Starting phenix.real_space_refine on Sat Jun 21 07:57:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t22_25609/06_2025/7t22_25609.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t22_25609/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7t22_25609/06_2025/7t22_25609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t22_25609/06_2025/7t22_25609.map" model { file = "/net/cci-nas-00/data/ceres_data/7t22_25609/06_2025/7t22_25609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t22_25609/06_2025/7t22_25609.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.28, per 1000 atoms: 0.58 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: 5.88 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 2.48 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: 8.83 Time building geometry restraints manager: 6.98 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 53.290 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.390 ------------------------------------------------------------------------------- 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 : 5.52 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.006 0.001 TRP B 48 HIS 0.003 0.001 HIS E 334 PHE 0.006 0.001 PHE D 166 TYR 0.008 0.001 TYR B 344 ARG 0.006 0.000 ARG E 387 Details of bonding type rmsd hydrogen bonds : bond 0.15030 ( 1466) hydrogen bonds : angle 4.78735 ( 4128) SS BOND : bond 0.00543 ( 3) SS BOND : angle 1.24451 ( 6) covalent geometry : bond 0.00415 (24900) covalent geometry : angle 1.41161 (33777) 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 : 2.859 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: 0.4537 time to fit residues: 458.4567 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 : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 7.9990 chunk 230 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 238 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 chunk 177 optimal weight: 9.9990 chunk 276 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 410 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.078084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.060875 restraints weight = 163497.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.062345 restraints weight = 116518.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.063419 restraints weight = 89871.311| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2521 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= 0.178 Angle : 1.049 30.987 33783 Z= 0.428 Chirality : 0.042 0.244 3852 Planarity : 0.005 0.118 4422 Dihedral : 7.557 121.786 3554 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.30 % Allowed : 2.01 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.15), residues: 3066 helix: 2.21 (0.12), residues: 1785 sheet: -0.59 (0.27), residues: 322 loop : 0.40 (0.22), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 48 HIS 0.008 0.002 HIS A 334 PHE 0.022 0.002 PHE F 240 TYR 0.026 0.002 TYR F 122 ARG 0.015 0.001 ARG E 387 Details of bonding type rmsd hydrogen bonds : bond 0.04138 ( 1466) hydrogen bonds : angle 4.39592 ( 4128) SS BOND : bond 0.02331 ( 3) SS BOND : angle 1.50040 ( 6) covalent geometry : bond 0.00390 (24900) covalent geometry : angle 1.04845 (33777) Misc. bond : bond 0.00265 ( 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: 8 poor density : 448 time to evaluate : 2.811 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: A 58 ASP cc_start: 0.9140 (m-30) cc_final: 0.8687 (p0) REVERT: A 135 MET cc_start: 0.8752 (ttm) cc_final: 0.8504 (ppp) REVERT: A 291 ASP cc_start: 0.8840 (m-30) cc_final: 0.8291 (p0) REVERT: A 345 LEU cc_start: 0.8074 (mt) cc_final: 0.7789 (mt) REVERT: B 72 MET cc_start: 0.8682 (mtt) cc_final: 0.8432 (mtt) REVERT: B 226 LEU cc_start: 0.8379 (tp) cc_final: 0.8086 (mm) REVERT: B 235 MET cc_start: 0.8845 (mmt) cc_final: 0.8539 (mmm) REVERT: B 240 PHE cc_start: 0.9095 (t80) cc_final: 0.8857 (t80) REVERT: B 269 MET cc_start: 0.8952 (tpp) cc_final: 0.8520 (tpp) REVERT: B 291 ASP cc_start: 0.9007 (m-30) cc_final: 0.8750 (p0) REVERT: B 297 ILE cc_start: 0.9481 (mm) cc_final: 0.9238 (pt) REVERT: B 301 MET cc_start: 0.8950 (tmm) cc_final: 0.8735 (tmm) REVERT: B 324 ARG cc_start: 0.9190 (ttm170) cc_final: 0.8700 (ttt180) REVERT: B 348 MET cc_start: 0.7267 (mtp) cc_final: 0.6760 (mpp) REVERT: B 414 LEU cc_start: 0.9154 (tp) cc_final: 0.8869 (tp) REVERT: C 235 MET cc_start: 0.9062 (mmp) cc_final: 0.8771 (mmm) REVERT: C 259 PHE cc_start: 0.9222 (m-80) cc_final: 0.8822 (m-80) REVERT: C 269 MET cc_start: 0.8819 (tpp) cc_final: 0.8617 (ttt) REVERT: C 312 ILE cc_start: 0.9427 (mp) cc_final: 0.9000 (tt) REVERT: C 382 LEU cc_start: 0.8815 (mt) cc_final: 0.8574 (mt) REVERT: C 427 ASN cc_start: 0.8148 (p0) cc_final: 0.7806 (p0) REVERT: D 34 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8727 (mt-10) REVERT: D 58 ASP cc_start: 0.9037 (m-30) cc_final: 0.8793 (p0) REVERT: D 118 ASN cc_start: 0.9470 (m-40) cc_final: 0.9178 (m-40) REVERT: D 160 LEU cc_start: 0.9201 (tp) cc_final: 0.8907 (tt) REVERT: D 237 LYS cc_start: 0.8687 (ttpt) cc_final: 0.8430 (ptpt) REVERT: D 269 MET cc_start: 0.8490 (ttm) cc_final: 0.8096 (ttm) REVERT: D 301 MET cc_start: 0.8913 (mtm) cc_final: 0.8580 (mtt) REVERT: D 337 ILE cc_start: 0.8711 (mt) cc_final: 0.8484 (mm) REVERT: E 60 PHE cc_start: 0.9067 (m-80) cc_final: 0.8856 (m-80) REVERT: E 92 GLU cc_start: 0.8841 (tt0) cc_final: 0.8585 (tm-30) REVERT: E 235 MET cc_start: 0.8848 (mmt) cc_final: 0.8238 (mmm) REVERT: E 267 GLN cc_start: 0.9175 (mp10) cc_final: 0.8947 (mp10) REVERT: E 363 GLU cc_start: 0.9183 (tp30) cc_final: 0.8886 (tp30) REVERT: F 98 ASP cc_start: 0.7864 (t0) cc_final: 0.7619 (p0) REVERT: F 235 MET cc_start: 0.7333 (mtt) cc_final: 0.6445 (mtp) REVERT: F 263 MET cc_start: 0.6986 (mpp) cc_final: 0.6710 (mpp) REVERT: F 282 THR cc_start: 0.9246 (m) cc_final: 0.8930 (p) REVERT: F 318 LEU cc_start: 0.8350 (mp) cc_final: 0.8083 (mp) REVERT: G 468 VAL cc_start: 0.6632 (t) cc_final: 0.6299 (t) REVERT: G 568 CYS cc_start: 0.8195 (m) cc_final: 0.7782 (t) REVERT: H 550 ARG cc_start: 0.8968 (mmp80) cc_final: 0.8708 (mmm160) REVERT: I 489 VAL cc_start: 0.4216 (t) cc_final: 0.3973 (t) REVERT: I 530 ILE cc_start: 0.8875 (tt) cc_final: 0.8671 (pt) outliers start: 8 outliers final: 1 residues processed: 452 average time/residue: 0.4006 time to fit residues: 274.9341 Evaluate side-chains 323 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 322 time to evaluate : 2.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 167 optimal weight: 7.9990 chunk 176 optimal weight: 30.0000 chunk 241 optimal weight: 20.0000 chunk 275 optimal weight: 8.9990 chunk 171 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 177 optimal weight: 20.0000 chunk 227 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** 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 D 65 HIS ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.074026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.057225 restraints weight = 172789.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.058577 restraints weight = 123861.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.059567 restraints weight = 96161.052| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 24908 Z= 0.240 Angle : 1.078 32.253 33783 Z= 0.449 Chirality : 0.043 0.215 3852 Planarity : 0.006 0.083 4422 Dihedral : 7.573 129.683 3554 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.11 % Allowed : 3.04 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.15), residues: 3066 helix: 1.62 (0.12), residues: 1792 sheet: -0.78 (0.27), residues: 328 loop : 0.24 (0.22), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 48 HIS 0.013 0.002 HIS D 65 PHE 0.018 0.002 PHE F 240 TYR 0.035 0.002 TYR B 122 ARG 0.009 0.001 ARG C 278 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 1466) hydrogen bonds : angle 4.59275 ( 4128) SS BOND : bond 0.01149 ( 3) SS BOND : angle 1.82736 ( 6) covalent geometry : bond 0.00498 (24900) covalent geometry : angle 1.07773 (33777) Misc. bond : bond 0.00251 ( 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 404 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 401 time to evaluate : 2.671 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: A 58 ASP cc_start: 0.9175 (m-30) cc_final: 0.8687 (p0) REVERT: A 135 MET cc_start: 0.8798 (ttm) cc_final: 0.8585 (ppp) REVERT: A 194 GLU cc_start: 0.9263 (mt-10) cc_final: 0.9010 (tp30) REVERT: A 242 MET cc_start: 0.8941 (ppp) cc_final: 0.8669 (ppp) REVERT: A 291 ASP cc_start: 0.8873 (m-30) cc_final: 0.8285 (p0) REVERT: A 345 LEU cc_start: 0.7971 (mt) cc_final: 0.7558 (mt) REVERT: A 416 MET cc_start: 0.8657 (mmp) cc_final: 0.8183 (mmm) REVERT: A 438 ILE cc_start: 0.8397 (mp) cc_final: 0.7962 (mp) REVERT: B 226 LEU cc_start: 0.8173 (tp) cc_final: 0.7637 (mm) REVERT: B 240 PHE cc_start: 0.9074 (t80) cc_final: 0.8823 (t80) REVERT: B 269 MET cc_start: 0.9021 (tpp) cc_final: 0.8613 (tpp) REVERT: B 291 ASP cc_start: 0.9061 (m-30) cc_final: 0.8786 (p0) REVERT: B 297 ILE cc_start: 0.9471 (mm) cc_final: 0.9209 (pt) REVERT: B 301 MET cc_start: 0.9043 (tmm) cc_final: 0.8763 (tmm) REVERT: B 348 MET cc_start: 0.7617 (mtp) cc_final: 0.7178 (ttm) REVERT: C 235 MET cc_start: 0.9026 (mmp) cc_final: 0.8763 (mmm) REVERT: C 250 MET cc_start: 0.8759 (tmm) cc_final: 0.8549 (tmm) REVERT: C 322 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8112 (mt-10) REVERT: C 382 LEU cc_start: 0.8896 (mt) cc_final: 0.8607 (mt) REVERT: C 427 ASN cc_start: 0.8279 (p0) cc_final: 0.8011 (p0) REVERT: D 118 ASN cc_start: 0.9516 (m-40) cc_final: 0.9261 (m-40) REVERT: D 160 LEU cc_start: 0.9248 (tp) cc_final: 0.8954 (tt) REVERT: D 301 MET cc_start: 0.8989 (mtm) cc_final: 0.8604 (mtt) REVERT: D 337 ILE cc_start: 0.8748 (mt) cc_final: 0.8539 (mm) REVERT: E 42 MET cc_start: 0.8388 (mtm) cc_final: 0.8141 (ptp) REVERT: E 92 GLU cc_start: 0.8870 (tt0) cc_final: 0.8536 (tp30) REVERT: E 134 GLU cc_start: 0.9447 (OUTLIER) cc_final: 0.9234 (pp20) REVERT: E 235 MET cc_start: 0.8961 (mmt) cc_final: 0.8415 (mmm) REVERT: E 344 TYR cc_start: 0.7796 (p90) cc_final: 0.7078 (p90) REVERT: E 363 GLU cc_start: 0.9226 (tp30) cc_final: 0.8909 (tp30) REVERT: E 443 ASN cc_start: 0.8463 (m-40) cc_final: 0.7285 (t0) REVERT: F 98 ASP cc_start: 0.7840 (t0) cc_final: 0.7566 (p0) REVERT: F 391 GLN cc_start: 0.9398 (mt0) cc_final: 0.9161 (mt0) REVERT: G 537 ASP cc_start: 0.8835 (t0) cc_final: 0.8520 (t0) REVERT: G 568 CYS cc_start: 0.8134 (m) cc_final: 0.7777 (t) REVERT: H 550 ARG cc_start: 0.8981 (mmp80) cc_final: 0.8711 (mmm160) REVERT: I 489 VAL cc_start: 0.4009 (t) cc_final: 0.3774 (t) REVERT: I 530 ILE cc_start: 0.8946 (tt) cc_final: 0.8734 (pt) outliers start: 3 outliers final: 0 residues processed: 403 average time/residue: 0.3951 time to fit residues: 244.7079 Evaluate side-chains 298 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 297 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 271 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 242 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 196 optimal weight: 0.4980 chunk 171 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 278 optimal weight: 30.0000 chunk 258 optimal weight: 10.0000 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 441 GLN B 281 GLN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 HIS F 252 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.075057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.058402 restraints weight = 172470.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.059731 restraints weight = 124608.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.060701 restraints weight = 97229.375| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24908 Z= 0.157 Angle : 1.020 30.303 33783 Z= 0.411 Chirality : 0.041 0.207 3852 Planarity : 0.004 0.066 4422 Dihedral : 7.296 130.231 3554 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.04 % Allowed : 1.97 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.15), residues: 3066 helix: 1.70 (0.12), residues: 1789 sheet: -0.65 (0.27), residues: 322 loop : 0.26 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 48 HIS 0.006 0.001 HIS A 334 PHE 0.016 0.002 PHE F 240 TYR 0.035 0.002 TYR B 122 ARG 0.008 0.001 ARG E 396 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 1466) hydrogen bonds : angle 4.42906 ( 4128) SS BOND : bond 0.00948 ( 3) SS BOND : angle 1.61938 ( 6) covalent geometry : bond 0.00342 (24900) covalent geometry : angle 1.02011 (33777) Misc. bond : bond 0.00169 ( 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 397 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 396 time to evaluate : 2.626 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: 0.9181 (m-30) cc_final: 0.8659 (p0) REVERT: A 194 GLU cc_start: 0.9234 (mt-10) cc_final: 0.9003 (tp30) REVERT: A 291 ASP cc_start: 0.8819 (m-30) cc_final: 0.8222 (p0) REVERT: A 345 LEU cc_start: 0.7941 (mt) cc_final: 0.7610 (mt) REVERT: A 416 MET cc_start: 0.8643 (mmp) cc_final: 0.8216 (mmm) REVERT: A 438 ILE cc_start: 0.8280 (mp) cc_final: 0.7901 (mp) REVERT: B 226 LEU cc_start: 0.8459 (tp) cc_final: 0.8223 (mm) REVERT: B 240 PHE cc_start: 0.9095 (t80) cc_final: 0.8853 (t80) REVERT: B 291 ASP cc_start: 0.9046 (m-30) cc_final: 0.8768 (p0) REVERT: B 297 ILE cc_start: 0.9444 (mm) cc_final: 0.9211 (pt) REVERT: B 301 MET cc_start: 0.9066 (tmm) cc_final: 0.8728 (tmm) REVERT: B 348 MET cc_start: 0.7537 (mtp) cc_final: 0.7070 (ttm) REVERT: C 235 MET cc_start: 0.8991 (mmp) cc_final: 0.8711 (mmm) REVERT: C 250 MET cc_start: 0.8786 (tmm) cc_final: 0.8534 (tmm) REVERT: C 270 MET cc_start: 0.8805 (mtp) cc_final: 0.8027 (ttm) REVERT: C 322 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8088 (mt-10) REVERT: C 382 LEU cc_start: 0.8862 (mt) cc_final: 0.8471 (mt) REVERT: C 419 TYR cc_start: 0.7699 (t80) cc_final: 0.7313 (t80) REVERT: C 427 ASN cc_start: 0.8243 (p0) cc_final: 0.7990 (p0) REVERT: D 42 MET cc_start: 0.7422 (mtp) cc_final: 0.7117 (mtp) REVERT: D 118 ASN cc_start: 0.9511 (m-40) cc_final: 0.9186 (m-40) REVERT: D 160 LEU cc_start: 0.9246 (tp) cc_final: 0.8956 (tt) REVERT: D 270 MET cc_start: 0.8924 (ttm) cc_final: 0.8567 (tpp) REVERT: D 284 ILE cc_start: 0.9256 (mt) cc_final: 0.8931 (mt) REVERT: D 301 MET cc_start: 0.8963 (mtm) cc_final: 0.8612 (mtt) REVERT: D 337 ILE cc_start: 0.8678 (mt) cc_final: 0.8468 (mm) REVERT: E 42 MET cc_start: 0.8339 (mtm) cc_final: 0.8048 (ptm) REVERT: E 92 GLU cc_start: 0.8980 (tt0) cc_final: 0.8570 (tp30) REVERT: E 235 MET cc_start: 0.8874 (mmt) cc_final: 0.8602 (mmm) REVERT: E 301 MET cc_start: 0.9203 (mtm) cc_final: 0.8864 (mtt) REVERT: E 348 MET cc_start: 0.8466 (mmp) cc_final: 0.7993 (mmp) REVERT: E 363 GLU cc_start: 0.9186 (tp30) cc_final: 0.8846 (tp30) REVERT: F 98 ASP cc_start: 0.7835 (t0) cc_final: 0.7558 (p0) REVERT: F 235 MET cc_start: 0.7437 (mtt) cc_final: 0.6605 (mtp) REVERT: F 263 MET cc_start: 0.6932 (mpp) cc_final: 0.6669 (mpp) REVERT: F 270 MET cc_start: 0.8480 (ttt) cc_final: 0.8259 (ttt) REVERT: F 391 GLN cc_start: 0.9423 (mt0) cc_final: 0.9156 (mt0) REVERT: G 537 ASP cc_start: 0.8754 (t0) cc_final: 0.8441 (t0) REVERT: G 568 CYS cc_start: 0.8191 (m) cc_final: 0.7777 (t) REVERT: H 550 ARG cc_start: 0.9007 (mmp80) cc_final: 0.8741 (mmm160) REVERT: I 489 VAL cc_start: 0.3982 (t) cc_final: 0.3742 (t) REVERT: I 530 ILE cc_start: 0.8914 (tt) cc_final: 0.8704 (pt) outliers start: 1 outliers final: 0 residues processed: 397 average time/residue: 0.4116 time to fit residues: 251.5157 Evaluate side-chains 287 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 2.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 276 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 201 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 189 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 210 optimal weight: 5.9990 chunk 191 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN D 45 ASN D 391 GLN ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 575 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.075455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.058884 restraints weight = 169526.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.060194 restraints weight = 122470.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.061195 restraints weight = 95206.584| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24908 Z= 0.132 Angle : 1.011 30.044 33783 Z= 0.403 Chirality : 0.041 0.174 3852 Planarity : 0.004 0.058 4422 Dihedral : 7.112 129.758 3554 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.04 % Allowed : 2.16 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.15), residues: 3066 helix: 1.77 (0.12), residues: 1796 sheet: -0.56 (0.27), residues: 322 loop : 0.32 (0.22), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 48 HIS 0.005 0.001 HIS A 334 PHE 0.042 0.002 PHE C 166 TYR 0.022 0.001 TYR D 122 ARG 0.013 0.000 ARG D 326 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 1466) hydrogen bonds : angle 4.31594 ( 4128) SS BOND : bond 0.01047 ( 3) SS BOND : angle 2.19676 ( 6) covalent geometry : bond 0.00290 (24900) covalent geometry : angle 1.01067 (33777) Misc. bond : bond 0.00127 ( 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 387 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 386 time to evaluate : 3.222 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: A 58 ASP cc_start: 0.9237 (m-30) cc_final: 0.8735 (p0) REVERT: A 194 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8975 (tp30) REVERT: A 242 MET cc_start: 0.8950 (ppp) cc_final: 0.8723 (ppp) REVERT: A 269 MET cc_start: 0.7097 (tpt) cc_final: 0.6591 (tpt) REVERT: A 291 ASP cc_start: 0.8831 (m-30) cc_final: 0.8222 (p0) REVERT: A 345 LEU cc_start: 0.8034 (mt) cc_final: 0.7709 (mt) REVERT: A 416 MET cc_start: 0.8682 (mmp) cc_final: 0.8266 (mmm) REVERT: A 438 ILE cc_start: 0.8192 (mp) cc_final: 0.7850 (mp) REVERT: B 187 ASP cc_start: 0.9115 (m-30) cc_final: 0.8907 (m-30) REVERT: B 240 PHE cc_start: 0.9121 (t80) cc_final: 0.8867 (t80) REVERT: B 291 ASP cc_start: 0.9011 (m-30) cc_final: 0.8737 (p0) REVERT: B 297 ILE cc_start: 0.9445 (mm) cc_final: 0.9211 (pt) REVERT: B 301 MET cc_start: 0.9118 (tmm) cc_final: 0.8773 (tmm) REVERT: B 348 MET cc_start: 0.7518 (mtp) cc_final: 0.6947 (mpp) REVERT: B 411 ASP cc_start: 0.8013 (m-30) cc_final: 0.7627 (m-30) REVERT: C 51 VAL cc_start: 0.8351 (t) cc_final: 0.8140 (p) REVERT: C 160 LEU cc_start: 0.9561 (tt) cc_final: 0.8931 (pp) REVERT: C 235 MET cc_start: 0.8964 (mmp) cc_final: 0.8652 (mmm) REVERT: C 250 MET cc_start: 0.8798 (tmm) cc_final: 0.8571 (tmm) REVERT: C 270 MET cc_start: 0.8773 (mtp) cc_final: 0.7895 (ttt) REVERT: C 322 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8134 (mt-10) REVERT: C 382 LEU cc_start: 0.8938 (mt) cc_final: 0.8532 (mt) REVERT: C 419 TYR cc_start: 0.7699 (t80) cc_final: 0.7193 (t80) REVERT: C 427 ASN cc_start: 0.8312 (p0) cc_final: 0.8076 (p0) REVERT: D 118 ASN cc_start: 0.9465 (m-40) cc_final: 0.9127 (m-40) REVERT: D 160 LEU cc_start: 0.9251 (tp) cc_final: 0.8964 (tt) REVERT: D 269 MET cc_start: 0.8850 (mtp) cc_final: 0.8634 (ptm) REVERT: D 301 MET cc_start: 0.8983 (mtm) cc_final: 0.8617 (mtt) REVERT: E 92 GLU cc_start: 0.8980 (tt0) cc_final: 0.8567 (tp30) REVERT: E 187 ASP cc_start: 0.8641 (m-30) cc_final: 0.8361 (p0) REVERT: E 235 MET cc_start: 0.8795 (mmt) cc_final: 0.8583 (mmm) REVERT: E 301 MET cc_start: 0.9144 (mtm) cc_final: 0.8694 (mtp) REVERT: E 348 MET cc_start: 0.8476 (mmp) cc_final: 0.8010 (mmp) REVERT: E 363 GLU cc_start: 0.9169 (tp30) cc_final: 0.8900 (tp30) REVERT: F 98 ASP cc_start: 0.7815 (t0) cc_final: 0.7566 (p0) REVERT: F 235 MET cc_start: 0.7408 (mtt) cc_final: 0.6528 (mtp) REVERT: F 270 MET cc_start: 0.8345 (ttt) cc_final: 0.8082 (ttt) REVERT: F 282 THR cc_start: 0.9228 (m) cc_final: 0.8952 (p) REVERT: F 391 GLN cc_start: 0.9426 (mt0) cc_final: 0.9132 (mt0) REVERT: G 537 ASP cc_start: 0.8723 (t0) cc_final: 0.8385 (t0) REVERT: G 568 CYS cc_start: 0.8116 (m) cc_final: 0.7721 (t) REVERT: H 550 ARG cc_start: 0.9010 (mmp80) cc_final: 0.8740 (mmm160) REVERT: I 489 VAL cc_start: 0.3968 (t) cc_final: 0.3744 (t) REVERT: I 530 ILE cc_start: 0.8898 (tt) cc_final: 0.8669 (pt) outliers start: 1 outliers final: 1 residues processed: 387 average time/residue: 0.4015 time to fit residues: 239.4817 Evaluate side-chains 290 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 289 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 296 optimal weight: 8.9990 chunk 241 optimal weight: 3.9990 chunk 197 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 173 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 301 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 293 optimal weight: 40.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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** A 281 GLN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN E 222 GLN F 45 ASN ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS H 541 HIS ** H 551 GLN ** 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 = 0.4008 r_free = 0.4008 target = 0.073412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.057059 restraints weight = 174208.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.058321 restraints weight = 125503.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.059255 restraints weight = 97996.780| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24908 Z= 0.186 Angle : 1.058 31.634 33783 Z= 0.430 Chirality : 0.042 0.331 3852 Planarity : 0.005 0.088 4422 Dihedral : 7.213 130.640 3554 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.15), residues: 3066 helix: 1.60 (0.12), residues: 1789 sheet: -0.64 (0.28), residues: 318 loop : 0.25 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 48 HIS 0.007 0.002 HIS G 541 PHE 0.016 0.002 PHE C 417 TYR 0.026 0.002 TYR D 122 ARG 0.013 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 1466) hydrogen bonds : angle 4.51425 ( 4128) SS BOND : bond 0.00949 ( 3) SS BOND : angle 1.73176 ( 6) covalent geometry : bond 0.00393 (24900) covalent geometry : angle 1.05821 (33777) Misc. bond : bond 0.00180 ( 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 362 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 2.712 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: 0.9188 (m-30) cc_final: 0.8656 (p0) REVERT: A 194 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8971 (tp30) REVERT: A 242 MET cc_start: 0.8956 (ppp) cc_final: 0.8643 (ppp) REVERT: A 291 ASP cc_start: 0.8882 (m-30) cc_final: 0.8259 (p0) REVERT: A 416 MET cc_start: 0.8651 (mmp) cc_final: 0.8230 (mmm) REVERT: A 438 ILE cc_start: 0.8167 (mp) cc_final: 0.7786 (mp) REVERT: B 187 ASP cc_start: 0.9126 (m-30) cc_final: 0.8914 (m-30) REVERT: B 225 ASP cc_start: 0.7924 (m-30) cc_final: 0.7596 (m-30) REVERT: B 235 MET cc_start: 0.8805 (mmt) cc_final: 0.8477 (mmm) REVERT: B 240 PHE cc_start: 0.9115 (t80) cc_final: 0.8828 (t80) REVERT: B 291 ASP cc_start: 0.9025 (m-30) cc_final: 0.8734 (p0) REVERT: B 297 ILE cc_start: 0.9448 (mm) cc_final: 0.9215 (pt) REVERT: B 301 MET cc_start: 0.9128 (tmm) cc_final: 0.8789 (tmm) REVERT: B 348 MET cc_start: 0.7657 (mtp) cc_final: 0.7184 (ttm) REVERT: C 235 MET cc_start: 0.8982 (mmp) cc_final: 0.8699 (mmm) REVERT: C 270 MET cc_start: 0.8850 (mtp) cc_final: 0.8564 (ttt) REVERT: C 322 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8081 (mt-10) REVERT: C 382 LEU cc_start: 0.8963 (mt) cc_final: 0.8717 (mt) REVERT: C 419 TYR cc_start: 0.7672 (t80) cc_final: 0.7116 (t80) REVERT: C 427 ASN cc_start: 0.8371 (p0) cc_final: 0.8151 (p0) REVERT: D 50 ASP cc_start: 0.8508 (m-30) cc_final: 0.7891 (p0) REVERT: D 118 ASN cc_start: 0.9529 (m-40) cc_final: 0.9219 (m-40) REVERT: D 160 LEU cc_start: 0.9236 (tp) cc_final: 0.8954 (tt) REVERT: D 301 MET cc_start: 0.8999 (mtm) cc_final: 0.8585 (mtt) REVERT: E 42 MET cc_start: 0.8676 (ptp) cc_final: 0.7755 (ppp) REVERT: E 89 GLU cc_start: 0.9471 (mp0) cc_final: 0.9179 (mp0) REVERT: E 92 GLU cc_start: 0.9042 (tt0) cc_final: 0.8589 (tp30) REVERT: E 301 MET cc_start: 0.9127 (mtm) cc_final: 0.8734 (mtp) REVERT: E 339 LEU cc_start: 0.8991 (tt) cc_final: 0.8257 (mt) REVERT: E 348 MET cc_start: 0.8645 (mmp) cc_final: 0.8140 (mmp) REVERT: E 363 GLU cc_start: 0.9166 (tp30) cc_final: 0.8909 (tp30) REVERT: F 72 MET cc_start: 0.8938 (ptt) cc_final: 0.8669 (ptt) REVERT: F 235 MET cc_start: 0.7468 (mtt) cc_final: 0.6546 (mtp) REVERT: F 391 GLN cc_start: 0.9414 (mt0) cc_final: 0.9086 (mt0) REVERT: G 537 ASP cc_start: 0.8769 (t0) cc_final: 0.8434 (t0) REVERT: G 568 CYS cc_start: 0.8172 (m) cc_final: 0.7765 (t) REVERT: H 541 HIS cc_start: 0.9172 (m-70) cc_final: 0.8971 (m-70) REVERT: H 550 ARG cc_start: 0.9016 (mmp80) cc_final: 0.8741 (mmm160) REVERT: I 530 ILE cc_start: 0.8890 (tt) cc_final: 0.8667 (pt) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.3846 time to fit residues: 213.8248 Evaluate side-chains 272 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 294 optimal weight: 30.0000 chunk 133 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 265 optimal weight: 30.0000 chunk 97 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** A 195 GLN C 45 ASN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 512 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.073699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.057232 restraints weight = 174439.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.058564 restraints weight = 125911.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.059506 restraints weight = 98019.098| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4334 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= 0.164 Angle : 1.037 30.688 33783 Z= 0.420 Chirality : 0.042 0.252 3852 Planarity : 0.005 0.127 4422 Dihedral : 7.177 131.238 3554 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.15), residues: 3066 helix: 1.62 (0.12), residues: 1792 sheet: -0.87 (0.27), residues: 320 loop : 0.18 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 457 HIS 0.005 0.001 HIS A 67 PHE 0.037 0.002 PHE C 166 TYR 0.036 0.002 TYR B 122 ARG 0.014 0.001 ARG E 329 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 1466) hydrogen bonds : angle 4.48012 ( 4128) SS BOND : bond 0.00878 ( 3) SS BOND : angle 1.60043 ( 6) covalent geometry : bond 0.00358 (24900) covalent geometry : angle 1.03683 (33777) Misc. bond : bond 0.00151 ( 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 365 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 2.860 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: A 58 ASP cc_start: 0.9204 (m-30) cc_final: 0.8674 (p0) REVERT: A 194 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8967 (tp30) REVERT: A 242 MET cc_start: 0.8847 (ppp) cc_final: 0.8613 (ppp) REVERT: A 269 MET cc_start: 0.6980 (tpt) cc_final: 0.6517 (tpt) REVERT: A 291 ASP cc_start: 0.8908 (m-30) cc_final: 0.8288 (p0) REVERT: A 416 MET cc_start: 0.8716 (mmp) cc_final: 0.8267 (mmm) REVERT: A 438 ILE cc_start: 0.8146 (mp) cc_final: 0.7761 (mp) REVERT: A 451 LEU cc_start: 0.9014 (mt) cc_final: 0.8796 (mt) REVERT: B 72 MET cc_start: 0.8737 (mtt) cc_final: 0.8196 (mtp) REVERT: B 82 ILE cc_start: 0.8544 (mt) cc_final: 0.8291 (mt) REVERT: B 187 ASP cc_start: 0.9143 (m-30) cc_final: 0.8931 (m-30) REVERT: B 225 ASP cc_start: 0.7861 (m-30) cc_final: 0.7603 (m-30) REVERT: B 240 PHE cc_start: 0.9088 (t80) cc_final: 0.8809 (t80) REVERT: B 291 ASP cc_start: 0.9022 (m-30) cc_final: 0.8733 (p0) REVERT: B 297 ILE cc_start: 0.9462 (mm) cc_final: 0.9228 (pt) REVERT: B 301 MET cc_start: 0.9152 (tmm) cc_final: 0.8818 (tmm) REVERT: B 348 MET cc_start: 0.7592 (mtp) cc_final: 0.7098 (ttm) REVERT: C 235 MET cc_start: 0.8954 (mmp) cc_final: 0.8635 (mmm) REVERT: C 250 MET cc_start: 0.8783 (tmm) cc_final: 0.8577 (tmm) REVERT: C 322 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8048 (mt-10) REVERT: C 337 ILE cc_start: 0.8893 (tt) cc_final: 0.8397 (mt) REVERT: C 339 LEU cc_start: 0.9387 (tt) cc_final: 0.9147 (tt) REVERT: C 382 LEU cc_start: 0.8950 (mt) cc_final: 0.8700 (mt) REVERT: C 419 TYR cc_start: 0.7615 (t80) cc_final: 0.7038 (t80) REVERT: C 427 ASN cc_start: 0.8411 (p0) cc_final: 0.8188 (p0) REVERT: D 50 ASP cc_start: 0.8524 (m-30) cc_final: 0.7903 (p0) REVERT: D 118 ASN cc_start: 0.9520 (m-40) cc_final: 0.9198 (m-40) REVERT: D 160 LEU cc_start: 0.9251 (tp) cc_final: 0.8965 (tt) REVERT: D 301 MET cc_start: 0.9001 (mtm) cc_final: 0.8572 (mtt) REVERT: E 92 GLU cc_start: 0.9084 (tt0) cc_final: 0.8620 (tp30) REVERT: E 301 MET cc_start: 0.9083 (mtm) cc_final: 0.8764 (mtp) REVERT: E 348 MET cc_start: 0.8628 (mmp) cc_final: 0.8132 (mmp) REVERT: E 363 GLU cc_start: 0.9181 (tp30) cc_final: 0.8942 (tp30) REVERT: F 72 MET cc_start: 0.8990 (ptt) cc_final: 0.8725 (ptt) REVERT: F 98 ASP cc_start: 0.7821 (t0) cc_final: 0.7544 (p0) REVERT: F 235 MET cc_start: 0.7414 (mtt) cc_final: 0.6517 (mtp) REVERT: F 391 GLN cc_start: 0.9404 (mt0) cc_final: 0.9114 (mt0) REVERT: G 512 ASN cc_start: 0.8029 (t0) cc_final: 0.6799 (m110) REVERT: G 537 ASP cc_start: 0.8728 (t0) cc_final: 0.8399 (t0) REVERT: G 568 CYS cc_start: 0.8167 (m) cc_final: 0.7794 (t) REVERT: H 541 HIS cc_start: 0.9131 (m-70) cc_final: 0.8926 (m-70) REVERT: H 550 ARG cc_start: 0.9032 (mmp80) cc_final: 0.8749 (mmm160) REVERT: I 530 ILE cc_start: 0.8857 (tt) cc_final: 0.8640 (pt) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.4147 time to fit residues: 237.8022 Evaluate side-chains 277 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 155 optimal weight: 0.3980 chunk 79 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 287 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 119 optimal weight: 0.0010 chunk 32 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 267 optimal weight: 20.0000 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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** A 195 GLN ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN G 541 HIS ** H 551 GLN ** 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 = 0.4069 r_free = 0.4069 target = 0.076405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.059991 restraints weight = 171000.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.061360 restraints weight = 123404.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.062337 restraints weight = 95998.776| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24908 Z= 0.118 Angle : 1.028 30.438 33783 Z= 0.411 Chirality : 0.042 0.260 3852 Planarity : 0.004 0.128 4422 Dihedral : 6.978 128.956 3554 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.15), residues: 3066 helix: 1.72 (0.12), residues: 1798 sheet: -0.68 (0.28), residues: 315 loop : 0.23 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 457 HIS 0.006 0.001 HIS G 541 PHE 0.016 0.001 PHE C 69 TYR 0.031 0.002 TYR B 122 ARG 0.009 0.001 ARG E 329 Details of bonding type rmsd hydrogen bonds : bond 0.03182 ( 1466) hydrogen bonds : angle 4.36038 ( 4128) SS BOND : bond 0.01117 ( 3) SS BOND : angle 1.77630 ( 6) covalent geometry : bond 0.00265 (24900) covalent geometry : angle 1.02807 (33777) Misc. bond : bond 0.00065 ( 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 375 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 2.555 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: A 58 ASP cc_start: 0.9262 (m-30) cc_final: 0.8735 (p0) REVERT: A 160 LEU cc_start: 0.9228 (tp) cc_final: 0.9023 (tp) REVERT: A 167 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8610 (mttt) REVERT: A 269 MET cc_start: 0.6739 (tpt) cc_final: 0.6290 (tpt) REVERT: A 291 ASP cc_start: 0.8924 (m-30) cc_final: 0.8325 (p0) REVERT: A 416 MET cc_start: 0.8694 (mmp) cc_final: 0.8251 (mmm) REVERT: A 438 ILE cc_start: 0.8015 (mp) cc_final: 0.7579 (mp) REVERT: A 451 LEU cc_start: 0.8987 (mt) cc_final: 0.8722 (mt) REVERT: B 187 ASP cc_start: 0.9103 (m-30) cc_final: 0.8871 (m-30) REVERT: B 240 PHE cc_start: 0.9108 (t80) cc_final: 0.8789 (t80) REVERT: B 269 MET cc_start: 0.8846 (tpt) cc_final: 0.8087 (tpp) REVERT: B 291 ASP cc_start: 0.8991 (m-30) cc_final: 0.8697 (p0) REVERT: B 301 MET cc_start: 0.9119 (tmm) cc_final: 0.8627 (ppp) REVERT: B 348 MET cc_start: 0.7491 (mtp) cc_final: 0.7171 (ttm) REVERT: B 364 ILE cc_start: 0.8730 (mt) cc_final: 0.8528 (mt) REVERT: C 235 MET cc_start: 0.8800 (mmp) cc_final: 0.8568 (mmm) REVERT: C 250 MET cc_start: 0.8799 (tmm) cc_final: 0.8496 (tmm) REVERT: C 268 ILE cc_start: 0.9319 (pt) cc_final: 0.8765 (pt) REVERT: C 270 MET cc_start: 0.8622 (ttt) cc_final: 0.8081 (tmm) REVERT: C 322 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8068 (mt-10) REVERT: C 337 ILE cc_start: 0.8862 (tt) cc_final: 0.8322 (mt) REVERT: C 339 LEU cc_start: 0.9184 (tt) cc_final: 0.8967 (tt) REVERT: C 382 LEU cc_start: 0.8830 (mt) cc_final: 0.8617 (mt) REVERT: C 419 TYR cc_start: 0.7516 (t80) cc_final: 0.7100 (t80) REVERT: C 427 ASN cc_start: 0.8431 (p0) cc_final: 0.8218 (p0) REVERT: D 50 ASP cc_start: 0.8554 (m-30) cc_final: 0.7902 (p0) REVERT: D 118 ASN cc_start: 0.9458 (m-40) cc_final: 0.9088 (m-40) REVERT: D 160 LEU cc_start: 0.9255 (tp) cc_final: 0.8965 (tt) REVERT: D 301 MET cc_start: 0.8907 (mtm) cc_final: 0.8518 (mtt) REVERT: E 92 GLU cc_start: 0.9066 (tt0) cc_final: 0.8594 (tp30) REVERT: E 301 MET cc_start: 0.8922 (mtm) cc_final: 0.8680 (mtp) REVERT: E 348 MET cc_start: 0.8586 (mmp) cc_final: 0.8046 (mmp) REVERT: E 373 LYS cc_start: 0.9554 (mmmt) cc_final: 0.9326 (mmmm) REVERT: F 72 MET cc_start: 0.8971 (ptt) cc_final: 0.8701 (ptt) REVERT: F 98 ASP cc_start: 0.7894 (t0) cc_final: 0.7620 (p0) REVERT: F 235 MET cc_start: 0.7366 (mtt) cc_final: 0.6467 (mtp) REVERT: F 301 MET cc_start: 0.8903 (mtm) cc_final: 0.8427 (mmm) REVERT: F 391 GLN cc_start: 0.9393 (mt0) cc_final: 0.9050 (mt0) REVERT: G 568 CYS cc_start: 0.8053 (m) cc_final: 0.7720 (t) REVERT: H 541 HIS cc_start: 0.9125 (m-70) cc_final: 0.8911 (m-70) REVERT: H 550 ARG cc_start: 0.9042 (mmp80) cc_final: 0.8753 (mmm160) REVERT: I 489 VAL cc_start: 0.3653 (t) cc_final: 0.3414 (t) REVERT: I 521 MET cc_start: 0.7313 (ppp) cc_final: 0.7073 (pmm) REVERT: I 530 ILE cc_start: 0.8835 (tt) cc_final: 0.8621 (pt) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.3797 time to fit residues: 219.9211 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 : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 225 optimal weight: 7.9990 chunk 218 optimal weight: 10.0000 chunk 278 optimal weight: 40.0000 chunk 170 optimal weight: 8.9990 chunk 246 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN G 541 HIS ** H 551 GLN ** 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 = 0.4012 r_free = 0.4012 target = 0.073451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.056874 restraints weight = 177046.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.058254 restraints weight = 126155.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.059249 restraints weight = 97284.557| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24908 Z= 0.185 Angle : 1.059 31.631 33783 Z= 0.434 Chirality : 0.042 0.214 3852 Planarity : 0.005 0.127 4422 Dihedral : 7.155 132.653 3554 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.15), residues: 3066 helix: 1.54 (0.12), residues: 1807 sheet: -0.85 (0.27), residues: 327 loop : 0.25 (0.22), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 48 HIS 0.007 0.001 HIS G 541 PHE 0.017 0.002 PHE A 240 TYR 0.030 0.002 TYR D 122 ARG 0.010 0.001 ARG F 387 Details of bonding type rmsd hydrogen bonds : bond 0.03343 ( 1466) hydrogen bonds : angle 4.59230 ( 4128) SS BOND : bond 0.00882 ( 3) SS BOND : angle 1.90944 ( 6) covalent geometry : bond 0.00399 (24900) covalent geometry : angle 1.05925 (33777) Misc. bond : bond 0.00172 ( 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 345 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 2.604 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: A 58 ASP cc_start: 0.9210 (m-30) cc_final: 0.8669 (p0) REVERT: A 291 ASP cc_start: 0.8939 (m-30) cc_final: 0.8338 (p0) REVERT: A 416 MET cc_start: 0.8769 (mmp) cc_final: 0.8314 (mmm) REVERT: A 438 ILE cc_start: 0.7982 (mp) cc_final: 0.7547 (mp) REVERT: A 451 LEU cc_start: 0.9022 (mt) cc_final: 0.8800 (mt) REVERT: B 42 MET cc_start: 0.8313 (mtp) cc_final: 0.7916 (mtp) REVERT: B 72 MET cc_start: 0.8734 (mtt) cc_final: 0.8321 (mtp) REVERT: B 82 ILE cc_start: 0.8627 (mt) cc_final: 0.8197 (mp) REVERT: B 187 ASP cc_start: 0.9132 (m-30) cc_final: 0.8896 (m-30) REVERT: B 225 ASP cc_start: 0.7434 (m-30) cc_final: 0.7228 (m-30) REVERT: B 240 PHE cc_start: 0.9065 (t80) cc_final: 0.8735 (t80) REVERT: B 291 ASP cc_start: 0.9047 (m-30) cc_final: 0.8724 (p0) REVERT: B 301 MET cc_start: 0.9150 (tmm) cc_final: 0.8836 (tmm) REVERT: B 348 MET cc_start: 0.7680 (mtp) cc_final: 0.7145 (ttm) REVERT: C 235 MET cc_start: 0.8849 (mmp) cc_final: 0.8613 (mmm) REVERT: C 250 MET cc_start: 0.8823 (tmm) cc_final: 0.8542 (tmm) REVERT: C 322 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8002 (mt-10) REVERT: C 337 ILE cc_start: 0.8882 (tt) cc_final: 0.8321 (mt) REVERT: C 339 LEU cc_start: 0.9306 (tt) cc_final: 0.9075 (tt) REVERT: C 382 LEU cc_start: 0.8939 (mt) cc_final: 0.8678 (mt) REVERT: C 392 ARG cc_start: 0.9024 (tmt170) cc_final: 0.8819 (tpt-90) REVERT: D 50 ASP cc_start: 0.8480 (m-30) cc_final: 0.7863 (p0) REVERT: D 118 ASN cc_start: 0.9558 (m-40) cc_final: 0.9304 (m-40) REVERT: D 135 MET cc_start: 0.8892 (ppp) cc_final: 0.8530 (ppp) REVERT: D 160 LEU cc_start: 0.9240 (tp) cc_final: 0.8968 (tt) REVERT: D 269 MET cc_start: 0.8629 (ptm) cc_final: 0.8100 (ppp) REVERT: D 270 MET cc_start: 0.9258 (ttt) cc_final: 0.8304 (tpp) REVERT: D 301 MET cc_start: 0.9005 (mtm) cc_final: 0.8654 (mtp) REVERT: D 348 MET cc_start: 0.8138 (tpp) cc_final: 0.7564 (tpp) REVERT: E 42 MET cc_start: 0.8365 (ptp) cc_final: 0.7713 (ppp) REVERT: E 92 GLU cc_start: 0.9098 (tt0) cc_final: 0.8656 (tp30) REVERT: E 301 MET cc_start: 0.8943 (mtm) cc_final: 0.8672 (ptp) REVERT: E 339 LEU cc_start: 0.9040 (tt) cc_final: 0.8217 (mt) REVERT: E 348 MET cc_start: 0.8696 (mmp) cc_final: 0.8204 (mmp) REVERT: E 363 GLU cc_start: 0.9170 (tp30) cc_final: 0.8958 (tp30) REVERT: F 72 MET cc_start: 0.9027 (ptt) cc_final: 0.8764 (ptt) REVERT: F 98 ASP cc_start: 0.7787 (t0) cc_final: 0.7521 (p0) REVERT: F 192 ARG cc_start: 0.8025 (ttt90) cc_final: 0.7763 (tpp-160) REVERT: F 235 MET cc_start: 0.7374 (mtt) cc_final: 0.6493 (mtt) REVERT: F 263 MET cc_start: 0.7318 (mpp) cc_final: 0.6988 (mpp) REVERT: F 391 GLN cc_start: 0.9374 (mt0) cc_final: 0.9048 (mt0) REVERT: F 418 ILE cc_start: 0.8205 (mp) cc_final: 0.7797 (mp) REVERT: G 537 ASP cc_start: 0.8780 (t0) cc_final: 0.8469 (t0) REVERT: G 568 CYS cc_start: 0.8158 (m) cc_final: 0.7814 (t) REVERT: H 541 HIS cc_start: 0.9064 (m-70) cc_final: 0.8822 (m-70) REVERT: H 550 ARG cc_start: 0.9020 (mmp80) cc_final: 0.8727 (mmm160) REVERT: I 489 VAL cc_start: 0.3779 (t) cc_final: 0.3552 (t) REVERT: I 530 ILE cc_start: 0.8849 (tt) cc_final: 0.8628 (pt) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.3761 time to fit residues: 201.1651 Evaluate side-chains 271 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 88 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 272 optimal weight: 8.9990 chunk 141 optimal weight: 0.7980 chunk 281 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 130 optimal weight: 7.9990 chunk 290 optimal weight: 30.0000 chunk 9 optimal weight: 8.9990 chunk 278 optimal weight: 1.9990 chunk 285 optimal weight: 8.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- 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 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 ASN D 456 GLN F 252 GLN G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.073188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.056706 restraints weight = 176663.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.058086 restraints weight = 125482.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.059071 restraints weight = 96613.827| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 24908 Z= 0.183 Angle : 1.070 31.092 33783 Z= 0.440 Chirality : 0.043 0.218 3852 Planarity : 0.006 0.188 4422 Dihedral : 7.243 132.900 3554 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % 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 : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.15), residues: 3066 helix: 1.41 (0.12), residues: 1797 sheet: -0.87 (0.27), residues: 325 loop : 0.19 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP E 48 HIS 0.005 0.001 HIS A 334 PHE 0.020 0.002 PHE E 60 TYR 0.032 0.002 TYR B 122 ARG 0.017 0.001 ARG D 329 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 1466) hydrogen bonds : angle 4.64364 ( 4128) SS BOND : bond 0.01283 ( 3) SS BOND : angle 2.53173 ( 6) covalent geometry : bond 0.00399 (24900) covalent geometry : angle 1.06922 (33777) Misc. bond : bond 0.00158 ( 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 336 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 2.625 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: A 58 ASP cc_start: 0.9209 (m-30) cc_final: 0.8590 (p0) REVERT: A 291 ASP cc_start: 0.8968 (m-30) cc_final: 0.8359 (p0) REVERT: A 416 MET cc_start: 0.8734 (mmp) cc_final: 0.8290 (mmm) REVERT: A 438 ILE cc_start: 0.8006 (mp) cc_final: 0.7647 (mp) REVERT: A 451 LEU cc_start: 0.9009 (mt) cc_final: 0.8797 (mt) REVERT: B 42 MET cc_start: 0.8270 (mtp) cc_final: 0.7756 (mtp) REVERT: B 72 MET cc_start: 0.8777 (mtt) cc_final: 0.8348 (mtp) REVERT: B 82 ILE cc_start: 0.8650 (mt) cc_final: 0.8229 (mp) REVERT: B 187 ASP cc_start: 0.9089 (m-30) cc_final: 0.8858 (m-30) REVERT: B 240 PHE cc_start: 0.9098 (t80) cc_final: 0.8780 (t80) REVERT: B 269 MET cc_start: 0.8809 (tpt) cc_final: 0.8005 (tpp) REVERT: B 291 ASP cc_start: 0.9022 (m-30) cc_final: 0.8710 (p0) REVERT: B 301 MET cc_start: 0.9165 (tmm) cc_final: 0.8862 (tmm) REVERT: B 348 MET cc_start: 0.7574 (mtp) cc_final: 0.7069 (ttm) REVERT: C 235 MET cc_start: 0.8867 (mmp) cc_final: 0.8573 (mmm) REVERT: C 250 MET cc_start: 0.8849 (tmm) cc_final: 0.8547 (tmm) REVERT: C 322 GLU cc_start: 0.8470 (mt-10) cc_final: 0.7936 (mt-10) REVERT: C 337 ILE cc_start: 0.8865 (tt) cc_final: 0.8308 (mt) REVERT: C 339 LEU cc_start: 0.9308 (tt) cc_final: 0.9060 (tt) REVERT: C 382 LEU cc_start: 0.8981 (mt) cc_final: 0.8715 (mt) REVERT: C 414 LEU cc_start: 0.9088 (tp) cc_final: 0.8752 (tp) REVERT: C 427 ASN cc_start: 0.8449 (p0) cc_final: 0.8159 (p0) REVERT: D 50 ASP cc_start: 0.8486 (m-30) cc_final: 0.7835 (p0) REVERT: D 118 ASN cc_start: 0.9539 (m-40) cc_final: 0.9234 (m-40) REVERT: D 160 LEU cc_start: 0.9204 (tp) cc_final: 0.8935 (tt) REVERT: D 269 MET cc_start: 0.8642 (ptm) cc_final: 0.8086 (ppp) REVERT: D 270 MET cc_start: 0.9290 (ttt) cc_final: 0.8270 (tpp) REVERT: D 301 MET cc_start: 0.8999 (mtm) cc_final: 0.8653 (mtp) REVERT: D 348 MET cc_start: 0.8185 (tpp) cc_final: 0.7572 (tpp) REVERT: E 42 MET cc_start: 0.8417 (ptp) cc_final: 0.7728 (ppp) REVERT: E 92 GLU cc_start: 0.9129 (tt0) cc_final: 0.8673 (tp30) REVERT: E 339 LEU cc_start: 0.8976 (tt) cc_final: 0.8170 (mt) REVERT: E 348 MET cc_start: 0.8718 (mmp) cc_final: 0.8218 (mmp) REVERT: E 363 GLU cc_start: 0.9123 (tp30) cc_final: 0.8890 (tp30) REVERT: F 72 MET cc_start: 0.9035 (ptt) cc_final: 0.8769 (ptt) REVERT: F 98 ASP cc_start: 0.7790 (t0) cc_final: 0.7538 (p0) REVERT: F 192 ARG cc_start: 0.8034 (ttt90) cc_final: 0.7758 (tpp-160) REVERT: F 235 MET cc_start: 0.7416 (mtt) cc_final: 0.6687 (mtp) REVERT: F 347 LEU cc_start: 0.8476 (mt) cc_final: 0.8160 (mt) REVERT: F 348 MET cc_start: 0.8153 (tpt) cc_final: 0.7887 (tpt) REVERT: F 391 GLN cc_start: 0.9375 (mt0) cc_final: 0.9063 (mt0) REVERT: G 537 ASP cc_start: 0.8791 (t0) cc_final: 0.8484 (t0) REVERT: G 568 CYS cc_start: 0.8030 (m) cc_final: 0.7707 (t) REVERT: H 541 HIS cc_start: 0.9087 (m-70) cc_final: 0.8846 (m-70) REVERT: H 550 ARG cc_start: 0.9027 (mmp80) cc_final: 0.8704 (mmm160) REVERT: I 489 VAL cc_start: 0.3577 (t) cc_final: 0.3361 (t) REVERT: I 521 MET cc_start: 0.7299 (ppp) cc_final: 0.7072 (pmm) REVERT: I 530 ILE cc_start: 0.8826 (tt) cc_final: 0.8609 (pt) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.3604 time to fit residues: 189.7565 Evaluate side-chains 272 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 2.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 127 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 266 optimal weight: 9.9990 chunk 296 optimal weight: 5.9990 chunk 232 optimal weight: 7.9990 chunk 128 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 26 optimal weight: 40.0000 chunk 151 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN D 281 GLN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN G 541 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.074143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.057707 restraints weight = 175211.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.059101 restraints weight = 124353.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.060089 restraints weight = 95852.149| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24908 Z= 0.145 Angle : 1.053 30.554 33783 Z= 0.429 Chirality : 0.043 0.320 3852 Planarity : 0.005 0.119 4422 Dihedral : 7.160 132.079 3554 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.15), residues: 3066 helix: 1.49 (0.12), residues: 1800 sheet: -0.83 (0.28), residues: 325 loop : 0.22 (0.22), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP E 48 HIS 0.005 0.001 HIS A 334 PHE 0.015 0.002 PHE C 60 TYR 0.034 0.002 TYR F 105 ARG 0.013 0.001 ARG F 403 Details of bonding type rmsd hydrogen bonds : bond 0.03285 ( 1466) hydrogen bonds : angle 4.56142 ( 4128) SS BOND : bond 0.01079 ( 3) SS BOND : angle 2.39280 ( 6) covalent geometry : bond 0.00325 (24900) covalent geometry : angle 1.05265 (33777) Misc. bond : bond 0.00121 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10592.88 seconds wall clock time: 186 minutes 14.74 seconds (11174.74 seconds total)