Starting phenix.real_space_refine on Sat Mar 16 12:50:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhi_24462/03_2024/7rhi_24462_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhi_24462/03_2024/7rhi_24462.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhi_24462/03_2024/7rhi_24462_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhi_24462/03_2024/7rhi_24462_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhi_24462/03_2024/7rhi_24462_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhi_24462/03_2024/7rhi_24462.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhi_24462/03_2024/7rhi_24462.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhi_24462/03_2024/7rhi_24462_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhi_24462/03_2024/7rhi_24462_updated.pdb" } resolution = 3.31 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= 0.001 sd= 0.004 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 4 5.49 5 S 82 5.16 5 C 9602 2.51 5 N 2396 2.21 5 O 2633 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 511": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14717 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3561 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 14, 'TRANS': 419} Chain breaks: 1 Chain: "C" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.34, per 1000 atoms: 0.50 Number of scatterers: 14717 At special positions: 0 Unit cell: (97.223, 98.04, 120.099, 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 82 16.00 P 4 15.00 O 2633 8.00 N 2396 7.00 C 9602 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: 5.68 Conformation dependent library (CDL) restraints added in 2.6 seconds 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3372 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 75 helices and 9 sheets defined 58.7% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 163 through 188 Proline residue: A 175 - end of helix removed outlier: 5.240A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 197 through 220 Processing helix chain 'A' and resid 233 through 242 Processing helix chain 'A' and resid 244 through 252 Processing helix chain 'A' and resid 256 through 263 removed outlier: 3.617A pdb=" N PHE A 261 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 262 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU A 263 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 291 removed outlier: 3.715A pdb=" N LEU A 272 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG A 277 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER A 279 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 288 " --> pdb=" O PHE A 285 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 289 " --> pdb=" O GLN A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 325 Processing helix chain 'A' and resid 345 through 360 Processing helix chain 'A' and resid 372 through 387 Processing helix chain 'A' and resid 389 through 403 Processing helix chain 'A' and resid 405 through 423 Processing helix chain 'A' and resid 428 through 443 Processing helix chain 'A' and resid 450 through 453 No H-bonds generated for 'chain 'A' and resid 450 through 453' Processing helix chain 'A' and resid 459 through 469 removed outlier: 3.675A pdb=" N ASN A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 476 removed outlier: 3.869A pdb=" N LYS A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 No H-bonds generated for 'chain 'A' and resid 488 through 491' Processing helix chain 'A' and resid 578 through 585 removed outlier: 3.639A pdb=" N ALA A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 602 removed outlier: 3.560A pdb=" N LYS A 598 " --> pdb=" O MET A 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 679 Proline residue: B 675 - end of helix Processing helix chain 'B' and resid 688 through 707 Processing helix chain 'B' and resid 710 through 712 No H-bonds generated for 'chain 'B' and resid 710 through 712' Processing helix chain 'B' and resid 725 through 734 Processing helix chain 'B' and resid 736 through 744 Processing helix chain 'B' and resid 759 through 767 Proline residue: B 764 - end of helix Processing helix chain 'B' and resid 770 through 781 Processing helix chain 'B' and resid 787 through 816 Processing helix chain 'B' and resid 831 through 843 Processing helix chain 'B' and resid 855 through 886 removed outlier: 3.614A pdb=" N SER B 873 " --> pdb=" O VAL B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 906 Processing helix chain 'B' and resid 911 through 927 removed outlier: 3.702A pdb=" N ARG B 916 " --> pdb=" O SER B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 937 Processing helix chain 'B' and resid 942 through 952 removed outlier: 3.631A pdb=" N ASP B 951 " --> pdb=" O ASP B 947 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 958 No H-bonds generated for 'chain 'B' and resid 955 through 958' Processing helix chain 'B' and resid 968 through 974 removed outlier: 3.510A pdb=" N PHE B 972 " --> pdb=" O ARG B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 1031 through 1033 No H-bonds generated for 'chain 'B' and resid 1031 through 1033' Processing helix chain 'B' and resid 1062 through 1066 Processing helix chain 'B' and resid 1070 through 1083 Processing helix chain 'C' and resid 163 through 188 Proline residue: C 175 - end of helix removed outlier: 3.671A pdb=" N VAL C 183 " --> pdb=" O ASN C 179 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 197 through 220 removed outlier: 3.576A pdb=" N ILE C 202 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 241 Processing helix chain 'C' and resid 244 through 253 Processing helix chain 'C' and resid 256 through 263 removed outlier: 3.856A pdb=" N PHE C 261 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU C 263 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 276 removed outlier: 4.182A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 291 removed outlier: 3.597A pdb=" N THR C 290 " --> pdb=" O GLN C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 325 Processing helix chain 'C' and resid 345 through 360 Processing helix chain 'C' and resid 372 through 403 Processing helix chain 'C' and resid 408 through 423 Processing helix chain 'C' and resid 428 through 444 Processing helix chain 'C' and resid 450 through 453 No H-bonds generated for 'chain 'C' and resid 450 through 453' Processing helix chain 'C' and resid 459 through 469 Processing helix chain 'C' and resid 471 through 476 removed outlier: 3.867A pdb=" N LYS C 475 " --> pdb=" O LEU C 471 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS C 476 " --> pdb=" O ASP C 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 471 through 476' Processing helix chain 'C' and resid 488 through 491 No H-bonds generated for 'chain 'C' and resid 488 through 491' Processing helix chain 'C' and resid 578 through 585 removed outlier: 3.508A pdb=" N GLU C 583 " --> pdb=" O ASP C 579 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 604 removed outlier: 4.030A pdb=" N THR C 593 " --> pdb=" O PRO C 589 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 188 removed outlier: 3.701A pdb=" N CYS D 171 " --> pdb=" O ASN D 167 " (cutoff:3.500A) Proline residue: D 175 - end of helix removed outlier: 3.623A pdb=" N VAL D 183 " --> pdb=" O ASN D 179 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 195 Processing helix chain 'D' and resid 197 through 220 Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 256 through 263 removed outlier: 3.637A pdb=" N PHE D 261 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU D 263 " --> pdb=" O TYR D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 289 removed outlier: 3.711A pdb=" N ARG D 271 " --> pdb=" O PRO D 268 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG D 274 " --> pdb=" O ARG D 271 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG D 277 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N SER D 279 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR D 288 " --> pdb=" O PHE D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 325 Processing helix chain 'D' and resid 345 through 360 Processing helix chain 'D' and resid 372 through 401 removed outlier: 4.055A pdb=" N PHE D 389 " --> pdb=" O GLY D 385 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA D 390 " --> pdb=" O VAL D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 423 removed outlier: 3.784A pdb=" N PHE D 423 " --> pdb=" O GLN D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 443 Processing helix chain 'D' and resid 450 through 456 removed outlier: 4.658A pdb=" N TYR D 456 " --> pdb=" O GLU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 Processing helix chain 'D' and resid 471 through 474 No H-bonds generated for 'chain 'D' and resid 471 through 474' Processing helix chain 'D' and resid 487 through 491 removed outlier: 3.687A pdb=" N LEU D 491 " --> pdb=" O LEU D 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 487 through 491' Processing helix chain 'D' and resid 578 through 585 Processing helix chain 'D' and resid 589 through 603 removed outlier: 3.642A pdb=" N THR D 593 " --> pdb=" O PRO D 589 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 223 through 225 removed outlier: 4.562A pdb=" N TYR A 223 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 230 " --> pdb=" O TYR A 223 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 496 through 500 Processing sheet with id= C, first strand: chain 'A' and resid 523 through 527 removed outlier: 4.301A pdb=" N LYS A 523 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 568 " --> pdb=" O LYS A 523 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 715 through 717 removed outlier: 3.800A pdb=" N PHE B 715 " --> pdb=" O ILE B 722 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 979 through 983 removed outlier: 3.718A pdb=" N ARG B 979 " --> pdb=" O ILE B1056 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE B1055 " --> pdb=" O ILE B1002 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE B1002 " --> pdb=" O PHE B1055 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU B1057 " --> pdb=" O TYR B1000 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR B1000 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 987 through 990 removed outlier: 4.019A pdb=" N ASP B 987 " --> pdb=" O ALA B1048 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL B1046 " --> pdb=" O VAL B 989 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B1020 " --> pdb=" O VAL B1009 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 496 through 500 Processing sheet with id= H, first strand: chain 'D' and resid 496 through 500 removed outlier: 6.058A pdb=" N PHE D 574 " --> pdb=" O ILE D 519 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ILE D 519 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 524 through 526 742 hydrogen bonds defined for protein. 2070 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.98 Time building geometry restraints manager: 6.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4540 1.34 - 1.46: 3479 1.46 - 1.58: 6911 1.58 - 1.70: 8 1.70 - 1.82: 138 Bond restraints: 15076 Sorted by residual: bond pdb=" C3' PCG A 701 " pdb=" C4' PCG A 701 " ideal model delta sigma weight residual 1.808 1.494 0.314 2.00e-02 2.50e+03 2.47e+02 bond pdb=" C3' PCG D 701 " pdb=" C4' PCG D 701 " ideal model delta sigma weight residual 1.808 1.494 0.314 2.00e-02 2.50e+03 2.46e+02 bond pdb=" C3' PCG C 701 " pdb=" C4' PCG C 701 " ideal model delta sigma weight residual 1.808 1.494 0.314 2.00e-02 2.50e+03 2.46e+02 bond pdb=" C3' PCG B1301 " pdb=" C4' PCG B1301 " ideal model delta sigma weight residual 1.808 1.496 0.312 2.00e-02 2.50e+03 2.43e+02 bond pdb=" C2' PCG B1301 " pdb=" C3' PCG B1301 " ideal model delta sigma weight residual 1.200 1.504 -0.304 2.00e-02 2.50e+03 2.31e+02 ... (remaining 15071 not shown) Histogram of bond angle deviations from ideal: 97.15 - 104.59: 209 104.59 - 112.03: 7198 112.03 - 119.46: 5217 119.46 - 126.90: 7639 126.90 - 134.34: 183 Bond angle restraints: 20446 Sorted by residual: angle pdb=" O3' PCG C 701 " pdb=" PA PCG C 701 " pdb=" O5' PCG C 701 " ideal model delta sigma weight residual 111.92 100.91 11.01 3.00e+00 1.11e-01 1.35e+01 angle pdb=" N TYR A 260 " pdb=" CA TYR A 260 " pdb=" C TYR A 260 " ideal model delta sigma weight residual 112.23 107.79 4.44 1.26e+00 6.30e-01 1.24e+01 angle pdb=" O3' PCG A 701 " pdb=" PA PCG A 701 " pdb=" O5' PCG A 701 " ideal model delta sigma weight residual 111.92 101.60 10.32 3.00e+00 1.11e-01 1.18e+01 angle pdb=" O3' PCG B1301 " pdb=" PA PCG B1301 " pdb=" O5' PCG B1301 " ideal model delta sigma weight residual 111.92 101.76 10.16 3.00e+00 1.11e-01 1.15e+01 angle pdb=" CA VAL C 526 " pdb=" CB VAL C 526 " pdb=" CG1 VAL C 526 " ideal model delta sigma weight residual 110.40 115.88 -5.48 1.70e+00 3.46e-01 1.04e+01 ... (remaining 20441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 7952 17.14 - 34.28: 803 34.28 - 51.41: 146 51.41 - 68.55: 10 68.55 - 85.69: 9 Dihedral angle restraints: 8920 sinusoidal: 3656 harmonic: 5264 Sorted by residual: dihedral pdb=" CA MET B 974 " pdb=" C MET B 974 " pdb=" N LEU B 975 " pdb=" CA LEU B 975 " ideal model delta harmonic sigma weight residual -180.00 -162.35 -17.65 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ARG B 997 " pdb=" C ARG B 997 " pdb=" N GLU B 998 " pdb=" CA GLU B 998 " ideal model delta harmonic sigma weight residual 180.00 -162.40 -17.60 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA THR A 181 " pdb=" C THR A 181 " pdb=" N MET A 182 " pdb=" CA MET A 182 " ideal model delta harmonic sigma weight residual -180.00 -162.85 -17.15 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 8917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2165 0.092 - 0.185: 105 0.185 - 0.277: 4 0.277 - 0.369: 3 0.369 - 0.462: 5 Chirality restraints: 2282 Sorted by residual: chirality pdb=" C3' PCG D 701 " pdb=" C2' PCG D 701 " pdb=" C4' PCG D 701 " pdb=" O3' PCG D 701 " both_signs ideal model delta sigma weight residual False -2.10 -2.56 0.46 2.00e-01 2.50e+01 5.33e+00 chirality pdb=" C3' PCG B1301 " pdb=" C2' PCG B1301 " pdb=" C4' PCG B1301 " pdb=" O3' PCG B1301 " both_signs ideal model delta sigma weight residual False -2.10 -2.56 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" C3' PCG C 701 " pdb=" C2' PCG C 701 " pdb=" C4' PCG C 701 " pdb=" O3' PCG C 701 " both_signs ideal model delta sigma weight residual False -2.10 -2.56 0.45 2.00e-01 2.50e+01 5.17e+00 ... (remaining 2279 not shown) Planarity restraints: 2518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 763 " 0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO B 764 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 764 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 764 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 254 " -0.034 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO D 255 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 255 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 255 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 259 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.57e+00 pdb=" C LEU A 259 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU A 259 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR A 260 " -0.011 2.00e-02 2.50e+03 ... (remaining 2515 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2505 2.76 - 3.30: 14536 3.30 - 3.83: 26029 3.83 - 4.37: 29726 4.37 - 4.90: 50883 Nonbonded interactions: 123679 Sorted by model distance: nonbonded pdb=" O THR D 357 " pdb=" OG1 THR D 361 " model vdw 2.230 2.440 nonbonded pdb=" O LEU D 169 " pdb=" OG1 THR D 173 " model vdw 2.235 2.440 nonbonded pdb=" O LEU A 169 " pdb=" OG1 THR A 173 " model vdw 2.247 2.440 nonbonded pdb=" OH TYR D 334 " pdb=" O PHE D 342 " model vdw 2.287 2.440 nonbonded pdb=" OG1 THR B 684 " pdb=" OD1 ASN B 687 " model vdw 2.295 2.440 ... (remaining 123674 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 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.500 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 38.630 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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 : 0.012 0.314 15076 Z= 0.742 Angle : 0.708 11.009 20446 Z= 0.343 Chirality : 0.050 0.462 2282 Planarity : 0.004 0.069 2518 Dihedral : 13.660 85.688 5548 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -0.39 (0.18), residues: 1774 helix: 0.18 (0.14), residues: 1062 sheet: -0.05 (0.55), residues: 91 loop : -0.87 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 168 HIS 0.005 0.001 HIS B 803 PHE 0.027 0.002 PHE D 382 TYR 0.015 0.001 TYR B 837 ARG 0.010 0.000 ARG C 478 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.733 Fit side-chains REVERT: C 267 TYR cc_start: 0.8324 (m-80) cc_final: 0.8074 (m-80) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2191 time to fit residues: 52.0219 Evaluate side-chains 116 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 161 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15076 Z= 0.157 Angle : 0.453 6.184 20446 Z= 0.233 Chirality : 0.038 0.141 2282 Planarity : 0.003 0.051 2518 Dihedral : 4.016 31.842 2019 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.19 % Allowed : 6.36 % Favored : 93.45 % 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: 0.33 (0.19), residues: 1774 helix: 0.87 (0.15), residues: 1088 sheet: 0.05 (0.56), residues: 91 loop : -0.86 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.004 0.001 HIS B 803 PHE 0.022 0.001 PHE D 574 TYR 0.011 0.001 TYR B 837 ARG 0.002 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 1.715 Fit side-chains REVERT: A 305 MET cc_start: 0.7901 (ttp) cc_final: 0.7688 (ttm) REVERT: B 994 GLU cc_start: 0.5359 (mm-30) cc_final: 0.5145 (mm-30) REVERT: C 267 TYR cc_start: 0.8321 (m-80) cc_final: 0.8052 (m-80) outliers start: 3 outliers final: 3 residues processed: 131 average time/residue: 0.2337 time to fit residues: 48.5108 Evaluate side-chains 123 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 134 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 174 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 chunk 160 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 129 optimal weight: 9.9990 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 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15076 Z= 0.133 Angle : 0.422 5.735 20446 Z= 0.217 Chirality : 0.037 0.141 2282 Planarity : 0.003 0.041 2518 Dihedral : 3.766 28.715 2019 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.50 % Allowed : 8.48 % Favored : 91.02 % 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: 0.71 (0.20), residues: 1774 helix: 1.17 (0.16), residues: 1107 sheet: 0.13 (0.56), residues: 91 loop : -0.75 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 168 HIS 0.004 0.001 HIS B 803 PHE 0.024 0.001 PHE C 389 TYR 0.011 0.001 TYR B 837 ARG 0.003 0.000 ARG C 478 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 1.667 Fit side-chains REVERT: B 994 GLU cc_start: 0.5391 (mm-30) cc_final: 0.5175 (mm-30) REVERT: C 267 TYR cc_start: 0.8287 (m-80) cc_final: 0.8031 (m-80) REVERT: D 491 LEU cc_start: 0.6448 (pp) cc_final: 0.5846 (tp) outliers start: 8 outliers final: 5 residues processed: 138 average time/residue: 0.2496 time to fit residues: 52.5197 Evaluate side-chains 125 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain D residue 496 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 2.9990 chunk 121 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 162 optimal weight: 7.9990 chunk 172 optimal weight: 0.1980 chunk 154 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15076 Z= 0.145 Angle : 0.419 5.649 20446 Z= 0.216 Chirality : 0.037 0.144 2282 Planarity : 0.003 0.036 2518 Dihedral : 3.708 27.596 2019 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.19 % Allowed : 9.73 % Favored : 89.08 % 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: 0.96 (0.20), residues: 1774 helix: 1.38 (0.16), residues: 1100 sheet: 0.20 (0.56), residues: 91 loop : -0.64 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.004 0.001 HIS B 803 PHE 0.024 0.001 PHE C 389 TYR 0.011 0.001 TYR A 349 ARG 0.002 0.000 ARG C 478 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 1.573 Fit side-chains REVERT: A 251 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8175 (tt) REVERT: B 836 TYR cc_start: 0.8719 (t80) cc_final: 0.8444 (t80) REVERT: C 267 TYR cc_start: 0.8297 (m-80) cc_final: 0.8010 (m-80) REVERT: D 491 LEU cc_start: 0.6460 (pp) cc_final: 0.5902 (tp) REVERT: D 511 ASP cc_start: 0.6126 (t0) cc_final: 0.5911 (t0) outliers start: 19 outliers final: 10 residues processed: 139 average time/residue: 0.2433 time to fit residues: 51.9762 Evaluate side-chains 132 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain B residue 1020 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 4.9990 chunk 2 optimal weight: 0.2980 chunk 128 optimal weight: 0.0020 chunk 70 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 154 optimal weight: 0.0010 chunk 43 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15076 Z= 0.150 Angle : 0.421 5.303 20446 Z= 0.217 Chirality : 0.037 0.145 2282 Planarity : 0.003 0.035 2518 Dihedral : 3.669 26.742 2019 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.06 % Allowed : 10.85 % Favored : 88.08 % 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: 1.03 (0.20), residues: 1774 helix: 1.43 (0.16), residues: 1106 sheet: 0.02 (0.55), residues: 94 loop : -0.60 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 168 HIS 0.004 0.001 HIS B 803 PHE 0.022 0.001 PHE C 423 TYR 0.013 0.001 TYR C 294 ARG 0.008 0.000 ARG B 997 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 1.892 Fit side-chains REVERT: A 251 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8192 (tt) REVERT: B 836 TYR cc_start: 0.8727 (t80) cc_final: 0.8453 (t80) REVERT: C 267 TYR cc_start: 0.8309 (m-80) cc_final: 0.7988 (m-80) REVERT: C 498 GLN cc_start: 0.7685 (mt0) cc_final: 0.7416 (pt0) REVERT: D 511 ASP cc_start: 0.6328 (t0) cc_final: 0.6059 (t0) outliers start: 17 outliers final: 11 residues processed: 133 average time/residue: 0.2249 time to fit residues: 47.8804 Evaluate side-chains 131 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain B residue 1020 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 TRP Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 172 optimal weight: 0.2980 chunk 142 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 166 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15076 Z= 0.130 Angle : 0.409 5.686 20446 Z= 0.211 Chirality : 0.037 0.156 2282 Planarity : 0.003 0.034 2518 Dihedral : 3.618 25.891 2019 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.65 % Favored : 97.29 % Rotamer: Outliers : 0.94 % Allowed : 11.60 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.20), residues: 1774 helix: 1.59 (0.16), residues: 1092 sheet: 0.26 (0.55), residues: 91 loop : -0.47 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 168 HIS 0.004 0.001 HIS B 803 PHE 0.019 0.001 PHE C 423 TYR 0.012 0.001 TYR C 294 ARG 0.005 0.000 ARG B 997 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 1.546 Fit side-chains REVERT: A 251 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8154 (tt) REVERT: B 836 TYR cc_start: 0.8707 (t80) cc_final: 0.8431 (t80) REVERT: C 498 GLN cc_start: 0.7658 (mt0) cc_final: 0.7403 (pt0) REVERT: D 511 ASP cc_start: 0.6315 (t0) cc_final: 0.6068 (t0) REVERT: D 521 GLU cc_start: 0.7882 (tt0) cc_final: 0.7526 (tt0) outliers start: 15 outliers final: 10 residues processed: 126 average time/residue: 0.2218 time to fit residues: 44.7755 Evaluate side-chains 126 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain B residue 1020 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain D residue 437 TRP Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15076 Z= 0.152 Angle : 0.419 6.170 20446 Z= 0.216 Chirality : 0.037 0.155 2282 Planarity : 0.003 0.033 2518 Dihedral : 3.603 25.466 2019 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.43 % Allowed : 12.23 % Favored : 86.34 % 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: 1.30 (0.20), residues: 1774 helix: 1.60 (0.16), residues: 1092 sheet: 0.40 (0.57), residues: 87 loop : -0.38 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 168 HIS 0.004 0.001 HIS B 803 PHE 0.025 0.001 PHE C 423 TYR 0.012 0.001 TYR C 294 ARG 0.005 0.000 ARG B 997 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 1.686 Fit side-chains REVERT: A 251 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8205 (tt) REVERT: B 836 TYR cc_start: 0.8721 (t80) cc_final: 0.8440 (t80) REVERT: C 498 GLN cc_start: 0.7652 (mt0) cc_final: 0.7384 (pt0) REVERT: C 573 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8108 (pp) REVERT: D 511 ASP cc_start: 0.6404 (t0) cc_final: 0.6172 (t0) REVERT: D 521 GLU cc_start: 0.7891 (tt0) cc_final: 0.7541 (tt0) outliers start: 23 outliers final: 15 residues processed: 134 average time/residue: 0.2352 time to fit residues: 50.2152 Evaluate side-chains 133 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 1020 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 TRP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 156 optimal weight: 0.5980 chunk 164 optimal weight: 10.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1073 GLN C 496 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15076 Z= 0.212 Angle : 0.453 6.393 20446 Z= 0.234 Chirality : 0.038 0.159 2282 Planarity : 0.003 0.033 2518 Dihedral : 3.716 26.294 2019 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.19 % Allowed : 13.10 % Favored : 85.71 % 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: 1.20 (0.20), residues: 1774 helix: 1.55 (0.16), residues: 1085 sheet: 0.12 (0.58), residues: 81 loop : -0.42 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 168 HIS 0.005 0.001 HIS B 803 PHE 0.022 0.001 PHE C 423 TYR 0.015 0.001 TYR A 349 ARG 0.005 0.000 ARG B 997 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 1.688 Fit side-chains REVERT: A 251 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8294 (tt) REVERT: B 836 TYR cc_start: 0.8750 (t80) cc_final: 0.8469 (t80) REVERT: C 498 GLN cc_start: 0.7668 (mt0) cc_final: 0.7442 (pt0) REVERT: C 573 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8220 (pp) REVERT: D 511 ASP cc_start: 0.6472 (t0) cc_final: 0.6261 (t0) REVERT: D 521 GLU cc_start: 0.7950 (tt0) cc_final: 0.7604 (tt0) outliers start: 19 outliers final: 14 residues processed: 127 average time/residue: 0.2299 time to fit residues: 46.5186 Evaluate side-chains 130 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain B residue 1020 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 TRP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 564 ASN Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 0.3980 chunk 159 optimal weight: 3.9990 chunk 164 optimal weight: 0.0050 chunk 96 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 144 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15076 Z= 0.154 Angle : 0.429 6.965 20446 Z= 0.220 Chirality : 0.037 0.153 2282 Planarity : 0.003 0.033 2518 Dihedral : 3.643 25.617 2019 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.25 % Allowed : 13.10 % Favored : 85.65 % 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: 1.30 (0.20), residues: 1774 helix: 1.62 (0.16), residues: 1084 sheet: 0.48 (0.62), residues: 72 loop : -0.39 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 168 HIS 0.004 0.001 HIS B 803 PHE 0.023 0.001 PHE C 423 TYR 0.011 0.001 TYR A 349 ARG 0.004 0.000 ARG B 997 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.781 Fit side-chains REVERT: A 251 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8253 (tt) REVERT: B 836 TYR cc_start: 0.8711 (t80) cc_final: 0.8440 (t80) REVERT: C 573 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8181 (pp) REVERT: D 260 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.8360 (m-10) REVERT: D 511 ASP cc_start: 0.6495 (t0) cc_final: 0.6275 (t0) REVERT: D 521 GLU cc_start: 0.7936 (tt0) cc_final: 0.7587 (tt0) outliers start: 20 outliers final: 16 residues processed: 129 average time/residue: 0.2285 time to fit residues: 47.3995 Evaluate side-chains 134 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 1020 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 TRP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 564 ASN Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 177 optimal weight: 0.0270 chunk 163 optimal weight: 0.0470 chunk 141 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 86 optimal weight: 0.0030 chunk 112 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 overall best weight: 0.2746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1073 GLN C 498 GLN D 302 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15076 Z= 0.113 Angle : 0.410 7.487 20446 Z= 0.209 Chirality : 0.036 0.139 2282 Planarity : 0.003 0.034 2518 Dihedral : 3.529 23.393 2019 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.06 % Allowed : 13.41 % Favored : 85.53 % 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: 1.49 (0.20), residues: 1774 helix: 1.78 (0.16), residues: 1085 sheet: 0.95 (0.58), residues: 79 loop : -0.41 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 168 HIS 0.003 0.000 HIS B 803 PHE 0.026 0.001 PHE C 389 TYR 0.014 0.001 TYR C 500 ARG 0.004 0.000 ARG B 997 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 1.636 Fit side-chains REVERT: A 251 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8125 (tt) REVERT: B 836 TYR cc_start: 0.8634 (t80) cc_final: 0.8364 (t80) REVERT: C 573 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7977 (pp) REVERT: D 260 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.8326 (m-10) REVERT: D 511 ASP cc_start: 0.6357 (t0) cc_final: 0.6153 (t0) REVERT: D 521 GLU cc_start: 0.7852 (tt0) cc_final: 0.7482 (tt0) outliers start: 17 outliers final: 12 residues processed: 134 average time/residue: 0.2292 time to fit residues: 48.7065 Evaluate side-chains 132 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain B residue 1020 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 437 TRP Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 564 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 145 optimal weight: 4.9990 chunk 17 optimal weight: 0.0470 chunk 26 optimal weight: 0.4980 chunk 124 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 534 GLN D 302 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.127939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.099355 restraints weight = 23947.654| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.37 r_work: 0.3233 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15076 Z= 0.124 Angle : 0.413 7.559 20446 Z= 0.211 Chirality : 0.036 0.145 2282 Planarity : 0.003 0.033 2518 Dihedral : 3.509 22.929 2019 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.12 % Allowed : 13.23 % Favored : 85.65 % 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 (0.20), residues: 1774 helix: 1.85 (0.16), residues: 1084 sheet: 0.72 (0.60), residues: 69 loop : -0.37 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 168 HIS 0.003 0.001 HIS B 803 PHE 0.027 0.001 PHE C 389 TYR 0.012 0.001 TYR D 205 ARG 0.004 0.000 ARG B 997 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2621.47 seconds wall clock time: 48 minutes 51.51 seconds (2931.51 seconds total)