Starting phenix.real_space_refine on Thu Mar 14 19:15:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cua_26997/03_2024/8cua_26997.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cua_26997/03_2024/8cua_26997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cua_26997/03_2024/8cua_26997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cua_26997/03_2024/8cua_26997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cua_26997/03_2024/8cua_26997.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cua_26997/03_2024/8cua_26997.pdb" } resolution = 2.44 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= 0.008 sd= 0.104 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Hg 3 10.96 5 K 3 8.98 5 S 63 5.16 5 C 6228 2.51 5 N 1512 2.21 5 O 1725 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C GLU 272": "OE1" <-> "OE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9534 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3166 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 11, 'TRANS': 404} Chain breaks: 2 Chain: "B" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3166 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 11, 'TRANS': 404} Chain breaks: 2 Chain: "C" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3166 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 11, 'TRANS': 404} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' HG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' HG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' HG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1605 SG CYS A 269 23.791 36.895 25.246 1.00 69.82 S ATOM 2886 SG CYS A 441 25.221 34.804 25.594 1.00 76.78 S ATOM 4771 SG CYS B 269 53.802 82.636 25.329 1.00 69.82 S ATOM 6052 SG CYS B 441 51.277 82.431 25.672 1.00 76.78 S ATOM 7937 SG CYS C 269 78.295 33.789 25.342 1.00 69.82 S ATOM 9218 SG CYS C 441 79.386 36.078 25.677 1.00 76.78 S Time building chain proxies: 5.19, per 1000 atoms: 0.54 Number of scatterers: 9534 At special positions: 0 Unit cell: (106.5, 103.092, 78.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Hg 3 79.96 K 3 19.00 S 63 16.00 O 1725 8.00 N 1512 7.00 C 6228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=0, symmetry=0 Time building additional restraints: 3.51 Conformation dependent library (CDL) restraints added in 1.8 seconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2310 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 3 sheets defined 86.1% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 removed outlier: 3.691A pdb=" N LEU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.831A pdb=" N ALA A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.558A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 81 removed outlier: 3.554A pdb=" N LEU A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 117 removed outlier: 3.629A pdb=" N ILE A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.519A pdb=" N LEU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 211 through 227 Processing helix chain 'A' and resid 229 through 232 removed outlier: 3.738A pdb=" N LYS A 232 " --> pdb=" O MET A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 233 through 270 removed outlier: 3.747A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.512A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.966A pdb=" N ARG A 280 " --> pdb=" O TRP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 299 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 312 through 319 Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.675A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix removed outlier: 3.672A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 removed outlier: 3.624A pdb=" N LEU A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 405 removed outlier: 3.653A pdb=" N SER A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 removed outlier: 4.243A pdb=" N VAL A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 438 removed outlier: 4.001A pdb=" N ILE A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 3.926A pdb=" N ARG A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 477 removed outlier: 3.716A pdb=" N ASP A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 42 removed outlier: 3.691A pdb=" N LEU B 22 " --> pdb=" O ASN B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.832A pdb=" N ALA B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 66 removed outlier: 3.558A pdb=" N ILE B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 81 removed outlier: 3.554A pdb=" N LEU B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 117 removed outlier: 3.629A pdb=" N ILE B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.519A pdb=" N LEU B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 158 Processing helix chain 'B' and resid 211 through 227 Processing helix chain 'B' and resid 229 through 232 removed outlier: 3.738A pdb=" N LYS B 232 " --> pdb=" O MET B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'B' and resid 233 through 270 removed outlier: 3.749A pdb=" N TRP B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 3.512A pdb=" N PHE B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 282 removed outlier: 3.967A pdb=" N ARG B 280 " --> pdb=" O TRP B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 299 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 312 through 319 Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 336 through 347 Processing helix chain 'B' and resid 351 through 366 removed outlier: 3.675A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Proline residue: B 360 - end of helix removed outlier: 3.672A pdb=" N THR B 364 " --> pdb=" O PRO B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 385 removed outlier: 3.624A pdb=" N LEU B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 405 removed outlier: 3.653A pdb=" N SER B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 427 removed outlier: 4.244A pdb=" N VAL B 417 " --> pdb=" O GLN B 413 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 438 removed outlier: 4.002A pdb=" N ILE B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA B 438 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 466 removed outlier: 3.926A pdb=" N ARG B 445 " --> pdb=" O CYS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 477 removed outlier: 3.715A pdb=" N ASP B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 476 " --> pdb=" O GLN B 472 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER B 477 " --> pdb=" O MET B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 42 removed outlier: 3.691A pdb=" N LEU C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.832A pdb=" N ALA C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 66 removed outlier: 3.558A pdb=" N ILE C 66 " --> pdb=" O MET C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 81 removed outlier: 3.554A pdb=" N LEU C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 117 removed outlier: 3.629A pdb=" N ILE C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.519A pdb=" N LEU C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 211 through 227 Processing helix chain 'C' and resid 229 through 232 removed outlier: 3.738A pdb=" N LYS C 232 " --> pdb=" O MET C 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 229 through 232' Processing helix chain 'C' and resid 233 through 270 removed outlier: 3.747A pdb=" N TRP C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 3.513A pdb=" N PHE C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 282 removed outlier: 3.966A pdb=" N ARG C 280 " --> pdb=" O TRP C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 299 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 312 through 319 Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 336 through 347 Processing helix chain 'C' and resid 351 through 366 removed outlier: 3.676A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Proline residue: C 360 - end of helix removed outlier: 3.671A pdb=" N THR C 364 " --> pdb=" O PRO C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 385 removed outlier: 3.624A pdb=" N LEU C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL C 376 " --> pdb=" O LEU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 405 removed outlier: 3.653A pdb=" N SER C 405 " --> pdb=" O ALA C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 427 removed outlier: 4.243A pdb=" N VAL C 417 " --> pdb=" O GLN C 413 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 438 removed outlier: 4.002A pdb=" N ILE C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA C 438 " --> pdb=" O THR C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 466 removed outlier: 3.926A pdb=" N ARG C 445 " --> pdb=" O CYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 477 removed outlier: 3.716A pdb=" N ASP C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 476 " --> pdb=" O GLN C 472 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 167 Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 167 708 hydrogen bonds defined for protein. 2106 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: 2.70 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2259 1.33 - 1.45: 1629 1.45 - 1.57: 5634 1.57 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 9639 Sorted by residual: bond pdb=" N ILE A 406 " pdb=" CA ILE A 406 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.87e+00 bond pdb=" N ILE C 406 " pdb=" CA ILE C 406 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.82e+00 bond pdb=" N ILE B 406 " pdb=" CA ILE B 406 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.80e+00 bond pdb=" N CYS C 441 " pdb=" CA CYS C 441 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.30e-02 5.92e+03 7.01e+00 bond pdb=" N CYS A 441 " pdb=" CA CYS A 441 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.30e-02 5.92e+03 6.99e+00 ... (remaining 9634 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.09: 204 107.09 - 113.82: 5790 113.82 - 120.55: 3902 120.55 - 127.28: 3133 127.28 - 134.01: 51 Bond angle restraints: 13080 Sorted by residual: angle pdb=" CB MET C 75 " pdb=" CG MET C 75 " pdb=" SD MET C 75 " ideal model delta sigma weight residual 112.70 103.31 9.39 3.00e+00 1.11e-01 9.79e+00 angle pdb=" CB MET B 75 " pdb=" CG MET B 75 " pdb=" SD MET B 75 " ideal model delta sigma weight residual 112.70 103.33 9.37 3.00e+00 1.11e-01 9.75e+00 angle pdb=" CB MET A 75 " pdb=" CG MET A 75 " pdb=" SD MET A 75 " ideal model delta sigma weight residual 112.70 103.33 9.37 3.00e+00 1.11e-01 9.75e+00 angle pdb=" N MET C 258 " pdb=" CA MET C 258 " pdb=" C MET C 258 " ideal model delta sigma weight residual 109.81 116.17 -6.36 2.21e+00 2.05e-01 8.29e+00 angle pdb=" N MET A 258 " pdb=" CA MET A 258 " pdb=" C MET A 258 " ideal model delta sigma weight residual 109.81 116.16 -6.35 2.21e+00 2.05e-01 8.24e+00 ... (remaining 13075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 5029 15.67 - 31.34: 495 31.34 - 47.01: 164 47.01 - 62.69: 66 62.69 - 78.36: 9 Dihedral angle restraints: 5763 sinusoidal: 2184 harmonic: 3579 Sorted by residual: dihedral pdb=" CG ARG B 315 " pdb=" CD ARG B 315 " pdb=" NE ARG B 315 " pdb=" CZ ARG B 315 " ideal model delta sinusoidal sigma weight residual -90.00 -39.98 -50.02 2 1.50e+01 4.44e-03 1.25e+01 dihedral pdb=" CG ARG C 315 " pdb=" CD ARG C 315 " pdb=" NE ARG C 315 " pdb=" CZ ARG C 315 " ideal model delta sinusoidal sigma weight residual -90.00 -40.02 -49.98 2 1.50e+01 4.44e-03 1.25e+01 dihedral pdb=" CG ARG A 315 " pdb=" CD ARG A 315 " pdb=" NE ARG A 315 " pdb=" CZ ARG A 315 " ideal model delta sinusoidal sigma weight residual -90.00 -40.02 -49.98 2 1.50e+01 4.44e-03 1.25e+01 ... (remaining 5760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1105 0.031 - 0.063: 352 0.063 - 0.094: 148 0.094 - 0.125: 40 0.125 - 0.157: 14 Chirality restraints: 1659 Sorted by residual: chirality pdb=" CA LEU B 443 " pdb=" N LEU B 443 " pdb=" C LEU B 443 " pdb=" CB LEU B 443 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CA LEU A 443 " pdb=" N LEU A 443 " pdb=" C LEU A 443 " pdb=" CB LEU A 443 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA LEU C 443 " pdb=" N LEU C 443 " pdb=" C LEU C 443 " pdb=" CB LEU C 443 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 1656 not shown) Planarity restraints: 1593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 295 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" C ILE A 295 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE A 295 " 0.012 2.00e-02 2.50e+03 pdb=" N HIS A 296 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 295 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C ILE C 295 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE C 295 " -0.012 2.00e-02 2.50e+03 pdb=" N HIS C 296 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 295 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" C ILE B 295 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE B 295 " 0.012 2.00e-02 2.50e+03 pdb=" N HIS B 296 " 0.010 2.00e-02 2.50e+03 ... (remaining 1590 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.59: 57 2.59 - 3.23: 9248 3.23 - 3.87: 18958 3.87 - 4.50: 25091 4.50 - 5.14: 40074 Nonbonded interactions: 93428 Sorted by model distance: nonbonded pdb=" SG CYS B 441 " pdb="HG HG B 601 " model vdw 1.957 2.880 nonbonded pdb=" SG CYS C 441 " pdb="HG HG C 601 " model vdw 1.957 2.880 nonbonded pdb=" SG CYS A 441 " pdb="HG HG A 601 " model vdw 1.957 2.880 nonbonded pdb=" OD2 ASP A 368 " pdb=" O HOH A 701 " model vdw 2.226 2.440 nonbonded pdb=" OD2 ASP C 368 " pdb=" O HOH C 701 " model vdw 2.226 2.440 ... (remaining 93423 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.910 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 27.580 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 0.003 0.035 9639 Z= 0.214 Angle : 0.575 9.388 13080 Z= 0.345 Chirality : 0.039 0.157 1659 Planarity : 0.004 0.027 1593 Dihedral : 15.571 78.357 3453 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 21.61 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.24), residues: 1230 helix: 1.92 (0.17), residues: 963 sheet: 0.89 (0.66), residues: 48 loop : -1.20 (0.36), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 256 HIS 0.001 0.000 HIS C 41 PHE 0.007 0.001 PHE A 218 TYR 0.009 0.001 TYR B 285 ARG 0.003 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.846 Fit side-chains REVERT: A 205 MET cc_start: 0.8426 (ptm) cc_final: 0.8177 (ptt) REVERT: A 385 ASN cc_start: 0.7509 (m-40) cc_final: 0.7298 (m110) REVERT: A 475 VAL cc_start: 0.7494 (p) cc_final: 0.7276 (m) REVERT: B 205 MET cc_start: 0.8250 (ptm) cc_final: 0.7960 (ptt) REVERT: B 315 ARG cc_start: 0.6984 (ttm-80) cc_final: 0.6409 (ttp80) REVERT: B 322 GLN cc_start: 0.7710 (mt0) cc_final: 0.7448 (tt0) REVERT: C 205 MET cc_start: 0.8319 (ptm) cc_final: 0.8055 (ptt) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 1.2785 time to fit residues: 185.3006 Evaluate side-chains 121 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 3.9990 chunk 93 optimal weight: 0.4980 chunk 51 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN A 366 ASN A 413 GLN B 252 GLN B 413 GLN C 252 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9639 Z= 0.191 Angle : 0.510 7.084 13080 Z= 0.267 Chirality : 0.037 0.144 1659 Planarity : 0.004 0.029 1593 Dihedral : 3.463 16.258 1308 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.02 % Allowed : 20.75 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.24), residues: 1230 helix: 1.83 (0.17), residues: 987 sheet: 0.09 (0.71), residues: 54 loop : -0.52 (0.42), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 19 HIS 0.001 0.001 HIS B 296 PHE 0.012 0.001 PHE C 240 TYR 0.012 0.002 TYR C 285 ARG 0.007 0.001 ARG C 315 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 1.133 Fit side-chains REVERT: A 39 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7335 (mtp-110) REVERT: B 205 MET cc_start: 0.8377 (ptm) cc_final: 0.8143 (ptm) REVERT: B 385 ASN cc_start: 0.7076 (m-40) cc_final: 0.6845 (m110) outliers start: 21 outliers final: 6 residues processed: 149 average time/residue: 1.2932 time to fit residues: 205.4511 Evaluate side-chains 137 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 474 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN A 385 ASN A 451 ASN B 252 GLN B 451 ASN C 252 GLN C 413 GLN C 451 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9639 Z= 0.169 Angle : 0.483 7.134 13080 Z= 0.253 Chirality : 0.037 0.143 1659 Planarity : 0.004 0.034 1593 Dihedral : 3.432 15.480 1308 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.40 % Allowed : 21.33 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.24), residues: 1230 helix: 1.92 (0.17), residues: 978 sheet: 1.27 (0.70), residues: 48 loop : -0.90 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 19 HIS 0.001 0.000 HIS B 296 PHE 0.015 0.001 PHE B 99 TYR 0.010 0.001 TYR C 285 ARG 0.008 0.001 ARG C 315 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 0.951 Fit side-chains REVERT: A 39 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7329 (mtp-110) REVERT: A 231 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6923 (mm-30) REVERT: B 205 MET cc_start: 0.8345 (ptm) cc_final: 0.8113 (ptm) REVERT: C 346 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7399 (mm-30) outliers start: 25 outliers final: 9 residues processed: 151 average time/residue: 1.2157 time to fit residues: 196.2476 Evaluate side-chains 141 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 364 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN B 385 ASN C 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9639 Z= 0.156 Angle : 0.474 7.049 13080 Z= 0.246 Chirality : 0.037 0.140 1659 Planarity : 0.003 0.035 1593 Dihedral : 3.399 15.343 1308 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.79 % Allowed : 20.65 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.24), residues: 1230 helix: 2.03 (0.17), residues: 978 sheet: 0.13 (0.74), residues: 54 loop : -0.72 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 19 HIS 0.001 0.000 HIS A 296 PHE 0.016 0.001 PHE B 99 TYR 0.010 0.001 TYR C 285 ARG 0.008 0.001 ARG C 315 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 1.083 Fit side-chains REVERT: A 39 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7288 (mtp-110) REVERT: A 231 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6876 (mm-30) REVERT: A 241 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8318 (t0) REVERT: B 205 MET cc_start: 0.8331 (ptm) cc_final: 0.8070 (ptm) REVERT: B 269 CYS cc_start: 0.7029 (m) cc_final: 0.6591 (t) REVERT: C 346 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7356 (mm-30) outliers start: 29 outliers final: 11 residues processed: 159 average time/residue: 1.1611 time to fit residues: 198.0554 Evaluate side-chains 144 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 474 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN B 385 ASN C 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9639 Z= 0.281 Angle : 0.569 7.697 13080 Z= 0.299 Chirality : 0.039 0.148 1659 Planarity : 0.004 0.040 1593 Dihedral : 3.685 15.693 1308 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.17 % Allowed : 20.27 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.24), residues: 1230 helix: 1.59 (0.17), residues: 993 sheet: 1.03 (0.67), residues: 48 loop : -0.91 (0.42), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 256 HIS 0.002 0.001 HIS A 296 PHE 0.017 0.002 PHE B 99 TYR 0.011 0.002 TYR C 285 ARG 0.008 0.001 ARG B 315 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 133 time to evaluate : 1.083 Fit side-chains REVERT: A 21 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6430 (mp) REVERT: A 39 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7417 (mtp-110) REVERT: A 231 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7109 (mm-30) REVERT: A 241 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8361 (t0) REVERT: A 471 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7932 (pt0) REVERT: B 115 SER cc_start: 0.7868 (t) cc_final: 0.7434 (m) REVERT: B 205 MET cc_start: 0.8319 (ptm) cc_final: 0.8036 (ptm) outliers start: 33 outliers final: 13 residues processed: 156 average time/residue: 1.1936 time to fit residues: 199.2658 Evaluate side-chains 148 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 340 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN C 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9639 Z= 0.163 Angle : 0.487 7.152 13080 Z= 0.252 Chirality : 0.037 0.139 1659 Planarity : 0.004 0.038 1593 Dihedral : 3.496 15.321 1308 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.98 % Allowed : 20.56 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.24), residues: 1230 helix: 1.99 (0.17), residues: 969 sheet: 0.06 (0.72), residues: 54 loop : -0.50 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 19 HIS 0.001 0.000 HIS A 296 PHE 0.018 0.001 PHE B 99 TYR 0.010 0.001 TYR B 285 ARG 0.009 0.001 ARG B 315 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7302 (mtp-110) REVERT: A 231 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6925 (mm-30) REVERT: A 241 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.8327 (t0) REVERT: B 64 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8161 (mtpt) REVERT: B 115 SER cc_start: 0.7761 (t) cc_final: 0.7329 (m) REVERT: B 205 MET cc_start: 0.8266 (ptm) cc_final: 0.8025 (ptm) REVERT: C 346 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7320 (mm-30) outliers start: 31 outliers final: 10 residues processed: 153 average time/residue: 1.2169 time to fit residues: 199.6651 Evaluate side-chains 141 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 346 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 118 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN B 385 ASN C 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9639 Z= 0.227 Angle : 0.533 7.400 13080 Z= 0.277 Chirality : 0.038 0.144 1659 Planarity : 0.004 0.042 1593 Dihedral : 3.612 15.550 1308 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.79 % Allowed : 20.65 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.24), residues: 1230 helix: 1.78 (0.17), residues: 981 sheet: 1.01 (0.67), residues: 48 loop : -1.03 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 19 HIS 0.002 0.001 HIS A 296 PHE 0.017 0.002 PHE B 99 TYR 0.010 0.002 TYR A 285 ARG 0.009 0.001 ARG B 315 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 1.099 Fit side-chains REVERT: A 39 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7339 (mtp-110) REVERT: A 231 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7114 (mm-30) REVERT: A 241 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8303 (t0) REVERT: B 39 ARG cc_start: 0.7860 (ttp80) cc_final: 0.7215 (ttp80) REVERT: B 64 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8178 (mtpt) REVERT: B 115 SER cc_start: 0.7860 (t) cc_final: 0.7428 (m) REVERT: B 205 MET cc_start: 0.8312 (ptm) cc_final: 0.8042 (ptm) REVERT: B 367 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7396 (mtm) outliers start: 29 outliers final: 15 residues processed: 150 average time/residue: 1.2166 time to fit residues: 195.2124 Evaluate side-chains 146 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 474 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 75 optimal weight: 0.0670 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN B 385 ASN C 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9639 Z= 0.147 Angle : 0.475 7.021 13080 Z= 0.245 Chirality : 0.037 0.136 1659 Planarity : 0.004 0.041 1593 Dihedral : 3.455 15.149 1308 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.88 % Allowed : 20.56 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.24), residues: 1230 helix: 2.08 (0.17), residues: 972 sheet: 0.06 (0.73), residues: 54 loop : -0.47 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 19 HIS 0.000 0.000 HIS C 296 PHE 0.019 0.001 PHE B 99 TYR 0.009 0.001 TYR B 285 ARG 0.010 0.001 ARG B 315 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 1.074 Fit side-chains REVERT: A 39 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7319 (mtp-110) REVERT: A 241 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8335 (t0) REVERT: A 329 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7220 (mmt) REVERT: A 469 GLU cc_start: 0.8130 (mp0) cc_final: 0.7589 (mp0) REVERT: B 39 ARG cc_start: 0.7836 (ttp80) cc_final: 0.7191 (ttp80) REVERT: B 64 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8157 (mtpt) REVERT: B 205 MET cc_start: 0.8314 (ptm) cc_final: 0.8059 (ptm) REVERT: B 231 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6983 (mm-30) REVERT: B 367 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7306 (mtm) REVERT: C 346 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7320 (mm-30) outliers start: 30 outliers final: 15 residues processed: 149 average time/residue: 1.1985 time to fit residues: 191.1872 Evaluate side-chains 138 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 346 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN B 385 ASN C 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9639 Z= 0.238 Angle : 0.547 7.509 13080 Z= 0.283 Chirality : 0.039 0.144 1659 Planarity : 0.004 0.046 1593 Dihedral : 3.625 15.630 1308 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.02 % Allowed : 21.71 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.24), residues: 1230 helix: 1.73 (0.17), residues: 993 sheet: 1.01 (0.67), residues: 48 loop : -0.96 (0.43), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 19 HIS 0.002 0.001 HIS A 296 PHE 0.018 0.002 PHE B 99 TYR 0.011 0.002 TYR A 285 ARG 0.009 0.001 ARG B 315 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 129 time to evaluate : 1.006 Fit side-chains REVERT: A 39 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7343 (mtp-110) REVERT: A 241 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8321 (t0) REVERT: A 329 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7282 (mmt) REVERT: A 469 GLU cc_start: 0.8187 (mp0) cc_final: 0.7549 (mp0) REVERT: B 64 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8182 (mtpt) REVERT: B 115 SER cc_start: 0.7898 (t) cc_final: 0.7476 (m) REVERT: B 205 MET cc_start: 0.8309 (ptm) cc_final: 0.8037 (ptm) REVERT: C 272 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7121 (mt-10) outliers start: 21 outliers final: 11 residues processed: 146 average time/residue: 1.1929 time to fit residues: 186.3891 Evaluate side-chains 142 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 340 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 0.0980 chunk 112 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN C 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9639 Z= 0.147 Angle : 0.483 7.135 13080 Z= 0.248 Chirality : 0.037 0.135 1659 Planarity : 0.004 0.043 1593 Dihedral : 3.459 15.209 1308 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.34 % Allowed : 22.38 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.24), residues: 1230 helix: 2.12 (0.17), residues: 969 sheet: 0.05 (0.73), residues: 54 loop : -0.54 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 19 HIS 0.000 0.000 HIS C 296 PHE 0.020 0.001 PHE B 99 TYR 0.010 0.001 TYR B 285 ARG 0.009 0.001 ARG A 315 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 1.125 Fit side-chains REVERT: A 39 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7315 (mtp-110) REVERT: A 241 ASN cc_start: 0.8665 (OUTLIER) cc_final: 0.8335 (t0) REVERT: A 329 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7188 (mmt) REVERT: A 469 GLU cc_start: 0.8133 (mp0) cc_final: 0.7600 (mp0) REVERT: B 205 MET cc_start: 0.8302 (ptm) cc_final: 0.8049 (ptm) REVERT: C 272 GLU cc_start: 0.7269 (mm-30) cc_final: 0.7036 (mt-10) outliers start: 14 outliers final: 9 residues processed: 134 average time/residue: 1.1791 time to fit residues: 169.5101 Evaluate side-chains 131 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 340 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 0.2980 chunk 97 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN C 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.168724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.122352 restraints weight = 2727.222| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 0.89 r_work: 0.3292 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9639 Z= 0.156 Angle : 0.490 7.142 13080 Z= 0.250 Chirality : 0.037 0.136 1659 Planarity : 0.004 0.043 1593 Dihedral : 3.430 15.159 1308 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.54 % Allowed : 22.29 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.24), residues: 1230 helix: 2.14 (0.17), residues: 969 sheet: 0.05 (0.73), residues: 54 loop : -0.58 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 19 HIS 0.001 0.000 HIS A 296 PHE 0.019 0.001 PHE B 99 TYR 0.010 0.001 TYR B 285 ARG 0.010 0.001 ARG A 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3577.74 seconds wall clock time: 63 minutes 37.23 seconds (3817.23 seconds total)