERT: A 451 LEU cc_start: 0.8971 (mt) cc_final: 0.8749 (mt) REVERT: B 42 MET cc_start: 0.8237 (mtp) cc_final: 0.8019 (mtp) REVERT: B 72 MET cc_start: 0.8795 (mtt) cc_final: 0.8337 (mtp) REVERT: B 82 ILE cc_start: 0.8531 (mt) cc_final: 0.8267 (mt) REVERT: B 187 ASP cc_start: 0.9045 (m-30) cc_final: 0.8816 (m-30) REVERT: B 235 MET cc_start: 0.8601 (mmp) cc_final: 0.8084 (mmm) REVERT: B 269 MET cc_start: 0.8918 (tpp) cc_final: 0.8525 (tpp) REVERT: B 291 ASP cc_start: 0.8910 (m-30) cc_final: 0.8651 (p0) REVERT: B 297 ILE cc_start: 0.9462 (mm) cc_final: 0.9235 (pt) REVERT: B 301 MET cc_start: 0.9131 (tmm) cc_final: 0.8812 (tmm) REVERT: C 235 MET cc_start: 0.8910 (mmp) cc_final: 0.8654 (mmm) REVERT: C 250 MET cc_start: 0.8846 (tmm) cc_final: 0.8589 (tmm) REVERT: C 312 ILE cc_start: 0.9600 (mt) cc_final: 0.9368 (tt) REVERT: C 322 GLU cc_start: 0.8441 (mt-10) cc_final: 0.7898 (mt-10) REVERT: C 337 ILE cc_start: 0.8800 (tt) cc_final: 0.8297 (mt) REVERT: C 419 TYR cc_start: 0.7540 (t80) cc_final: 0.6970 (t80) REVERT: C 427 ASN cc_start: 0.8431 (p0) cc_final: 0.8149 (p0) REVERT: D 50 ASP cc_start: 0.8512 (m-30) cc_final: 0.7803 (p0) REVERT: D 118 ASN cc_start: 0.9556 (m-40) cc_final: 0.9235 (m-40) REVERT: D 135 MET cc_start: 0.8953 (ppp) cc_final: 0.8527 (ppp) REVERT: D 301 MET cc_start: 0.8931 (mtm) cc_final: 0.8530 (mtt) REVERT: D 348 MET cc_start: 0.8584 (tpp) cc_final: 0.8229 (tpp) REVERT: E 42 MET cc_start: 0.8461 (ptp) cc_final: 0.7686 (ppp) REVERT: E 92 GLU cc_start: 0.8907 (tt0) cc_final: 0.8485 (tm-30) REVERT: E 135 MET cc_start: 0.8916 (ppp) cc_final: 0.8685 (ppp) REVERT: E 348 MET cc_start: 0.8776 (tpt) cc_final: 0.8259 (tpt) REVERT: E 363 GLU cc_start: 0.9159 (tp30) cc_final: 0.8873 (tp30) REVERT: F 72 MET cc_start: 0.8924 (ptt) cc_final: 0.8612 (ptt) REVERT: F 98 ASP cc_start: 0.7917 (t0) cc_final: 0.7631 (p0) REVERT: F 235 MET cc_start: 0.7441 (mtt) cc_final: 0.6535 (mtt) REVERT: F 341 MET cc_start: 0.8806 (tpp) cc_final: 0.8604 (tpp) REVERT: F 347 LEU cc_start: 0.8488 (mt) cc_final: 0.8206 (mt) REVERT: F 348 MET cc_start: 0.8131 (tpt) cc_final: 0.7888 (tpt) REVERT: F 391 GLN cc_start: 0.9351 (mt0) cc_final: 0.8968 (mt0) REVERT: F 418 ILE cc_start: 0.8157 (mp) cc_final: 0.7712 (mp) REVERT: G 512 ASN cc_start: 0.8108 (t160) cc_final: 0.6720 (m110) REVERT: G 537 ASP cc_start: 0.8720 (t0) cc_final: 0.8402 (t0) REVERT: G 568 CYS cc_start: 0.8095 (m) cc_final: 0.7797 (t) REVERT: H 541 HIS cc_start: 0.9118 (m-70) cc_final: 0.8879 (m-70) REVERT: H 550 ARG cc_start: 0.9048 (mmp80) cc_final: 0.8713 (mmm160) REVERT: I 530 ILE cc_start: 0.8815 (tt) cc_final: 0.8574 (pt) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.1669 time to fit residues: 90.9186 Evaluate side-chains 258 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 176 optimal weight: 0.7980 chunk 296 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 161 optimal weight: 20.0000 chunk 171 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 284 optimal weight: 0.7980 chunk 272 optimal weight: 4.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 GLN ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN G 541 HIS ** I 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 490 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.073474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.057072 restraints weight = 176173.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.058446 restraints weight = 124562.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.059452 restraints weight = 95849.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.060200 restraints weight = 78148.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.060687 restraints weight = 66940.280| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 24908 Z= 0.158 Angle : 1.052 30.755 33783 Z= 0.428 Chirality : 0.042 0.296 3852 Planarity : 0.004 0.050 4422 Dihedral : 7.111 133.136 3554 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.15), residues: 3066 helix: 1.42 (0.12), residues: 1803 sheet: -0.90 (0.28), residues: 313 loop : 0.06 (0.22), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 349 TYR 0.032 0.002 TYR F 105 PHE 0.024 0.002 PHE B 240 TRP 0.056 0.002 TRP E 48 HIS 0.005 0.001 HIS H 541 Details of bonding type rmsd covalent geometry : bond 0.00355 (24900) covalent geometry : angle 1.05156 (33777) SS BOND : bond 0.01048 ( 3) SS BOND : angle 2.31534 ( 6) hydrogen bonds : bond 0.03296 ( 1466) hydrogen bonds : angle 4.54741 ( 4128) Misc. bond : bond 0.00121 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5284.65 seconds wall clock time: 91 minutes 38.82 seconds (5498.82 seconds total)