Starting phenix.real_space_refine on Wed Feb 14 12:08:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bi0_16075/02_2024/8bi0_16075_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bi0_16075/02_2024/8bi0_16075.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bi0_16075/02_2024/8bi0_16075_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bi0_16075/02_2024/8bi0_16075_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bi0_16075/02_2024/8bi0_16075_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bi0_16075/02_2024/8bi0_16075.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bi0_16075/02_2024/8bi0_16075.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bi0_16075/02_2024/8bi0_16075_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bi0_16075/02_2024/8bi0_16075_updated.pdb" } resolution = 3.2 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= 0.005 sd= 0.050 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 P 8 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 6004 2.51 5 N 1478 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 96": "NH1" <-> "NH2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 217": "OD1" <-> "OD2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 217": "OD1" <-> "OD2" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9198 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4445 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 20, 'TRANS': 550} Chain breaks: 4 Chain: "B" Number of atoms: 4445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4445 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 20, 'TRANS': 550} Chain breaks: 4 Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 130 Unusual residues: {' MG': 1, 'ATP': 1, 'CLR': 2, 'PLC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 178 Unusual residues: {' MG': 1, 'ATP': 1, 'CLR': 2, 'PLC': 1, 'R1H': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 5.67, per 1000 atoms: 0.62 Number of scatterers: 9198 At special positions: 0 Unit cell: (95.7, 91.74, 122.1, 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) S 58 16.00 P 8 15.00 Mg 2 11.99 O 1648 8.00 N 1478 7.00 C 6004 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 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: 4.17 Conformation dependent library (CDL) restraints added in 1.7 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2116 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 6 sheets defined 57.3% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 86 through 94 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 154 through 168 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 188 through 202 removed outlier: 3.663A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR A 202 " --> pdb=" O MET A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 232 Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.666A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 280 removed outlier: 3.619A pdb=" N ALA A 280 " --> pdb=" O TYR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 298 Processing helix chain 'A' and resid 328 through 337 removed outlier: 3.590A pdb=" N ILE A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 352 Processing helix chain 'A' and resid 373 through 390 Processing helix chain 'A' and resid 392 through 412 removed outlier: 4.521A pdb=" N ALA A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLN A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 450 removed outlier: 4.082A pdb=" N SER A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N VAL A 442 " --> pdb=" O CYS A 438 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N SER A 443 " --> pdb=" O PHE A 439 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 466 through 476 Processing helix chain 'A' and resid 478 through 497 removed outlier: 3.603A pdb=" N MET A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Proline residue: A 485 - end of helix removed outlier: 4.640A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 528 Processing helix chain 'A' and resid 534 through 551 removed outlier: 3.870A pdb=" N PHE A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 571 removed outlier: 4.132A pdb=" N TRP A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU A 568 " --> pdb=" O TRP A 564 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLN A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TYR A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE A 571 " --> pdb=" O TRP A 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 563 through 571' Processing helix chain 'A' and resid 573 through 585 Processing helix chain 'A' and resid 610 through 616 Processing helix chain 'A' and resid 623 through 649 removed outlier: 3.819A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 94 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 136 through 147 Processing helix chain 'B' and resid 154 through 168 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 188 through 202 removed outlier: 3.662A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR B 202 " --> pdb=" O MET B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 232 Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.666A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 280 removed outlier: 3.619A pdb=" N ALA B 280 " --> pdb=" O TYR B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 298 Processing helix chain 'B' and resid 328 through 337 removed outlier: 3.590A pdb=" N ILE B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 352 Processing helix chain 'B' and resid 373 through 390 Processing helix chain 'B' and resid 392 through 412 removed outlier: 4.523A pdb=" N ALA B 397 " --> pdb=" O GLN B 393 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLN B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 450 removed outlier: 4.083A pdb=" N SER B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N VAL B 442 " --> pdb=" O CYS B 438 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N SER B 443 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA B 444 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 461 Processing helix chain 'B' and resid 466 through 476 Processing helix chain 'B' and resid 478 through 497 removed outlier: 3.602A pdb=" N MET B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Proline residue: B 485 - end of helix removed outlier: 4.640A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 528 Processing helix chain 'B' and resid 534 through 551 removed outlier: 3.869A pdb=" N PHE B 551 " --> pdb=" O PHE B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 571 removed outlier: 4.132A pdb=" N TRP B 567 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLN B 569 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TYR B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE B 571 " --> pdb=" O TRP B 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 563 through 571' Processing helix chain 'B' and resid 573 through 585 Processing helix chain 'B' and resid 610 through 616 Processing helix chain 'B' and resid 623 through 649 removed outlier: 3.820A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 69 through 71 removed outlier: 3.641A pdb=" N ASP A 105 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 263 through 269 removed outlier: 6.898A pdb=" N LEU A 258 " --> pdb=" O MET A 265 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N HIS A 267 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU A 256 " --> pdb=" O HIS A 267 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 44 through 46 removed outlier: 3.820A pdb=" N LEU A 64 " --> pdb=" O TYR A 44 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A 46 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N GLU A 62 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 69 through 71 removed outlier: 3.641A pdb=" N ASP B 105 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 263 through 269 removed outlier: 6.899A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N HIS B 267 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU B 256 " --> pdb=" O HIS B 267 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 44 through 46 removed outlier: 3.819A pdb=" N LEU B 64 " --> pdb=" O TYR B 44 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL B 46 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N GLU B 62 " --> pdb=" O VAL B 46 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1368 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: 2.71 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1399 1.31 - 1.44: 2535 1.44 - 1.57: 5345 1.57 - 1.70: 28 1.70 - 1.83: 94 Bond restraints: 9401 Sorted by residual: bond pdb=" C13 R1H B1505 " pdb=" N08 R1H B1505 " ideal model delta sigma weight residual 1.455 1.292 0.163 2.00e-02 2.50e+03 6.62e+01 bond pdb=" C4 ATP A1501 " pdb=" C5 ATP A1501 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.78e+01 bond pdb=" C4 ATP B1501 " pdb=" C5 ATP B1501 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.78e+01 bond pdb=" C5 ATP B1501 " pdb=" C6 ATP B1501 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.89e+01 bond pdb=" C5 ATP A1501 " pdb=" C6 ATP A1501 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.88e+01 ... (remaining 9396 not shown) Histogram of bond angle deviations from ideal: 98.45 - 106.08: 229 106.08 - 113.71: 5390 113.71 - 121.34: 5157 121.34 - 128.97: 1920 128.97 - 136.60: 48 Bond angle restraints: 12744 Sorted by residual: angle pdb=" PB ATP A1501 " pdb=" O3B ATP A1501 " pdb=" PG ATP A1501 " ideal model delta sigma weight residual 139.87 121.57 18.30 1.00e+00 1.00e+00 3.35e+02 angle pdb=" PB ATP B1501 " pdb=" O3B ATP B1501 " pdb=" PG ATP B1501 " ideal model delta sigma weight residual 139.87 121.63 18.24 1.00e+00 1.00e+00 3.33e+02 angle pdb=" PA ATP B1501 " pdb=" O3A ATP B1501 " pdb=" PB ATP B1501 " ideal model delta sigma weight residual 136.83 119.53 17.30 1.00e+00 1.00e+00 2.99e+02 angle pdb=" PA ATP A1501 " pdb=" O3A ATP A1501 " pdb=" PB ATP A1501 " ideal model delta sigma weight residual 136.83 119.57 17.26 1.00e+00 1.00e+00 2.98e+02 angle pdb=" C5 ATP B1501 " pdb=" C4 ATP B1501 " pdb=" N3 ATP B1501 " ideal model delta sigma weight residual 126.80 119.16 7.64 1.00e+00 1.00e+00 5.84e+01 ... (remaining 12739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.02: 5522 22.02 - 44.05: 229 44.05 - 66.07: 40 66.07 - 88.10: 7 88.10 - 110.12: 6 Dihedral angle restraints: 5804 sinusoidal: 2512 harmonic: 3292 Sorted by residual: dihedral pdb=" CB CYS A 603 " pdb=" SG CYS A 603 " pdb=" SG CYS B 603 " pdb=" CB CYS B 603 " ideal model delta sinusoidal sigma weight residual 93.00 140.59 -47.59 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" SG CYS A 603 " pdb=" CB CYS B 603 " pdb=" SG CYS B 603 " pdb=" CA CYS B 603 " ideal model delta sinusoidal sigma weight residual 79.00 4.00 75.00 1 2.00e+01 2.50e-03 1.78e+01 dihedral pdb=" C07 R1H B1505 " pdb=" C09 R1H B1505 " pdb=" N08 R1H B1505 " pdb=" C10 R1H B1505 " ideal model delta sinusoidal sigma weight residual -53.85 56.27 -110.12 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 5801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1339 0.073 - 0.147: 103 0.147 - 0.220: 14 0.220 - 0.294: 6 0.294 - 0.367: 4 Chirality restraints: 1466 Sorted by residual: chirality pdb=" C17 CLR B1502 " pdb=" C13 CLR B1502 " pdb=" C16 CLR B1502 " pdb=" C20 CLR B1502 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" C17 CLR A1502 " pdb=" C13 CLR A1502 " pdb=" C16 CLR A1502 " pdb=" C20 CLR A1502 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" C17 CLR B1503 " pdb=" C13 CLR B1503 " pdb=" C16 CLR B1503 " pdb=" C20 CLR B1503 " both_signs ideal model delta sigma weight residual False 2.55 2.88 -0.32 2.00e-01 2.50e+01 2.64e+00 ... (remaining 1463 not shown) Planarity restraints: 1538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 211 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.92e+00 pdb=" N PRO A 212 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 211 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO B 212 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 212 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 212 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 500 " -0.018 5.00e-02 4.00e+02 2.64e-02 1.12e+00 pdb=" N PRO A 501 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 501 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 501 " -0.015 5.00e-02 4.00e+02 ... (remaining 1535 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 5 1.99 - 2.71: 287 2.71 - 3.44: 13697 3.44 - 4.17: 20343 4.17 - 4.90: 39498 Nonbonded interactions: 73830 Sorted by model distance: nonbonded pdb=" O1G ATP B1501 " pdb="MG MG B1506 " model vdw 1.257 2.170 nonbonded pdb=" O1G ATP A1501 " pdb="MG MG A1505 " model vdw 1.521 2.170 nonbonded pdb=" NE2 GLN A 126 " pdb="MG MG A1505 " model vdw 1.897 2.250 nonbonded pdb=" OE1 GLN A 126 " pdb="MG MG A1505 " model vdw 1.918 2.170 nonbonded pdb=" O1B ATP B1501 " pdb="MG MG B1506 " model vdw 1.956 2.170 ... (remaining 73825 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' and (resid 34 through 654 or resid 1501 through 1504)) selection = (chain 'B' and (resid 34 through 654 or resid 1501 through 1504)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=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: 3.810 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: 12.160 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.880 Find NCS groups from input model: 0.550 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: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.007 0.163 9401 Z= 0.481 Angle : 0.878 18.295 12744 Z= 0.522 Chirality : 0.049 0.367 1466 Planarity : 0.003 0.035 1538 Dihedral : 12.779 110.123 3679 Min Nonbonded Distance : 1.257 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.48 % Favored : 96.35 % Rotamer: Outliers : 0.20 % Allowed : 4.20 % Favored : 95.59 % 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: 0.83 (0.25), residues: 1122 helix: 1.55 (0.20), residues: 654 sheet: -0.68 (0.62), residues: 68 loop : -0.87 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 564 HIS 0.003 0.001 HIS B 267 PHE 0.011 0.001 PHE A 39 TYR 0.014 0.001 TYR A 463 ARG 0.003 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 0.993 Fit side-chains REVERT: B 585 GLU cc_start: 0.7706 (tp30) cc_final: 0.7475 (tp30) outliers start: 2 outliers final: 0 residues processed: 158 average time/residue: 0.2396 time to fit residues: 51.1049 Evaluate side-chains 70 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 299 ASN A 375 HIS B 288 ASN B 617 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9401 Z= 0.252 Angle : 0.565 9.367 12744 Z= 0.292 Chirality : 0.041 0.157 1466 Planarity : 0.003 0.025 1538 Dihedral : 10.677 95.347 1629 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.14 % Favored : 97.68 % Rotamer: Outliers : 1.64 % Allowed : 9.43 % Favored : 88.93 % 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: 1.37 (0.26), residues: 1122 helix: 2.12 (0.20), residues: 662 sheet: -0.04 (0.58), residues: 76 loop : -1.09 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.008 0.001 HIS A 40 PHE 0.023 0.001 PHE A 293 TYR 0.014 0.001 TYR B 605 ARG 0.004 0.000 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 1.172 Fit side-chains REVERT: B 585 GLU cc_start: 0.7971 (tp30) cc_final: 0.7738 (tp30) outliers start: 16 outliers final: 12 residues processed: 92 average time/residue: 0.1783 time to fit residues: 24.8621 Evaluate side-chains 82 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 532 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 70 optimal weight: 0.1980 chunk 28 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9401 Z= 0.195 Angle : 0.513 8.946 12744 Z= 0.262 Chirality : 0.039 0.143 1466 Planarity : 0.003 0.030 1538 Dihedral : 10.007 84.879 1629 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.74 % Allowed : 10.55 % Favored : 87.70 % 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: 1.57 (0.26), residues: 1122 helix: 2.34 (0.20), residues: 662 sheet: 0.21 (0.57), residues: 76 loop : -1.19 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 379 HIS 0.004 0.001 HIS A 40 PHE 0.018 0.001 PHE A 293 TYR 0.014 0.001 TYR B 605 ARG 0.003 0.000 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 1.051 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 99 average time/residue: 0.1750 time to fit residues: 26.5601 Evaluate side-chains 83 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 532 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 104 optimal weight: 0.2980 chunk 110 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9401 Z= 0.244 Angle : 0.526 8.826 12744 Z= 0.270 Chirality : 0.040 0.143 1466 Planarity : 0.003 0.033 1538 Dihedral : 9.759 78.069 1629 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.84 % Allowed : 11.58 % Favored : 86.58 % 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: 1.55 (0.26), residues: 1122 helix: 2.26 (0.20), residues: 668 sheet: 0.55 (0.66), residues: 50 loop : -1.09 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 379 HIS 0.005 0.001 HIS B 283 PHE 0.017 0.001 PHE A 293 TYR 0.012 0.001 TYR B 605 ARG 0.003 0.000 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 1.041 Fit side-chains outliers start: 18 outliers final: 13 residues processed: 86 average time/residue: 0.1727 time to fit residues: 23.1820 Evaluate side-chains 82 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 532 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN B 629 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9401 Z= 0.380 Angle : 0.590 8.888 12744 Z= 0.301 Chirality : 0.042 0.142 1466 Planarity : 0.003 0.038 1538 Dihedral : 9.862 77.740 1629 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.15 % Allowed : 11.37 % Favored : 86.48 % 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: 1.26 (0.26), residues: 1122 helix: 2.02 (0.20), residues: 668 sheet: 0.69 (0.65), residues: 50 loop : -1.23 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 379 HIS 0.004 0.001 HIS A 630 PHE 0.019 0.002 PHE A 293 TYR 0.015 0.001 TYR A 463 ARG 0.002 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 69 time to evaluate : 1.124 Fit side-chains REVERT: A 525 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8632 (mp) REVERT: B 246 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8093 (mtm180) outliers start: 21 outliers final: 15 residues processed: 88 average time/residue: 0.1968 time to fit residues: 25.9441 Evaluate side-chains 83 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 532 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 0.0870 chunk 27 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 629 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 9401 Z= 0.150 Angle : 0.469 8.518 12744 Z= 0.240 Chirality : 0.037 0.141 1466 Planarity : 0.003 0.037 1538 Dihedral : 9.422 74.111 1629 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.74 % Allowed : 12.19 % Favored : 86.07 % 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: 1.61 (0.26), residues: 1122 helix: 2.33 (0.21), residues: 668 sheet: 0.96 (0.66), residues: 50 loop : -1.18 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 379 HIS 0.003 0.001 HIS A 40 PHE 0.016 0.001 PHE A 293 TYR 0.009 0.001 TYR B 605 ARG 0.001 0.000 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 1.068 Fit side-chains REVERT: A 515 MET cc_start: 0.8239 (mmm) cc_final: 0.8006 (mmp) REVERT: A 525 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8639 (mp) outliers start: 17 outliers final: 11 residues processed: 84 average time/residue: 0.1793 time to fit residues: 22.7785 Evaluate side-chains 77 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 532 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 629 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9401 Z= 0.289 Angle : 0.524 8.519 12744 Z= 0.267 Chirality : 0.040 0.145 1466 Planarity : 0.003 0.041 1538 Dihedral : 9.490 74.179 1629 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.95 % Allowed : 12.50 % Favored : 85.55 % 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: 1.45 (0.26), residues: 1122 helix: 2.24 (0.20), residues: 668 sheet: 0.69 (0.55), residues: 76 loop : -1.42 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.003 0.001 HIS B 40 PHE 0.017 0.001 PHE A 293 TYR 0.012 0.001 TYR B 336 ARG 0.002 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 68 time to evaluate : 1.071 Fit side-chains REVERT: A 161 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.9012 (mp) REVERT: A 525 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8630 (mp) REVERT: B 130 VAL cc_start: 0.9142 (OUTLIER) cc_final: 0.8910 (m) outliers start: 19 outliers final: 13 residues processed: 84 average time/residue: 0.1761 time to fit residues: 22.6079 Evaluate side-chains 84 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 532 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 ASN B 375 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9401 Z= 0.274 Angle : 0.516 8.485 12744 Z= 0.263 Chirality : 0.039 0.143 1466 Planarity : 0.003 0.043 1538 Dihedral : 9.404 74.147 1629 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.15 % Allowed : 12.91 % Favored : 84.94 % 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: 1.50 (0.26), residues: 1122 helix: 2.19 (0.20), residues: 672 sheet: 1.13 (0.67), residues: 50 loop : -1.18 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.003 0.001 HIS B 40 PHE 0.017 0.001 PHE A 293 TYR 0.011 0.001 TYR A 463 ARG 0.002 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 67 time to evaluate : 1.083 Fit side-chains REVERT: A 525 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8621 (mp) REVERT: B 489 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8420 (m-80) outliers start: 21 outliers final: 15 residues processed: 84 average time/residue: 0.1724 time to fit residues: 22.5033 Evaluate side-chains 84 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 67 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 532 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9401 Z= 0.182 Angle : 0.485 8.417 12744 Z= 0.248 Chirality : 0.038 0.143 1466 Planarity : 0.003 0.043 1538 Dihedral : 9.221 73.576 1629 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.74 % Allowed : 12.91 % Favored : 85.35 % 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: 1.66 (0.26), residues: 1122 helix: 2.32 (0.20), residues: 672 sheet: 1.21 (0.67), residues: 50 loop : -1.12 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 379 HIS 0.002 0.001 HIS A 40 PHE 0.016 0.001 PHE A 293 TYR 0.009 0.001 TYR B 336 ARG 0.002 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 1.006 Fit side-chains REVERT: A 525 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8631 (mp) REVERT: B 246 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7956 (mtm180) REVERT: B 489 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8383 (m-80) outliers start: 17 outliers final: 12 residues processed: 79 average time/residue: 0.2094 time to fit residues: 24.6811 Evaluate side-chains 80 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 532 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9401 Z= 0.239 Angle : 0.504 8.353 12744 Z= 0.257 Chirality : 0.039 0.144 1466 Planarity : 0.003 0.045 1538 Dihedral : 9.182 74.055 1629 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.74 % Allowed : 12.81 % Favored : 85.45 % 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: 1.59 (0.26), residues: 1122 helix: 2.26 (0.20), residues: 672 sheet: 1.15 (0.66), residues: 50 loop : -1.14 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.003 0.001 HIS A 40 PHE 0.016 0.001 PHE A 293 TYR 0.010 0.001 TYR A 413 ARG 0.002 0.000 ARG A 113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 67 time to evaluate : 1.088 Fit side-chains REVERT: A 525 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8642 (mp) REVERT: B 130 VAL cc_start: 0.9198 (OUTLIER) cc_final: 0.8989 (m) REVERT: B 246 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7988 (mtm180) REVERT: B 489 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8392 (m-80) outliers start: 17 outliers final: 13 residues processed: 80 average time/residue: 0.1864 time to fit residues: 22.5174 Evaluate side-chains 83 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 532 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 5 optimal weight: 0.0030 chunk 65 optimal weight: 6.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 629 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.101397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.081584 restraints weight = 16152.977| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.32 r_work: 0.2941 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9401 Z= 0.154 Angle : 0.462 8.238 12744 Z= 0.235 Chirality : 0.037 0.139 1466 Planarity : 0.003 0.043 1538 Dihedral : 8.933 72.831 1629 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.64 % Allowed : 13.01 % Favored : 85.35 % 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: 1.79 (0.27), residues: 1122 helix: 2.43 (0.20), residues: 670 sheet: 1.26 (0.67), residues: 50 loop : -1.05 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 379 HIS 0.002 0.001 HIS A 40 PHE 0.015 0.001 PHE A 293 TYR 0.009 0.001 TYR B 336 ARG 0.001 0.000 ARG A 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2140.29 seconds wall clock time: 39 minutes 58.84 seconds (2398.84 seconds total)