Starting phenix.real_space_refine on Fri Feb 16 12:06:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5e_10695/02_2024/6y5e_10695_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5e_10695/02_2024/6y5e_10695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5e_10695/02_2024/6y5e_10695.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5e_10695/02_2024/6y5e_10695.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5e_10695/02_2024/6y5e_10695_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5e_10695/02_2024/6y5e_10695_updated.pdb" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 306 5.49 5 S 27 5.16 5 C 8699 2.51 5 N 2815 2.21 5 O 3444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "D TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 56": "NH1" <-> "NH2" Residue "F TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 196": "NH1" <-> "NH2" Residue "K TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 216": "OE1" <-> "OE2" Residue "K PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 325": "OE1" <-> "OE2" Residue "K PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 478": "OE1" <-> "OE2" Residue "K GLU 487": "OE1" <-> "OE2" Residue "K GLU 515": "OE1" <-> "OE2" Residue "K PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15292 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3119 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "J" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3154 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "K" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2980 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-2': 2, 'PTD:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "K" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' ZN': 1, 'PTD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14165 SG CYS K 396 77.673 20.971 33.960 0.00 21.29 S ATOM 14171 SG CYS K 397 79.534 19.817 37.046 0.00 21.76 S ATOM 14230 SG CYS K 404 81.302 21.908 34.439 0.00600.00 S Time building chain proxies: 9.23, per 1000 atoms: 0.60 Number of scatterers: 15292 At special positions: 0 Unit cell: (121.26, 126.42, 122.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 27 16.00 P 306 15.00 O 3444 8.00 N 2815 7.00 C 8699 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.38 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 390 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 404 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 396 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 397 " Number of angles added : 3 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 3 sheets defined 57.6% alpha, 4.2% beta 153 base pairs and 281 stacking pairs defined. Time for finding SS restraints: 8.15 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 65 through 78 removed outlier: 3.770A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 114 Processing helix chain 'A' and resid 122 through 131 Processing helix chain 'B' and resid 26 through 29 Processing helix chain 'B' and resid 32 through 41 Processing helix chain 'B' and resid 51 through 76 removed outlier: 4.037A pdb=" N VAL B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 94 removed outlier: 4.182A pdb=" N GLN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 29 through 36 Processing helix chain 'C' and resid 48 through 73 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'D' and resid 39 through 49 Processing helix chain 'D' and resid 57 through 84 Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'D' and resid 107 through 124 Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 65 through 78 removed outlier: 3.932A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 114 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'F' and resid 27 through 29 No H-bonds generated for 'chain 'F' and resid 27 through 29' Processing helix chain 'F' and resid 32 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.689A pdb=" N TYR F 52 " --> pdb=" O GLY F 49 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU F 53 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR F 55 " --> pdb=" O TYR F 52 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS F 60 " --> pdb=" O GLY F 57 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE F 67 " --> pdb=" O GLU F 64 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG F 68 " --> pdb=" O ASN F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 94 removed outlier: 4.014A pdb=" N GLN F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 21 No H-bonds generated for 'chain 'G' and resid 18 through 21' Processing helix chain 'G' and resid 29 through 36 removed outlier: 4.006A pdb=" N ARG G 36 " --> pdb=" O HIS G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 73 Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 114 through 116 No H-bonds generated for 'chain 'G' and resid 114 through 116' Processing helix chain 'H' and resid 39 through 49 removed outlier: 3.511A pdb=" N GLN H 48 " --> pdb=" O LYS H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 84 Processing helix chain 'H' and resid 92 through 102 Processing helix chain 'H' and resid 105 through 124 removed outlier: 3.907A pdb=" N LYS H 109 " --> pdb=" O GLY H 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 162 through 176 removed outlier: 3.866A pdb=" N ARG K 176 " --> pdb=" O LEU K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 199 removed outlier: 3.658A pdb=" N ALA K 183 " --> pdb=" O SER K 180 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP K 191 " --> pdb=" O GLY K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 261 through 265 removed outlier: 3.998A pdb=" N GLN K 264 " --> pdb=" O PRO K 261 " (cutoff:3.500A) Processing helix chain 'K' and resid 273 through 290 removed outlier: 3.569A pdb=" N ASN K 289 " --> pdb=" O LYS K 285 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP K 290 " --> pdb=" O GLU K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 332 through 334 No H-bonds generated for 'chain 'K' and resid 332 through 334' Processing helix chain 'K' and resid 346 through 354 Processing helix chain 'K' and resid 380 through 389 Processing helix chain 'K' and resid 400 through 402 No H-bonds generated for 'chain 'K' and resid 400 through 402' Processing helix chain 'K' and resid 406 through 423 Processing helix chain 'K' and resid 435 through 448 Processing helix chain 'K' and resid 452 through 455 Processing helix chain 'K' and resid 457 through 477 removed outlier: 4.982A pdb=" N GLY K 461 " --> pdb=" O LYS K 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE K 464 " --> pdb=" O GLY K 461 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR K 477 " --> pdb=" O CYS K 474 " (cutoff:3.500A) Processing helix chain 'K' and resid 498 through 514 Processing helix chain 'K' and resid 517 through 519 No H-bonds generated for 'chain 'K' and resid 517 through 519' Processing sheet with id= A, first strand: chain 'K' and resid 225 through 233 removed outlier: 6.441A pdb=" N SER K 317 " --> pdb=" O PHE K 226 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL K 228 " --> pdb=" O SER K 317 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ASP K 319 " --> pdb=" O VAL K 228 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N PHE K 230 " --> pdb=" O ASP K 319 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N THR K 321 " --> pdb=" O PHE K 230 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU K 232 " --> pdb=" O THR K 321 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA K 323 " --> pdb=" O LEU K 232 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 237 through 241 Processing sheet with id= C, first strand: chain 'K' and resid 364 through 366 460 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 391 hydrogen bonds 782 hydrogen bond angles 0 basepair planarities 153 basepair parallelities 281 stacking parallelities Total time for adding SS restraints: 7.17 Time building geometry restraints manager: 6.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2598 1.32 - 1.45: 5560 1.45 - 1.57: 7372 1.57 - 1.69: 612 1.69 - 1.82: 44 Bond restraints: 16186 Sorted by residual: bond pdb=" C4 PTD C 201 " pdb=" C5 PTD C 201 " ideal model delta sigma weight residual 1.501 1.615 -0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" CD ARG E 64 " pdb=" NE ARG E 64 " ideal model delta sigma weight residual 1.458 1.378 0.080 1.40e-02 5.10e+03 3.25e+01 bond pdb=" CD ARG F 36 " pdb=" NE ARG F 36 " ideal model delta sigma weight residual 1.458 1.385 0.073 1.40e-02 5.10e+03 2.71e+01 bond pdb=" CD ARG A 64 " pdb=" NE ARG A 64 " ideal model delta sigma weight residual 1.458 1.390 0.068 1.40e-02 5.10e+03 2.37e+01 bond pdb=" CD ARG B 93 " pdb=" NE ARG B 93 " ideal model delta sigma weight residual 1.458 1.391 0.067 1.40e-02 5.10e+03 2.32e+01 ... (remaining 16181 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.38: 1508 105.38 - 112.49: 8740 112.49 - 119.59: 4975 119.59 - 126.70: 7105 126.70 - 133.80: 795 Bond angle restraints: 23123 Sorted by residual: angle pdb=" N GLY G 38 " pdb=" CA GLY G 38 " pdb=" C GLY G 38 " ideal model delta sigma weight residual 115.30 104.72 10.58 1.39e+00 5.18e-01 5.79e+01 angle pdb=" C LEU G 117 " pdb=" N PRO G 118 " pdb=" CA PRO G 118 " ideal model delta sigma weight residual 119.85 126.73 -6.88 1.01e+00 9.80e-01 4.64e+01 angle pdb=" N GLY C 38 " pdb=" CA GLY C 38 " pdb=" C GLY C 38 " ideal model delta sigma weight residual 115.30 105.98 9.32 1.39e+00 5.18e-01 4.50e+01 angle pdb=" C HIS D 50 " pdb=" N PRO D 51 " pdb=" CA PRO D 51 " ideal model delta sigma weight residual 119.47 127.16 -7.69 1.16e+00 7.43e-01 4.40e+01 angle pdb=" C ASN K 449 " pdb=" N PRO K 450 " pdb=" CA PRO K 450 " ideal model delta sigma weight residual 119.64 126.30 -6.66 1.01e+00 9.80e-01 4.34e+01 ... (remaining 23118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.13: 7531 34.13 - 68.25: 1419 68.25 - 102.38: 31 102.38 - 136.50: 0 136.50 - 170.63: 5 Dihedral angle restraints: 8986 sinusoidal: 5726 harmonic: 3260 Sorted by residual: dihedral pdb=" CA SER K 305 " pdb=" C SER K 305 " pdb=" N PRO K 306 " pdb=" CA PRO K 306 " ideal model delta harmonic sigma weight residual 180.00 153.69 26.31 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" C4' DC I 81 " pdb=" C3' DC I 81 " pdb=" O3' DC I 81 " pdb=" P DC I 82 " ideal model delta sinusoidal sigma weight residual 220.00 49.37 170.63 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT I 150 " pdb=" C3' DT I 150 " pdb=" O3' DT I 150 " pdb=" P DG I 151 " ideal model delta sinusoidal sigma weight residual 220.00 51.04 168.96 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 8983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1874 0.067 - 0.134: 626 0.134 - 0.202: 84 0.202 - 0.269: 13 0.269 - 0.336: 3 Chirality restraints: 2600 Sorted by residual: chirality pdb=" CA LYS G 37 " pdb=" N LYS G 37 " pdb=" C LYS G 37 " pdb=" CB LYS G 37 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA CYS K 397 " pdb=" N CYS K 397 " pdb=" C CYS K 397 " pdb=" CB CYS K 397 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA LYS B 32 " pdb=" N LYS B 32 " pdb=" C LYS B 32 " pdb=" CB LYS B 32 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 2597 not shown) Planarity restraints: 1867 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 55 " -0.070 2.00e-02 2.50e+03 3.81e-02 2.91e+01 pdb=" CG TYR E 55 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR E 55 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR E 55 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR E 55 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR E 55 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR E 55 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 55 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 37 " 0.027 2.00e-02 2.50e+03 5.38e-02 2.90e+01 pdb=" C LYS G 37 " -0.093 2.00e-02 2.50e+03 pdb=" O LYS G 37 " 0.036 2.00e-02 2.50e+03 pdb=" N GLY G 38 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 358 " 0.067 2.00e-02 2.50e+03 3.56e-02 2.54e+01 pdb=" CG TYR K 358 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR K 358 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR K 358 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR K 358 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR K 358 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR K 358 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR K 358 " 0.049 2.00e-02 2.50e+03 ... (remaining 1864 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 6012 2.92 - 3.42: 13538 3.42 - 3.91: 29664 3.91 - 4.41: 36012 4.41 - 4.90: 46930 Nonbonded interactions: 132156 Sorted by model distance: nonbonded pdb=" N GLY G 38 " pdb=" N ASN G 39 " model vdw 2.429 2.560 nonbonded pdb=" O PHE K 491 " pdb=" NZ LYS K 501 " model vdw 2.455 2.520 nonbonded pdb=" N GLY C 38 " pdb=" N ASN C 39 " model vdw 2.468 2.560 nonbonded pdb=" O ASN G 39 " pdb=" C TYR G 40 " model vdw 2.488 3.270 nonbonded pdb=" N ALA K 273 " pdb=" OE1 GLU K 373 " model vdw 2.493 2.520 ... (remaining 132151 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 'E' and (resid 39 through 134 or resid 201)) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 103) } ncs_group { reference = (chain 'C' and resid 12 through 118) selection = (chain 'G' and resid 12 through 118) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 33 through 125 or resid 301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.93 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 7.400 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 51.970 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.080 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 : 0.014 0.128 16186 Z= 0.912 Angle : 1.162 10.579 23123 Z= 0.780 Chirality : 0.066 0.336 2600 Planarity : 0.010 0.054 1867 Dihedral : 25.715 170.629 6878 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.91 % Favored : 98.00 % Rotamer: Outliers : 0.21 % Allowed : 0.31 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.23), residues: 1102 helix: 0.67 (0.18), residues: 690 sheet: -0.43 (0.63), residues: 54 loop : 0.14 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.009 TRP K 343 HIS 0.008 0.002 HIS H 110 PHE 0.045 0.009 PHE K 265 TYR 0.070 0.011 TYR E 55 ARG 0.019 0.002 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 249 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9245 (p) cc_final: 0.8999 (p) REVERT: C 93 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7182 (mt-10) REVERT: G 16 LYS cc_start: 0.7726 (ttmt) cc_final: 0.7498 (tttt) REVERT: G 111 ASN cc_start: 0.8498 (t0) cc_final: 0.8277 (p0) REVERT: H 35 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8268 (mttt) REVERT: K 229 MET cc_start: 0.6850 (ttm) cc_final: 0.6515 (mmm) REVERT: K 233 GLU cc_start: 0.8056 (tt0) cc_final: 0.7590 (tm-30) REVERT: K 325 GLU cc_start: 0.7556 (tt0) cc_final: 0.7162 (tm-30) REVERT: K 359 LEU cc_start: 0.8157 (mt) cc_final: 0.7746 (mt) outliers start: 2 outliers final: 0 residues processed: 249 average time/residue: 0.2639 time to fit residues: 98.2400 Evaluate side-chains 179 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 50.0000 chunk 104 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 125 optimal weight: 20.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS B 26 ASN D 64 ASN F 94 GLN K 260 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16186 Z= 0.217 Angle : 0.619 12.176 23123 Z= 0.360 Chirality : 0.037 0.146 2600 Planarity : 0.004 0.039 1867 Dihedral : 29.387 177.125 4600 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.82 % Favored : 99.09 % Rotamer: Outliers : 2.08 % Allowed : 7.81 % Favored : 90.10 % 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: 1.74 (0.24), residues: 1102 helix: 1.89 (0.19), residues: 687 sheet: -0.79 (0.60), residues: 53 loop : 0.14 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 330 HIS 0.003 0.001 HIS K 390 PHE 0.012 0.001 PHE K 471 TYR 0.019 0.002 TYR K 415 ARG 0.003 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 217 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 89 TYR cc_start: 0.8707 (m-80) cc_final: 0.8480 (m-80) REVERT: H 35 LYS cc_start: 0.8707 (mmmt) cc_final: 0.8333 (mttt) REVERT: K 359 LEU cc_start: 0.7941 (mt) cc_final: 0.7633 (mt) REVERT: K 375 TRP cc_start: 0.6931 (m100) cc_final: 0.6562 (m100) outliers start: 20 outliers final: 14 residues processed: 226 average time/residue: 0.2878 time to fit residues: 94.2554 Evaluate side-chains 195 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 181 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 72 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 125 optimal weight: 30.0000 chunk 135 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 64 ASN G 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16186 Z= 0.255 Angle : 0.582 7.328 23123 Z= 0.340 Chirality : 0.037 0.159 2600 Planarity : 0.004 0.042 1867 Dihedral : 29.337 177.194 4600 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.54 % Favored : 98.28 % Rotamer: Outliers : 2.19 % Allowed : 8.54 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.25), residues: 1102 helix: 2.12 (0.20), residues: 688 sheet: -0.58 (0.63), residues: 53 loop : 0.01 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 343 HIS 0.003 0.001 HIS K 390 PHE 0.011 0.001 PHE E 68 TYR 0.012 0.001 TYR H 122 ARG 0.004 0.000 ARG G 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 196 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8820 (t) REVERT: H 35 LYS cc_start: 0.8816 (mmmt) cc_final: 0.8486 (mttt) REVERT: K 359 LEU cc_start: 0.7960 (mt) cc_final: 0.7706 (mt) REVERT: K 375 TRP cc_start: 0.6980 (m100) cc_final: 0.6694 (m100) outliers start: 21 outliers final: 13 residues processed: 206 average time/residue: 0.3115 time to fit residues: 91.5964 Evaluate side-chains 186 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 172 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 72 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 125 optimal weight: 40.0000 chunk 133 optimal weight: 0.0980 chunk 119 optimal weight: 0.0970 chunk 35 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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: 0.8106 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16186 Z= 0.170 Angle : 0.543 7.740 23123 Z= 0.320 Chirality : 0.034 0.193 2600 Planarity : 0.004 0.034 1867 Dihedral : 28.871 176.538 4600 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.18 % Favored : 98.73 % Rotamer: Outliers : 1.77 % Allowed : 10.73 % Favored : 87.50 % 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: 2.14 (0.25), residues: 1102 helix: 2.25 (0.20), residues: 685 sheet: -0.07 (0.65), residues: 53 loop : 0.12 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 343 HIS 0.002 0.000 HIS D 110 PHE 0.012 0.001 PHE K 265 TYR 0.012 0.001 TYR K 470 ARG 0.007 0.000 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 191 time to evaluate : 1.324 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: C 77 THR cc_start: 0.9119 (p) cc_final: 0.8906 (t) REVERT: H 35 LYS cc_start: 0.8782 (mmmt) cc_final: 0.8501 (mttt) REVERT: K 359 LEU cc_start: 0.8043 (mt) cc_final: 0.7808 (mt) REVERT: K 375 TRP cc_start: 0.6962 (m100) cc_final: 0.6687 (m100) outliers start: 17 outliers final: 12 residues processed: 199 average time/residue: 0.2827 time to fit residues: 81.4213 Evaluate side-chains 190 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 178 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain K residue 404 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 0 optimal weight: 0.6980 chunk 68 optimal weight: 0.1980 chunk 119 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.8116 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16186 Z= 0.175 Angle : 0.532 7.946 23123 Z= 0.316 Chirality : 0.034 0.171 2600 Planarity : 0.004 0.032 1867 Dihedral : 28.743 176.343 4600 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.63 % Favored : 98.28 % Rotamer: Outliers : 2.60 % Allowed : 9.58 % Favored : 87.81 % 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: 2.21 (0.25), residues: 1102 helix: 2.29 (0.20), residues: 685 sheet: 0.33 (0.67), residues: 53 loop : 0.08 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP K 343 HIS 0.003 0.001 HIS D 110 PHE 0.009 0.001 PHE K 265 TYR 0.011 0.001 TYR K 470 ARG 0.006 0.000 ARG H 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 187 time to evaluate : 1.271 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: G 77 THR cc_start: 0.9139 (p) cc_final: 0.8936 (t) REVERT: H 35 LYS cc_start: 0.8785 (mmmt) cc_final: 0.8485 (mttt) REVERT: K 359 LEU cc_start: 0.8060 (mt) cc_final: 0.7831 (mt) REVERT: K 375 TRP cc_start: 0.6853 (m100) cc_final: 0.6560 (m100) outliers start: 25 outliers final: 22 residues processed: 197 average time/residue: 0.3049 time to fit residues: 86.5926 Evaluate side-chains 194 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 172 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 404 CYS Chi-restraints excluded: chain K residue 429 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 128 optimal weight: 50.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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: 0.8205 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 16186 Z= 0.317 Angle : 0.585 9.332 23123 Z= 0.339 Chirality : 0.037 0.183 2600 Planarity : 0.004 0.036 1867 Dihedral : 29.152 178.946 4600 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.81 % Favored : 98.09 % Rotamer: Outliers : 2.19 % Allowed : 11.15 % Favored : 86.67 % 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: 2.02 (0.25), residues: 1102 helix: 2.19 (0.20), residues: 682 sheet: 0.80 (0.69), residues: 53 loop : -0.17 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 343 HIS 0.003 0.001 HIS A 40 PHE 0.011 0.001 PHE K 265 TYR 0.023 0.002 TYR K 214 ARG 0.005 0.001 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 175 time to evaluate : 1.345 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: E 57 LYS cc_start: 0.9374 (ttmt) cc_final: 0.9157 (ttpp) REVERT: H 35 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8459 (mttt) REVERT: K 359 LEU cc_start: 0.8066 (mt) cc_final: 0.7861 (mt) REVERT: K 375 TRP cc_start: 0.6722 (m100) cc_final: 0.6507 (m100) outliers start: 21 outliers final: 20 residues processed: 184 average time/residue: 0.3102 time to fit residues: 82.0405 Evaluate side-chains 177 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 157 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain G residue 37 LYS Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 404 CYS Chi-restraints excluded: chain K residue 429 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 16186 Z= 0.426 Angle : 0.638 8.147 23123 Z= 0.366 Chirality : 0.040 0.168 2600 Planarity : 0.005 0.053 1867 Dihedral : 29.698 177.434 4600 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.00 % Favored : 97.91 % Rotamer: Outliers : 2.60 % Allowed : 10.83 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.25), residues: 1102 helix: 1.96 (0.19), residues: 677 sheet: 0.80 (0.71), residues: 52 loop : -0.44 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 343 HIS 0.004 0.001 HIS A 40 PHE 0.010 0.001 PHE K 503 TYR 0.014 0.002 TYR K 215 ARG 0.004 0.001 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 LEU cc_start: 0.7000 (mp) cc_final: 0.6537 (mt) REVERT: H 35 LYS cc_start: 0.8883 (mmmt) cc_final: 0.8464 (mttt) outliers start: 25 outliers final: 21 residues processed: 171 average time/residue: 0.3050 time to fit residues: 74.7353 Evaluate side-chains 162 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain G residue 37 LYS Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 404 CYS Chi-restraints excluded: chain K residue 429 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 0.0060 chunk 12 optimal weight: 0.9980 chunk 104 optimal weight: 0.0770 chunk 120 optimal weight: 4.9990 overall best weight: 0.5754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16186 Z= 0.173 Angle : 0.549 10.179 23123 Z= 0.321 Chirality : 0.034 0.169 2600 Planarity : 0.003 0.030 1867 Dihedral : 29.092 179.726 4600 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.56 % Allowed : 12.50 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.25), residues: 1102 helix: 2.21 (0.20), residues: 675 sheet: 1.33 (0.73), residues: 50 loop : -0.35 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 343 HIS 0.002 0.000 HIS H 83 PHE 0.017 0.001 PHE K 519 TYR 0.013 0.001 TYR H 41 ARG 0.005 0.000 ARG E 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 171 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 LEU cc_start: 0.7039 (mp) cc_final: 0.6540 (mt) REVERT: G 39 ASN cc_start: 0.7695 (m110) cc_final: 0.7270 (m110) REVERT: H 35 LYS cc_start: 0.8881 (mmmt) cc_final: 0.8479 (mttt) outliers start: 15 outliers final: 13 residues processed: 176 average time/residue: 0.2851 time to fit residues: 72.2289 Evaluate side-chains 173 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain K residue 185 MET Chi-restraints excluded: chain K residue 404 CYS Chi-restraints excluded: chain K residue 429 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 38 optimal weight: 0.0770 chunk 112 optimal weight: 0.9990 chunk 117 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 overall best weight: 3.6146 ------------------------------------------------------------------------------- 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: 0.8239 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 16186 Z= 0.372 Angle : 0.611 9.781 23123 Z= 0.352 Chirality : 0.038 0.216 2600 Planarity : 0.004 0.067 1867 Dihedral : 29.343 178.737 4600 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.77 % Allowed : 12.60 % Favored : 85.62 % 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: 1.87 (0.25), residues: 1102 helix: 2.11 (0.20), residues: 676 sheet: 1.41 (0.73), residues: 50 loop : -0.39 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 375 HIS 0.004 0.001 HIS C 32 PHE 0.013 0.001 PHE K 265 TYR 0.023 0.002 TYR D 84 ARG 0.006 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 155 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 LEU cc_start: 0.7117 (mp) cc_final: 0.6603 (mt) REVERT: H 35 LYS cc_start: 0.8927 (mmmt) cc_final: 0.8502 (mttt) outliers start: 17 outliers final: 16 residues processed: 161 average time/residue: 0.2902 time to fit residues: 67.4914 Evaluate side-chains 168 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 152 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain G residue 37 LYS Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain K residue 185 MET Chi-restraints excluded: chain K residue 404 CYS Chi-restraints excluded: chain K residue 429 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 137 optimal weight: 0.1980 chunk 126 optimal weight: 30.0000 chunk 109 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 39 ASN H 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16186 Z= 0.221 Angle : 0.564 10.600 23123 Z= 0.326 Chirality : 0.034 0.220 2600 Planarity : 0.003 0.030 1867 Dihedral : 29.049 179.595 4600 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.88 % Allowed : 12.81 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.25), residues: 1102 helix: 2.13 (0.20), residues: 684 sheet: 1.44 (0.73), residues: 50 loop : -0.35 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 343 HIS 0.003 0.001 HIS B 76 PHE 0.010 0.001 PHE K 265 TYR 0.013 0.001 TYR K 415 ARG 0.005 0.000 ARG H 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 160 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 LEU cc_start: 0.7130 (mp) cc_final: 0.6596 (mt) REVERT: G 39 ASN cc_start: 0.7735 (OUTLIER) cc_final: 0.7339 (m110) REVERT: H 35 LYS cc_start: 0.8921 (mmmt) cc_final: 0.8528 (mttt) outliers start: 18 outliers final: 14 residues processed: 167 average time/residue: 0.2894 time to fit residues: 70.1557 Evaluate side-chains 173 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 404 CYS Chi-restraints excluded: chain K residue 429 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 109 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.0270 chunk 96 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.095225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.064052 restraints weight = 44453.834| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.28 r_work: 0.2887 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.267 16186 Z= 0.383 Angle : 0.992 66.844 23123 Z= 0.514 Chirality : 0.043 1.059 2600 Planarity : 0.003 0.030 1867 Dihedral : 29.061 179.588 4600 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.63 % Favored : 98.28 % Rotamer: Outliers : 1.77 % Allowed : 12.81 % Favored : 85.42 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.97 (0.25), residues: 1102 helix: 2.15 (0.20), residues: 684 sheet: 1.44 (0.73), residues: 50 loop : -0.33 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 343 HIS 0.004 0.001 HIS H 83 PHE 0.009 0.001 PHE K 265 TYR 0.011 0.001 TYR H 41 ARG 0.007 0.000 ARG C 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3006.42 seconds wall clock time: 54 minutes 48.95 seconds (3288.95 seconds total)