Starting phenix.real_space_refine on Wed Feb 14 05:11:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqy_20456/02_2024/6pqy_20456.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqy_20456/02_2024/6pqy_20456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqy_20456/02_2024/6pqy_20456.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqy_20456/02_2024/6pqy_20456.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqy_20456/02_2024/6pqy_20456.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqy_20456/02_2024/6pqy_20456.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 64 5.49 5 S 34 5.16 5 C 5324 2.51 5 N 1496 2.21 5 O 1772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A ARG 106": "NH1" <-> "NH2" Residue "A ASP 109": "OD1" <-> "OD2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 159": "OD1" <-> "OD2" Residue "A ASP 161": "OD1" <-> "OD2" Residue "A TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 319": "OD1" <-> "OD2" Residue "A ASP 320": "OD1" <-> "OD2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 416": "OD1" <-> "OD2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "A ARG 445": "NH1" <-> "NH2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A ASP 481": "OD1" <-> "OD2" Residue "A PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 500": "OD1" <-> "OD2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D ARG 106": "NH1" <-> "NH2" Residue "D ASP 109": "OD1" <-> "OD2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 159": "OD1" <-> "OD2" Residue "D ASP 161": "OD1" <-> "OD2" Residue "D TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 176": "NH1" <-> "NH2" Residue "D TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 276": "NH1" <-> "NH2" Residue "D TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 319": "OD1" <-> "OD2" Residue "D ASP 320": "OD1" <-> "OD2" Residue "D PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 388": "NH1" <-> "NH2" Residue "D TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 396": "OE1" <-> "OE2" Residue "D TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 416": "OD1" <-> "OD2" Residue "D GLU 431": "OE1" <-> "OE2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D ARG 437": "NH1" <-> "NH2" Residue "D PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 443": "NH1" <-> "NH2" Residue "D ARG 445": "NH1" <-> "NH2" Residue "D GLU 446": "OE1" <-> "OE2" Residue "D ASP 481": "OD1" <-> "OD2" Residue "D PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 500": "OD1" <-> "OD2" Residue "D PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8690 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3689 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 442} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "C" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 323 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3689 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 442} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "F" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 323 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 5.14, per 1000 atoms: 0.59 Number of scatterers: 8690 At special positions: 0 Unit cell: (85.05, 122.85, 92.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 64 15.00 O 1772 8.00 N 1496 7.00 C 5324 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: 4.06 Conformation dependent library (CDL) restraints added in 1.4 seconds 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1764 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 4 sheets defined 52.6% alpha, 14.8% beta 28 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'A' and resid 25 through 37 removed outlier: 4.031A pdb=" N GLY A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 53 removed outlier: 3.582A pdb=" N GLU A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 73 removed outlier: 3.722A pdb=" N VAL A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 106 removed outlier: 4.271A pdb=" N ILE A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 removed outlier: 4.030A pdb=" N TYR A 174 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 201 Processing helix chain 'A' and resid 226 through 232 Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 275 through 289 removed outlier: 3.697A pdb=" N VAL A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 322 removed outlier: 3.690A pdb=" N ASN A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 344 Processing helix chain 'A' and resid 347 through 355 Processing helix chain 'A' and resid 358 through 374 removed outlier: 3.504A pdb=" N ILE A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER A 374 " --> pdb=" O GLN A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 398 Processing helix chain 'A' and resid 404 through 412 removed outlier: 3.571A pdb=" N HIS A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 removed outlier: 3.512A pdb=" N GLU A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 448 Processing helix chain 'A' and resid 454 through 470 removed outlier: 3.892A pdb=" N ASN A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 496 removed outlier: 3.554A pdb=" N LEU A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 37 removed outlier: 4.031A pdb=" N GLY D 31 " --> pdb=" O GLU D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 53 removed outlier: 3.582A pdb=" N GLU D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 73 removed outlier: 3.721A pdb=" N VAL D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 106 removed outlier: 4.270A pdb=" N ILE D 105 " --> pdb=" O ILE D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 175 removed outlier: 4.031A pdb=" N TYR D 174 " --> pdb=" O SER D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 201 Processing helix chain 'D' and resid 226 through 232 Processing helix chain 'D' and resid 272 through 274 No H-bonds generated for 'chain 'D' and resid 272 through 274' Processing helix chain 'D' and resid 275 through 289 removed outlier: 3.698A pdb=" N VAL D 279 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 322 removed outlier: 3.690A pdb=" N ASN D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 344 Processing helix chain 'D' and resid 347 through 355 Processing helix chain 'D' and resid 358 through 374 removed outlier: 3.505A pdb=" N ILE D 362 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE D 372 " --> pdb=" O ILE D 368 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR D 373 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER D 374 " --> pdb=" O GLN D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 398 Processing helix chain 'D' and resid 404 through 412 removed outlier: 3.572A pdb=" N HIS D 408 " --> pdb=" O SER D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 421 removed outlier: 3.512A pdb=" N GLU D 420 " --> pdb=" O ASP D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 448 Processing helix chain 'D' and resid 454 through 470 removed outlier: 3.892A pdb=" N ASN D 458 " --> pdb=" O ARG D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 496 removed outlier: 3.554A pdb=" N LEU D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.408A pdb=" N THR A 149 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE A 180 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHE A 147 " --> pdb=" O PHE A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.408A pdb=" N THR A 149 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE A 180 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHE A 147 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP A 125 " --> pdb=" O MET A 148 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE A 119 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU A 156 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE A 117 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 10.174A pdb=" N LEU A 116 " --> pdb=" O HIS A 216 " (cutoff:3.500A) removed outlier: 11.586A pdb=" N LEU A 218 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 10.387A pdb=" N LEU A 118 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 11.390A pdb=" N MET A 220 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 11.195A pdb=" N SER A 120 " --> pdb=" O MET A 220 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N MET A 222 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP A 122 " --> pdb=" O MET A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 80 through 81 removed outlier: 6.408A pdb=" N THR D 149 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE D 180 " --> pdb=" O PHE D 147 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE D 147 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 80 through 81 removed outlier: 6.408A pdb=" N THR D 149 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE D 180 " --> pdb=" O PHE D 147 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE D 147 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP D 125 " --> pdb=" O MET D 148 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE D 119 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LEU D 156 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE D 117 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 10.174A pdb=" N LEU D 116 " --> pdb=" O HIS D 216 " (cutoff:3.500A) removed outlier: 11.587A pdb=" N LEU D 218 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 10.386A pdb=" N LEU D 118 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 11.390A pdb=" N MET D 220 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 11.194A pdb=" N SER D 120 " --> pdb=" O MET D 220 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N MET D 222 " --> pdb=" O SER D 120 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP D 122 " --> pdb=" O MET D 222 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 2.87 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2151 1.33 - 1.45: 1973 1.45 - 1.57: 4688 1.57 - 1.69: 124 1.69 - 1.81: 52 Bond restraints: 8988 Sorted by residual: bond pdb=" O3' DC F 12 " pdb=" P DC F 13 " ideal model delta sigma weight residual 1.607 1.647 -0.040 1.50e-02 4.44e+03 7.16e+00 bond pdb=" O3' DC C 12 " pdb=" P DC C 13 " ideal model delta sigma weight residual 1.607 1.644 -0.037 1.50e-02 4.44e+03 6.15e+00 bond pdb=" C1' DT B 22 " pdb=" N1 DT B 22 " ideal model delta sigma weight residual 1.490 1.441 0.049 3.00e-02 1.11e+03 2.67e+00 bond pdb=" C1' DT E 22 " pdb=" N1 DT E 22 " ideal model delta sigma weight residual 1.490 1.441 0.049 3.00e-02 1.11e+03 2.63e+00 bond pdb=" CB TRP D 41 " pdb=" CG TRP D 41 " ideal model delta sigma weight residual 1.498 1.449 0.049 3.10e-02 1.04e+03 2.47e+00 ... (remaining 8983 not shown) Histogram of bond angle deviations from ideal: 98.95 - 105.96: 488 105.96 - 112.97: 4873 112.97 - 119.98: 3182 119.98 - 126.99: 3642 126.99 - 134.00: 215 Bond angle restraints: 12400 Sorted by residual: angle pdb=" C4' DC F 12 " pdb=" C3' DC F 12 " pdb=" O3' DC F 12 " ideal model delta sigma weight residual 110.00 121.29 -11.29 1.50e+00 4.44e-01 5.66e+01 angle pdb=" C4' DC C 12 " pdb=" C3' DC C 12 " pdb=" O3' DC C 12 " ideal model delta sigma weight residual 110.00 120.69 -10.69 1.50e+00 4.44e-01 5.08e+01 angle pdb=" O3' DT C 15 " pdb=" C3' DT C 15 " pdb=" C2' DT C 15 " ideal model delta sigma weight residual 111.50 120.80 -9.30 1.50e+00 4.44e-01 3.84e+01 angle pdb=" C3' DC F 12 " pdb=" C2' DC F 12 " pdb=" C1' DC F 12 " ideal model delta sigma weight residual 101.60 107.16 -5.56 1.50e+00 4.44e-01 1.37e+01 angle pdb=" C3' DC C 12 " pdb=" C2' DC C 12 " pdb=" C1' DC C 12 " ideal model delta sigma weight residual 101.60 106.93 -5.33 1.50e+00 4.44e-01 1.26e+01 ... (remaining 12395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 4952 35.87 - 71.75: 328 71.75 - 107.62: 10 107.62 - 143.49: 0 143.49 - 179.36: 10 Dihedral angle restraints: 5300 sinusoidal: 2588 harmonic: 2712 Sorted by residual: dihedral pdb=" CA ASP D 161 " pdb=" C ASP D 161 " pdb=" N THR D 162 " pdb=" CA THR D 162 " ideal model delta harmonic sigma weight residual 180.00 154.62 25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ASP A 161 " pdb=" C ASP A 161 " pdb=" N THR A 162 " pdb=" CA THR A 162 " ideal model delta harmonic sigma weight residual 180.00 154.62 25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA SER A 453 " pdb=" C SER A 453 " pdb=" N ARG A 454 " pdb=" CA ARG A 454 " ideal model delta harmonic sigma weight residual 180.00 155.18 24.82 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 5297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1122 0.073 - 0.146: 238 0.146 - 0.219: 31 0.219 - 0.292: 6 0.292 - 0.364: 3 Chirality restraints: 1400 Sorted by residual: chirality pdb=" C3' DC F 12 " pdb=" C4' DC F 12 " pdb=" O3' DC F 12 " pdb=" C2' DC F 12 " both_signs ideal model delta sigma weight residual False -2.66 -2.30 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C3' DC C 12 " pdb=" C4' DC C 12 " pdb=" O3' DC C 12 " pdb=" C2' DC C 12 " both_signs ideal model delta sigma weight residual False -2.66 -2.30 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C3' DT C 15 " pdb=" C4' DT C 15 " pdb=" O3' DT C 15 " pdb=" C2' DT C 15 " both_signs ideal model delta sigma weight residual False -2.66 -2.34 -0.33 2.00e-01 2.50e+01 2.64e+00 ... (remaining 1397 not shown) Planarity restraints: 1348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC C 12 " 0.041 2.00e-02 2.50e+03 2.75e-02 1.71e+01 pdb=" N1 DC C 12 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DC C 12 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DC C 12 " -0.033 2.00e-02 2.50e+03 pdb=" N3 DC C 12 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DC C 12 " 0.047 2.00e-02 2.50e+03 pdb=" N4 DC C 12 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DC C 12 " -0.025 2.00e-02 2.50e+03 pdb=" C6 DC C 12 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT C 15 " -0.051 2.00e-02 2.50e+03 2.26e-02 1.28e+01 pdb=" N1 DT C 15 " 0.024 2.00e-02 2.50e+03 pdb=" C2 DT C 15 " 0.018 2.00e-02 2.50e+03 pdb=" O2 DT C 15 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DT C 15 " -0.009 2.00e-02 2.50e+03 pdb=" C4 DT C 15 " 0.000 2.00e-02 2.50e+03 pdb=" O4 DT C 15 " -0.026 2.00e-02 2.50e+03 pdb=" C5 DT C 15 " 0.013 2.00e-02 2.50e+03 pdb=" C7 DT C 15 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT C 15 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA B 30 " 0.019 2.00e-02 2.50e+03 2.07e-02 1.18e+01 pdb=" N9 DA B 30 " -0.053 2.00e-02 2.50e+03 pdb=" C8 DA B 30 " 0.037 2.00e-02 2.50e+03 pdb=" N7 DA B 30 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DA B 30 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DA B 30 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA B 30 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DA B 30 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DA B 30 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA B 30 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA B 30 " -0.006 2.00e-02 2.50e+03 ... (remaining 1345 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1501 2.76 - 3.30: 9795 3.30 - 3.83: 15952 3.83 - 4.37: 17791 4.37 - 4.90: 25995 Nonbonded interactions: 71034 Sorted by model distance: nonbonded pdb=" OG1 THR A 149 " pdb=" OE1 GLN A 179 " model vdw 2.225 2.440 nonbonded pdb=" OG1 THR D 149 " pdb=" OE1 GLN D 179 " model vdw 2.226 2.440 nonbonded pdb=" N ASP D 500 " pdb=" OD1 ASP D 500 " model vdw 2.239 2.520 nonbonded pdb=" N ASP A 500 " pdb=" OD1 ASP A 500 " model vdw 2.239 2.520 nonbonded pdb=" O VAL D 81 " pdb=" NE2 GLN D 455 " model vdw 2.244 2.520 ... (remaining 71029 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 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.000 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.160 Find NCS groups from input model: 0.440 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 0.049 8988 Z= 0.448 Angle : 0.987 11.285 12400 Z= 0.578 Chirality : 0.064 0.364 1400 Planarity : 0.007 0.066 1348 Dihedral : 22.029 179.364 3536 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 25.09 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.83 % Favored : 92.51 % Rotamer: Outliers : 0.49 % Allowed : 5.38 % Favored : 94.13 % 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: -4.46 (0.22), residues: 908 helix: -2.68 (0.18), residues: 438 sheet: -3.07 (0.55), residues: 60 loop : -3.19 (0.26), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 41 HIS 0.015 0.003 HIS A 448 PHE 0.028 0.003 PHE A 102 TYR 0.023 0.005 TYR A 174 ARG 0.044 0.008 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 143 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8183 (mmm) cc_final: 0.7776 (mmp) REVERT: A 280 MET cc_start: 0.7800 (ppp) cc_final: 0.7234 (ppp) REVERT: A 337 ASP cc_start: 0.4447 (m-30) cc_final: 0.3873 (m-30) REVERT: D 193 GLU cc_start: 0.9064 (tp30) cc_final: 0.8540 (tp30) REVERT: D 197 MET cc_start: 0.8507 (mmm) cc_final: 0.7847 (mmp) REVERT: D 204 LEU cc_start: 0.8835 (pp) cc_final: 0.8560 (pt) REVERT: D 280 MET cc_start: 0.7380 (ppp) cc_final: 0.6939 (ppp) REVERT: D 337 ASP cc_start: 0.3946 (m-30) cc_final: 0.3736 (m-30) outliers start: 4 outliers final: 1 residues processed: 147 average time/residue: 0.2563 time to fit residues: 48.9712 Evaluate side-chains 90 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 0.0870 chunk 24 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8988 Z= 0.178 Angle : 0.624 6.102 12400 Z= 0.344 Chirality : 0.040 0.149 1400 Planarity : 0.004 0.033 1348 Dihedral : 25.194 179.172 1688 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % 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: -2.32 (0.26), residues: 908 helix: -0.73 (0.23), residues: 452 sheet: -2.04 (0.60), residues: 54 loop : -2.41 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 400 HIS 0.005 0.001 HIS A 307 PHE 0.013 0.002 PHE D 102 TYR 0.014 0.001 TYR A 288 ARG 0.004 0.001 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8552 (tp) cc_final: 0.8235 (tp) REVERT: A 32 LEU cc_start: 0.8993 (tp) cc_final: 0.8698 (tt) REVERT: A 115 GLN cc_start: 0.6824 (tp40) cc_final: 0.6169 (tp-100) REVERT: A 173 MET cc_start: 0.6712 (mtm) cc_final: 0.6237 (mtm) REVERT: A 176 ARG cc_start: 0.8555 (mtp85) cc_final: 0.7668 (mtp85) REVERT: A 197 MET cc_start: 0.7898 (mmm) cc_final: 0.7668 (mmp) REVERT: A 280 MET cc_start: 0.7971 (ppp) cc_final: 0.7506 (ppp) REVERT: A 310 LYS cc_start: 0.6859 (tppt) cc_final: 0.6560 (tppt) REVERT: A 472 LEU cc_start: 0.8981 (tp) cc_final: 0.8677 (tp) REVERT: D 146 ILE cc_start: 0.8785 (mm) cc_final: 0.8473 (mm) REVERT: D 197 MET cc_start: 0.8413 (mmm) cc_final: 0.8093 (mmp) REVERT: D 280 MET cc_start: 0.7011 (ppp) cc_final: 0.6642 (tpp) REVERT: D 289 ARG cc_start: 0.6133 (mtt-85) cc_final: 0.5869 (mtt180) REVERT: D 443 ARG cc_start: 0.8637 (ttp-170) cc_final: 0.7985 (mmm160) REVERT: D 472 LEU cc_start: 0.9187 (tp) cc_final: 0.8887 (tp) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2563 time to fit residues: 51.1621 Evaluate side-chains 114 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 24 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8988 Z= 0.280 Angle : 0.685 6.833 12400 Z= 0.380 Chirality : 0.043 0.233 1400 Planarity : 0.005 0.042 1348 Dihedral : 24.641 179.422 1688 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 22.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.12 % Allowed : 5.38 % Favored : 94.50 % 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: -1.91 (0.26), residues: 908 helix: -0.37 (0.23), residues: 450 sheet: -1.93 (0.59), residues: 54 loop : -2.20 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 41 HIS 0.004 0.001 HIS A 408 PHE 0.048 0.002 PHE A 102 TYR 0.014 0.002 TYR D 174 ARG 0.004 0.001 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ILE cc_start: 0.8993 (mm) cc_final: 0.8671 (mm) REVERT: A 197 MET cc_start: 0.8437 (mmm) cc_final: 0.8161 (mmp) REVERT: A 280 MET cc_start: 0.7712 (ppp) cc_final: 0.7224 (ppp) REVERT: D 124 PHE cc_start: 0.8852 (p90) cc_final: 0.8650 (p90) REVERT: D 146 ILE cc_start: 0.8908 (mm) cc_final: 0.8648 (mm) REVERT: D 173 MET cc_start: 0.7596 (mtt) cc_final: 0.7315 (mtp) REVERT: D 197 MET cc_start: 0.8602 (mmm) cc_final: 0.7982 (mmp) REVERT: D 280 MET cc_start: 0.7085 (ppp) cc_final: 0.6701 (tpp) REVERT: D 289 ARG cc_start: 0.6134 (mtt-85) cc_final: 0.5904 (mtt180) REVERT: D 443 ARG cc_start: 0.8610 (ttp-170) cc_final: 0.7720 (mmm160) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.2554 time to fit residues: 41.2896 Evaluate side-chains 93 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 9 optimal weight: 0.1980 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8988 Z= 0.241 Angle : 0.654 6.361 12400 Z= 0.363 Chirality : 0.041 0.161 1400 Planarity : 0.004 0.066 1348 Dihedral : 24.565 179.690 1688 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.12 % Allowed : 2.81 % Favored : 97.07 % 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 (0.27), residues: 908 helix: -0.18 (0.24), residues: 450 sheet: -1.54 (0.62), residues: 54 loop : -2.01 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 400 HIS 0.004 0.001 HIS A 408 PHE 0.049 0.002 PHE A 102 TYR 0.021 0.002 TYR D 73 ARG 0.012 0.001 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8956 (tp) cc_final: 0.8566 (tt) REVERT: A 36 LEU cc_start: 0.8959 (mp) cc_final: 0.8728 (mp) REVERT: A 146 ILE cc_start: 0.8921 (mm) cc_final: 0.8644 (mm) REVERT: A 197 MET cc_start: 0.8527 (mmm) cc_final: 0.8088 (mmp) REVERT: A 233 GLU cc_start: 0.6548 (mp0) cc_final: 0.6189 (tm-30) REVERT: A 280 MET cc_start: 0.7747 (ppp) cc_final: 0.7244 (ppp) REVERT: D 106 ARG cc_start: 0.6334 (tmt170) cc_final: 0.5708 (tmt170) REVERT: D 146 ILE cc_start: 0.8915 (mm) cc_final: 0.8624 (mm) REVERT: D 152 VAL cc_start: 0.9222 (t) cc_final: 0.9017 (t) REVERT: D 197 MET cc_start: 0.8697 (mmm) cc_final: 0.8096 (mmp) REVERT: D 280 MET cc_start: 0.7141 (ppp) cc_final: 0.6845 (tpp) REVERT: D 417 ILE cc_start: 0.7807 (mm) cc_final: 0.7552 (mm) REVERT: D 443 ARG cc_start: 0.8620 (ttp-170) cc_final: 0.7744 (mmm160) outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.2299 time to fit residues: 40.8224 Evaluate side-chains 103 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 83 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN D 307 HIS D 463 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8988 Z= 0.163 Angle : 0.598 7.417 12400 Z= 0.330 Chirality : 0.040 0.161 1400 Planarity : 0.004 0.040 1348 Dihedral : 24.483 178.309 1688 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.24 % Allowed : 1.96 % Favored : 97.80 % 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: -1.05 (0.28), residues: 908 helix: 0.30 (0.24), residues: 454 sheet: -0.96 (0.65), residues: 54 loop : -1.84 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 400 HIS 0.006 0.001 HIS D 307 PHE 0.037 0.002 PHE A 102 TYR 0.012 0.001 TYR A 288 ARG 0.012 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.9022 (tp) cc_final: 0.8717 (tt) REVERT: A 36 LEU cc_start: 0.8998 (mp) cc_final: 0.8788 (mp) REVERT: A 115 GLN cc_start: 0.6844 (tp40) cc_final: 0.6488 (tp40) REVERT: A 124 PHE cc_start: 0.8622 (p90) cc_final: 0.8316 (p90) REVERT: A 197 MET cc_start: 0.8370 (mmm) cc_final: 0.8120 (mmp) REVERT: A 219 MET cc_start: 0.7778 (mmp) cc_final: 0.7573 (mmp) REVERT: A 233 GLU cc_start: 0.6663 (mp0) cc_final: 0.5978 (tm-30) REVERT: A 280 MET cc_start: 0.7335 (ppp) cc_final: 0.6807 (ppp) REVERT: A 464 MET cc_start: 0.8628 (tpt) cc_final: 0.8411 (tpp) REVERT: A 488 TYR cc_start: 0.5214 (m-10) cc_final: 0.4628 (m-10) REVERT: D 106 ARG cc_start: 0.6173 (tmt170) cc_final: 0.5483 (tmt170) REVERT: D 146 ILE cc_start: 0.8870 (mm) cc_final: 0.8610 (mm) REVERT: D 161 ASP cc_start: 0.7019 (p0) cc_final: 0.6419 (m-30) REVERT: D 197 MET cc_start: 0.8633 (mmm) cc_final: 0.8017 (mmp) REVERT: D 219 MET cc_start: 0.7852 (mmp) cc_final: 0.7638 (mmp) REVERT: D 443 ARG cc_start: 0.8573 (ttp-170) cc_final: 0.7619 (mmm160) outliers start: 2 outliers final: 0 residues processed: 135 average time/residue: 0.2106 time to fit residues: 38.9441 Evaluate side-chains 102 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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: 0.7716 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8988 Z= 0.199 Angle : 0.606 6.963 12400 Z= 0.337 Chirality : 0.039 0.184 1400 Planarity : 0.004 0.043 1348 Dihedral : 24.385 177.265 1688 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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: -1.00 (0.28), residues: 908 helix: 0.30 (0.24), residues: 454 sheet: -0.87 (0.67), residues: 54 loop : -1.77 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 41 HIS 0.003 0.001 HIS D 413 PHE 0.039 0.002 PHE A 102 TYR 0.023 0.002 TYR A 288 ARG 0.013 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.9073 (tp) cc_final: 0.8739 (tt) REVERT: A 36 LEU cc_start: 0.8975 (mp) cc_final: 0.8752 (mp) REVERT: A 146 ILE cc_start: 0.8951 (mm) cc_final: 0.8695 (mm) REVERT: A 197 MET cc_start: 0.8428 (mmm) cc_final: 0.8118 (mmp) REVERT: A 219 MET cc_start: 0.8026 (mmp) cc_final: 0.7787 (mmp) REVERT: A 233 GLU cc_start: 0.6755 (mp0) cc_final: 0.5906 (tm-30) REVERT: A 280 MET cc_start: 0.7319 (ppp) cc_final: 0.6793 (ppp) REVERT: A 310 LYS cc_start: 0.6678 (mmmt) cc_final: 0.6394 (tppt) REVERT: A 488 TYR cc_start: 0.5361 (m-10) cc_final: 0.4616 (m-10) REVERT: D 30 LEU cc_start: 0.9014 (tp) cc_final: 0.8543 (tp) REVERT: D 106 ARG cc_start: 0.6300 (tmt170) cc_final: 0.5609 (tmt170) REVERT: D 146 ILE cc_start: 0.8897 (mm) cc_final: 0.8621 (mm) REVERT: D 161 ASP cc_start: 0.6951 (p0) cc_final: 0.6443 (m-30) REVERT: D 197 MET cc_start: 0.8646 (mmm) cc_final: 0.8230 (mmp) REVERT: D 219 MET cc_start: 0.7958 (mmp) cc_final: 0.7750 (mmp) REVERT: D 233 GLU cc_start: 0.7005 (mp0) cc_final: 0.6397 (tm-30) REVERT: D 344 PHE cc_start: 0.5769 (m-80) cc_final: 0.5423 (m-80) REVERT: D 416 ASP cc_start: 0.8134 (t0) cc_final: 0.7640 (p0) REVERT: D 443 ARG cc_start: 0.8655 (ttp-170) cc_final: 0.7750 (mmm160) REVERT: D 464 MET cc_start: 0.8603 (tpp) cc_final: 0.8075 (tpp) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2289 time to fit residues: 40.1892 Evaluate side-chains 100 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 92 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8988 Z= 0.162 Angle : 0.585 7.582 12400 Z= 0.325 Chirality : 0.039 0.185 1400 Planarity : 0.003 0.039 1348 Dihedral : 24.342 177.380 1688 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.12 % Allowed : 1.34 % Favored : 98.53 % 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: -0.75 (0.28), residues: 908 helix: 0.42 (0.24), residues: 458 sheet: -0.57 (0.65), residues: 64 loop : -1.59 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 400 HIS 0.006 0.001 HIS D 307 PHE 0.030 0.002 PHE A 102 TYR 0.027 0.002 TYR A 73 ARG 0.006 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8952 (tp) cc_final: 0.8655 (tt) REVERT: A 36 LEU cc_start: 0.8960 (mp) cc_final: 0.8728 (mp) REVERT: A 115 GLN cc_start: 0.6945 (tp40) cc_final: 0.6686 (tp40) REVERT: A 197 MET cc_start: 0.8381 (mmm) cc_final: 0.8100 (mmp) REVERT: A 233 GLU cc_start: 0.6663 (mp0) cc_final: 0.6045 (tm-30) REVERT: A 280 MET cc_start: 0.7224 (ppp) cc_final: 0.6692 (ppp) REVERT: A 464 MET cc_start: 0.8747 (ttm) cc_final: 0.8144 (ttm) REVERT: A 488 TYR cc_start: 0.5084 (m-10) cc_final: 0.4714 (m-10) REVERT: D 30 LEU cc_start: 0.9015 (tp) cc_final: 0.8564 (tp) REVERT: D 146 ILE cc_start: 0.8864 (mm) cc_final: 0.8620 (mm) REVERT: D 161 ASP cc_start: 0.6843 (p0) cc_final: 0.6314 (m-30) REVERT: D 176 ARG cc_start: 0.8776 (mtp85) cc_final: 0.8008 (mtp85) REVERT: D 197 MET cc_start: 0.8631 (mmm) cc_final: 0.8190 (mmp) REVERT: D 233 GLU cc_start: 0.6829 (mp0) cc_final: 0.6148 (tm-30) REVERT: D 416 ASP cc_start: 0.8205 (t0) cc_final: 0.7708 (p0) REVERT: D 443 ARG cc_start: 0.8571 (ttp-170) cc_final: 0.7668 (mmm160) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.2253 time to fit residues: 41.9400 Evaluate side-chains 104 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 0.0870 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 72 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8988 Z= 0.169 Angle : 0.582 6.865 12400 Z= 0.320 Chirality : 0.039 0.155 1400 Planarity : 0.003 0.040 1348 Dihedral : 24.267 176.459 1688 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: -0.66 (0.29), residues: 908 helix: 0.47 (0.24), residues: 458 sheet: -0.45 (0.65), residues: 64 loop : -1.53 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 295 HIS 0.002 0.001 HIS A 408 PHE 0.026 0.001 PHE A 444 TYR 0.023 0.001 TYR A 73 ARG 0.002 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8921 (tp) cc_final: 0.8507 (tp) REVERT: A 32 LEU cc_start: 0.8969 (tp) cc_final: 0.8576 (tt) REVERT: A 102 PHE cc_start: 0.7390 (m-10) cc_final: 0.6376 (m-10) REVERT: A 106 ARG cc_start: 0.6679 (ptt90) cc_final: 0.6219 (ptt90) REVERT: A 197 MET cc_start: 0.8417 (mmm) cc_final: 0.8111 (mmp) REVERT: A 233 GLU cc_start: 0.6719 (mp0) cc_final: 0.6107 (tm-30) REVERT: A 280 MET cc_start: 0.7210 (ppp) cc_final: 0.6812 (tpt) REVERT: A 310 LYS cc_start: 0.7144 (tppt) cc_final: 0.6406 (pptt) REVERT: A 416 ASP cc_start: 0.8014 (t0) cc_final: 0.7370 (p0) REVERT: A 444 PHE cc_start: 0.7641 (m-80) cc_final: 0.6645 (m-10) REVERT: A 464 MET cc_start: 0.8708 (ttm) cc_final: 0.8375 (ttp) REVERT: A 488 TYR cc_start: 0.4917 (m-10) cc_final: 0.4588 (m-10) REVERT: D 106 ARG cc_start: 0.6091 (tmt170) cc_final: 0.5419 (tmt170) REVERT: D 146 ILE cc_start: 0.8869 (mm) cc_final: 0.8601 (mm) REVERT: D 161 ASP cc_start: 0.6832 (p0) cc_final: 0.6354 (m-30) REVERT: D 176 ARG cc_start: 0.8847 (mtp85) cc_final: 0.8170 (mtp85) REVERT: D 197 MET cc_start: 0.8617 (mmm) cc_final: 0.8185 (mmp) REVERT: D 233 GLU cc_start: 0.6775 (mp0) cc_final: 0.6155 (tm-30) REVERT: D 416 ASP cc_start: 0.8188 (t0) cc_final: 0.7697 (p0) REVERT: D 417 ILE cc_start: 0.8391 (tp) cc_final: 0.8155 (tp) REVERT: D 439 LYS cc_start: 0.8757 (ttpt) cc_final: 0.8244 (ptmt) REVERT: D 443 ARG cc_start: 0.8563 (ttp-170) cc_final: 0.7725 (mmm160) REVERT: D 464 MET cc_start: 0.8537 (tpp) cc_final: 0.7840 (tpp) REVERT: D 465 LEU cc_start: 0.8915 (mt) cc_final: 0.8691 (tp) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2398 time to fit residues: 44.1620 Evaluate side-chains 107 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8988 Z= 0.162 Angle : 0.582 6.514 12400 Z= 0.318 Chirality : 0.039 0.146 1400 Planarity : 0.003 0.040 1348 Dihedral : 24.176 176.392 1688 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.12 % Allowed : 0.24 % Favored : 99.63 % 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: -0.60 (0.29), residues: 908 helix: 0.43 (0.24), residues: 464 sheet: -0.47 (0.63), residues: 64 loop : -1.39 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 400 HIS 0.007 0.001 HIS D 307 PHE 0.032 0.002 PHE D 102 TYR 0.024 0.001 TYR A 73 ARG 0.002 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8870 (tp) cc_final: 0.8483 (tp) REVERT: A 32 LEU cc_start: 0.8896 (tp) cc_final: 0.8661 (tt) REVERT: A 103 GLU cc_start: 0.8182 (pp20) cc_final: 0.7966 (pp20) REVERT: A 152 VAL cc_start: 0.9185 (t) cc_final: 0.8958 (t) REVERT: A 197 MET cc_start: 0.8384 (mmm) cc_final: 0.8047 (mmp) REVERT: A 233 GLU cc_start: 0.6573 (mp0) cc_final: 0.6134 (tm-30) REVERT: A 280 MET cc_start: 0.7098 (ppp) cc_final: 0.6761 (tpt) REVERT: A 310 LYS cc_start: 0.7200 (tppt) cc_final: 0.6479 (pptt) REVERT: A 344 PHE cc_start: 0.5842 (m-80) cc_final: 0.5635 (m-80) REVERT: A 416 ASP cc_start: 0.8031 (t0) cc_final: 0.7419 (p0) REVERT: A 439 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8163 (ptmt) REVERT: A 446 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8107 (tp30) REVERT: D 106 ARG cc_start: 0.6034 (tmt170) cc_final: 0.5536 (tmt170) REVERT: D 146 ILE cc_start: 0.8853 (mm) cc_final: 0.8592 (mm) REVERT: D 161 ASP cc_start: 0.6639 (p0) cc_final: 0.6293 (m-30) REVERT: D 176 ARG cc_start: 0.8826 (mtp85) cc_final: 0.8128 (mtp85) REVERT: D 197 MET cc_start: 0.8632 (mmm) cc_final: 0.8206 (mmp) REVERT: D 233 GLU cc_start: 0.6516 (mp0) cc_final: 0.5888 (tm-30) REVERT: D 416 ASP cc_start: 0.8182 (t0) cc_final: 0.7734 (p0) REVERT: D 417 ILE cc_start: 0.8452 (tp) cc_final: 0.8209 (tp) REVERT: D 439 LYS cc_start: 0.8767 (ttpt) cc_final: 0.8244 (ptmt) REVERT: D 443 ARG cc_start: 0.8544 (ttp-170) cc_final: 0.7680 (mmm160) REVERT: D 464 MET cc_start: 0.8513 (tpp) cc_final: 0.7863 (tpp) REVERT: D 465 LEU cc_start: 0.8892 (mt) cc_final: 0.8659 (tp) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.2278 time to fit residues: 42.8370 Evaluate side-chains 113 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8988 Z= 0.260 Angle : 0.659 7.285 12400 Z= 0.361 Chirality : 0.041 0.200 1400 Planarity : 0.004 0.039 1348 Dihedral : 24.176 178.525 1688 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -0.91 (0.28), residues: 908 helix: 0.16 (0.24), residues: 462 sheet: -0.87 (0.70), residues: 54 loop : -1.45 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 41 HIS 0.004 0.001 HIS D 413 PHE 0.037 0.002 PHE A 444 TYR 0.026 0.002 TYR A 73 ARG 0.003 0.001 ARG A 316 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.9041 (tp) cc_final: 0.8763 (tt) REVERT: A 197 MET cc_start: 0.8407 (mmm) cc_final: 0.8035 (mmp) REVERT: A 219 MET cc_start: 0.8149 (mmp) cc_final: 0.7904 (mmp) REVERT: A 233 GLU cc_start: 0.6699 (mp0) cc_final: 0.6136 (tm-30) REVERT: A 280 MET cc_start: 0.7204 (ppp) cc_final: 0.6815 (tpp) REVERT: A 283 LEU cc_start: 0.7140 (pp) cc_final: 0.6908 (pp) REVERT: A 310 LYS cc_start: 0.7162 (tppt) cc_final: 0.6516 (pptt) REVERT: A 416 ASP cc_start: 0.8050 (t0) cc_final: 0.7441 (p0) REVERT: A 439 LYS cc_start: 0.8770 (ttpt) cc_final: 0.8416 (ptmt) REVERT: D 146 ILE cc_start: 0.8861 (mm) cc_final: 0.8597 (mm) REVERT: D 161 ASP cc_start: 0.6931 (p0) cc_final: 0.6544 (m-30) REVERT: D 197 MET cc_start: 0.8620 (mmm) cc_final: 0.8172 (mmp) REVERT: D 233 GLU cc_start: 0.6734 (mp0) cc_final: 0.6096 (tp30) REVERT: D 291 ASP cc_start: 0.8214 (t0) cc_final: 0.7976 (t0) REVERT: D 416 ASP cc_start: 0.8201 (t0) cc_final: 0.7748 (p0) REVERT: D 417 ILE cc_start: 0.8531 (tp) cc_final: 0.8298 (tp) REVERT: D 439 LYS cc_start: 0.8935 (ttpt) cc_final: 0.8464 (ptmt) REVERT: D 443 ARG cc_start: 0.8641 (ttp-170) cc_final: 0.7772 (mmm160) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2241 time to fit residues: 38.8863 Evaluate side-chains 101 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.6980 chunk 70 optimal weight: 0.0170 chunk 11 optimal weight: 8.9990 chunk 21 optimal weight: 0.0000 chunk 76 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.133846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.103069 restraints weight = 30095.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.106668 restraints weight = 16363.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.108961 restraints weight = 10834.793| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8988 Z= 0.162 Angle : 0.588 6.515 12400 Z= 0.321 Chirality : 0.040 0.206 1400 Planarity : 0.003 0.040 1348 Dihedral : 24.159 177.519 1688 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.12 % Allowed : 0.24 % Favored : 99.63 % 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: -0.66 (0.28), residues: 908 helix: 0.34 (0.24), residues: 464 sheet: -0.51 (0.62), residues: 64 loop : -1.34 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 295 HIS 0.008 0.001 HIS D 307 PHE 0.044 0.002 PHE A 102 TYR 0.028 0.001 TYR D 73 ARG 0.002 0.000 ARG A 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1811.01 seconds wall clock time: 34 minutes 6.17 seconds (2046.17 seconds total)