Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 14:45:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5e_10695/04_2023/6y5e_10695_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5e_10695/04_2023/6y5e_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_10695/04_2023/6y5e_10695.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5e_10695/04_2023/6y5e_10695.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5e_10695/04_2023/6y5e_10695_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5e_10695/04_2023/6y5e_10695_updated.pdb" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 8.11, per 1000 atoms: 0.53 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: 6.99 Conformation dependent library (CDL) restraints added in 1.7 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: 6.77 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: 7.56 Time building geometry restraints manager: 7.25 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: 7275 34.13 - 68.25: 1403 68.25 - 102.38: 31 102.38 - 136.50: 0 136.50 - 170.63: 5 Dihedral angle restraints: 8714 sinusoidal: 5454 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 8711 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: 1.440 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: 0.020 Extract box with map and model: 8.080 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 51.990 Find NCS groups from input model: 0.570 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.510 ------------------------------------------------------------------------------- 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 : 25.820 170.629 6606 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 % 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 *********************** 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 : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 249 average time/residue: 0.2642 time to fit residues: 96.7435 Evaluate side-chains 176 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.253 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5218 ------------------------------------------------------------------------------- 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: 9.9990 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: B 26 ASN D 64 ASN F 94 GLN K 260 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 16186 Z= 0.226 Angle : 0.626 11.151 23123 Z= 0.364 Chirality : 0.038 0.193 2600 Planarity : 0.005 0.038 1867 Dihedral : 29.974 178.049 4328 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.73 % Favored : 99.18 % Rotamer Outliers : 1.98 % 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: 1.73 (0.24), residues: 1102 helix: 1.88 (0.19), residues: 684 sheet: -0.81 (0.63), residues: 53 loop : 0.16 (0.31), residues: 365 *********************** 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 231 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 212 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 220 average time/residue: 0.2871 time to fit residues: 91.5862 Evaluate side-chains 194 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 179 time to evaluate : 1.343 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1387 time to fit residues: 5.4816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 104 optimal weight: 0.5980 chunk 85 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS D 64 ASN F 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 16186 Z= 0.244 Angle : 0.583 9.818 23123 Z= 0.340 Chirality : 0.037 0.161 2600 Planarity : 0.004 0.039 1867 Dihedral : 29.917 177.141 4328 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.27 % Favored : 98.64 % Rotamer Outliers : 0.94 % 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: 1.89 (0.25), residues: 1102 helix: 2.08 (0.20), residues: 687 sheet: -0.38 (0.68), residues: 53 loop : -0.03 (0.31), residues: 362 *********************** 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 199 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 190 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 197 average time/residue: 0.3110 time to fit residues: 87.1402 Evaluate side-chains 175 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 171 time to evaluate : 1.387 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1337 time to fit residues: 2.6540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 13 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 125 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 chunk 119 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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: 0.8194 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 16186 Z= 0.295 Angle : 0.585 10.018 23123 Z= 0.340 Chirality : 0.037 0.201 2600 Planarity : 0.004 0.034 1867 Dihedral : 29.866 175.641 4328 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.45 % Favored : 98.46 % Rotamer Outliers : 1.67 % 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: 1.94 (0.25), residues: 1102 helix: 2.16 (0.19), residues: 685 sheet: -0.10 (0.68), residues: 53 loop : -0.14 (0.31), residues: 364 *********************** 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 197 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 181 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 188 average time/residue: 0.3144 time to fit residues: 84.5886 Evaluate side-chains 174 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 163 time to evaluate : 1.410 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1413 time to fit residues: 4.4959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 99 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 0 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3626 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= 0.170 Angle : 0.541 8.526 23123 Z= 0.319 Chirality : 0.034 0.128 2600 Planarity : 0.003 0.038 1867 Dihedral : 29.414 176.549 4328 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.27 % Favored : 98.64 % Rotamer Outliers : 0.83 % 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: 2.13 (0.25), residues: 1102 helix: 2.27 (0.20), residues: 686 sheet: 0.20 (0.70), residues: 53 loop : -0.04 (0.31), residues: 363 *********************** 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 194 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 186 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 191 average time/residue: 0.3321 time to fit residues: 89.6939 Evaluate side-chains 173 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 1.398 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1587 time to fit residues: 2.5853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.0170 chunk 26 optimal weight: 0.0870 chunk 78 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 110 optimal weight: 20.0000 chunk 61 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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: 0.8108 moved from start: 0.3867 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= 0.154 Angle : 0.531 8.918 23123 Z= 0.313 Chirality : 0.034 0.146 2600 Planarity : 0.004 0.038 1867 Dihedral : 29.225 179.652 4328 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.45 % Favored : 98.46 % Rotamer Outliers : 0.83 % 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: 2.20 (0.25), residues: 1102 helix: 2.35 (0.20), residues: 680 sheet: 0.42 (0.70), residues: 52 loop : -0.04 (0.31), residues: 370 *********************** 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 192 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 184 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 186 average time/residue: 0.2990 time to fit residues: 80.6062 Evaluate side-chains 175 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 171 time to evaluate : 1.376 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1567 time to fit residues: 2.7530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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: 0.8243 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.045 16186 Z= 0.420 Angle : 0.627 9.133 23123 Z= 0.360 Chirality : 0.040 0.138 2600 Planarity : 0.005 0.047 1867 Dihedral : 30.010 179.581 4328 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.91 % Favored : 98.00 % Rotamer Outliers : 0.83 % 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: 1.84 (0.25), residues: 1102 helix: 2.05 (0.20), residues: 685 sheet: 0.61 (0.70), residues: 52 loop : -0.26 (0.31), residues: 365 *********************** 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 178 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 170 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 171 average time/residue: 0.3216 time to fit residues: 78.3128 Evaluate side-chains 161 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 155 time to evaluate : 1.293 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1352 time to fit residues: 3.1877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 104 optimal weight: 30.0000 chunk 120 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 126 GLN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 16186 Z= 0.212 Angle : 0.552 9.865 23123 Z= 0.322 Chirality : 0.034 0.192 2600 Planarity : 0.004 0.039 1867 Dihedral : 29.621 179.835 4328 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 0.31 % 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: 2.00 (0.25), residues: 1102 helix: 2.22 (0.20), residues: 680 sheet: 0.68 (0.71), residues: 52 loop : -0.24 (0.30), residues: 370 *********************** 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 177 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 174 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 174 average time/residue: 0.3066 time to fit residues: 76.3876 Evaluate side-chains 164 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 1.361 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1276 time to fit residues: 1.8828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 123 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 117 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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: 0.8233 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.042 16186 Z= 0.358 Angle : 0.600 9.897 23123 Z= 0.346 Chirality : 0.037 0.133 2600 Planarity : 0.004 0.039 1867 Dihedral : 29.866 179.074 4328 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 0.73 % 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: 1.85 (0.25), residues: 1102 helix: 2.13 (0.20), residues: 675 sheet: 0.70 (0.72), residues: 52 loop : -0.35 (0.30), residues: 375 *********************** 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 167 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 160 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 164 average time/residue: 0.3247 time to fit residues: 76.7718 Evaluate side-chains 153 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 149 time to evaluate : 1.437 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1496 time to fit residues: 2.8557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 40.0000 chunk 109 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 GLN E 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 16186 Z= 0.174 Angle : 0.547 10.656 23123 Z= 0.319 Chirality : 0.033 0.229 2600 Planarity : 0.003 0.040 1867 Dihedral : 29.512 179.707 4328 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer Outliers : 0.31 % 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: 1.98 (0.25), residues: 1102 helix: 2.21 (0.20), residues: 680 sheet: 0.77 (0.72), residues: 52 loop : -0.30 (0.30), residues: 370 ********************** 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 175 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 172 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 172 average time/residue: 0.3067 time to fit residues: 75.7880 Evaluate side-chains 165 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 1.451 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1348 time to fit residues: 1.9114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.096635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.065780 restraints weight = 44400.194| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.31 r_work: 0.2926 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 16186 Z= 0.178 Angle : 0.548 11.404 23123 Z= 0.317 Chirality : 0.034 0.315 2600 Planarity : 0.004 0.039 1867 Dihedral : 29.316 179.456 4328 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % 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: 2.01 (0.25), residues: 1102 helix: 2.24 (0.20), residues: 680 sheet: 0.78 (0.72), residues: 52 loop : -0.29 (0.30), residues: 370 =============================================================================== Job complete usr+sys time: 2886.65 seconds wall clock time: 52 minutes 57.50 seconds (3177.50 seconds total)