Starting phenix.real_space_refine on Fri Feb 16 09:20:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jo9_22408/02_2024/7jo9_22408.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jo9_22408/02_2024/7jo9_22408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jo9_22408/02_2024/7jo9_22408.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jo9_22408/02_2024/7jo9_22408.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jo9_22408/02_2024/7jo9_22408.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jo9_22408/02_2024/7jo9_22408.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 290 5.49 5 S 25 5.16 5 C 8556 2.51 5 N 2771 2.21 5 O 3351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "H ARG 33": "NH1" <-> "NH2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 176": "OE1" <-> "OE2" Residue "K ARG 222": "NH1" <-> "NH2" Residue "K PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 253": "OE1" <-> "OE2" Residue "K GLU 276": "OE1" <-> "OE2" Residue "K GLU 302": "OE1" <-> "OE2" Residue "K GLU 303": "OE1" <-> "OE2" Residue "K GLU 411": "OE1" <-> "OE2" Residue "K PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 463": "OE1" <-> "OE2" Residue "K PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 494": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14994 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 683 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "G" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2961 Unusual residues: {' ZN': 1} Classifications: {'peptide': 358, 'undetermined': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 342, None: 1} Not linked: pdbres="ASP K 505 " pdbres=" ZN K 601 " List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13969 SG CYS K 384 40.430 21.150 77.314 1.00 84.47 S ATOM 13975 SG CYS K 385 36.531 21.814 76.213 1.00 87.46 S ATOM 14020 SG CYS K 392 36.749 21.709 79.807 1.00 89.32 S Time building chain proxies: 8.62, per 1000 atoms: 0.57 Number of scatterers: 14994 At special positions: 0 Unit cell: (121.03, 135.59, 125.58, 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 25 16.00 P 290 15.00 O 3351 8.00 N 2771 7.00 C 8556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.84 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=" SG CYS K 385 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 378 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 392 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 384 " Number of angles added : 3 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 12 sheets defined 63.0% alpha, 7.4% beta 138 base pairs and 252 stacking pairs defined. Time for finding SS restraints: 7.23 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.512A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.530A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.527A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.670A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 77 removed outlier: 4.219A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.500A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.610A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 4.043A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.739A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.629A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.703A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 removed outlier: 4.109A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.977A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.596A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.611A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.575A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.102A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.583A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.611A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 4.043A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.739A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.629A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.703A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 4.109A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 185 removed outlier: 4.019A pdb=" N ARG K 161 " --> pdb=" O LEU K 157 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LYS K 162 " --> pdb=" O ARG K 158 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP K 163 " --> pdb=" O LEU K 159 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE K 164 " --> pdb=" O LYS K 160 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU K 166 " --> pdb=" O LYS K 162 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ALA K 167 " --> pdb=" O ASP K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 250 No H-bonds generated for 'chain 'K' and resid 248 through 250' Processing helix chain 'K' and resid 258 through 276 removed outlier: 3.741A pdb=" N GLU K 276 " --> pdb=" O GLU K 272 " (cutoff:3.500A) Processing helix chain 'K' and resid 319 through 325 removed outlier: 4.400A pdb=" N GLU K 324 " --> pdb=" O SER K 321 " (cutoff:3.500A) Processing helix chain 'K' and resid 333 through 342 removed outlier: 3.535A pdb=" N ARG K 337 " --> pdb=" O GLY K 333 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 377 Processing helix chain 'K' and resid 393 through 412 Processing helix chain 'K' and resid 413 through 416 Processing helix chain 'K' and resid 419 through 434 removed outlier: 3.999A pdb=" N VAL K 423 " --> pdb=" O CYS K 419 " (cutoff:3.500A) Processing helix chain 'K' and resid 436 through 443 removed outlier: 4.028A pdb=" N ASP K 441 " --> pdb=" O SER K 438 " (cutoff:3.500A) Proline residue: K 442 - end of helix Processing helix chain 'K' and resid 444 through 463 Processing helix chain 'K' and resid 482 through 499 Processing helix chain 'K' and resid 501 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.137A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.629A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.957A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.489A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.767A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 193 through 195 removed outlier: 4.619A pdb=" N MET K 215 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE K 212 " --> pdb=" O ASP K 307 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE K 309 " --> pdb=" O PHE K 212 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL K 214 " --> pdb=" O ILE K 309 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA K 311 " --> pdb=" O VAL K 214 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N PHE K 216 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU K 313 " --> pdb=" O PHE K 216 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU K 218 " --> pdb=" O GLU K 313 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP K 281 " --> pdb=" O ARG K 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 193 through 195 removed outlier: 4.619A pdb=" N MET K 215 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE K 212 " --> pdb=" O ASP K 307 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE K 309 " --> pdb=" O PHE K 212 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL K 214 " --> pdb=" O ILE K 309 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA K 311 " --> pdb=" O VAL K 214 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N PHE K 216 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU K 313 " --> pdb=" O PHE K 216 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU K 218 " --> pdb=" O GLU K 313 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU K 310 " --> pdb=" O PRO K 349 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 223 through 227 Processing sheet with id=AB3, first strand: chain 'K' and resid 252 through 253 511 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 356 hydrogen bonds 712 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 252 stacking parallelities Total time for adding SS restraints: 7.64 Time building geometry restraints manager: 8.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3006 1.33 - 1.45: 4768 1.45 - 1.57: 7469 1.57 - 1.69: 578 1.69 - 1.81: 40 Bond restraints: 15861 Sorted by residual: bond pdb=" C LEU D 102 " pdb=" N PRO D 103 " ideal model delta sigma weight residual 1.334 1.317 0.016 1.11e-02 8.12e+03 2.19e+00 bond pdb=" C LEU H 102 " pdb=" N PRO H 103 " ideal model delta sigma weight residual 1.334 1.319 0.015 1.11e-02 8.12e+03 1.91e+00 bond pdb=" CB LEU D 80 " pdb=" CG LEU D 80 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.59e+00 bond pdb=" CB LEU H 80 " pdb=" CG LEU H 80 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.53e+00 bond pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.49e+00 ... (remaining 15856 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.28: 1365 105.28 - 112.46: 8823 112.46 - 119.64: 5238 119.64 - 126.82: 6394 126.82 - 134.00: 814 Bond angle restraints: 22634 Sorted by residual: angle pdb=" CA GLY H 53 " pdb=" C GLY H 53 " pdb=" N ILE H 54 " ideal model delta sigma weight residual 115.27 117.77 -2.50 7.60e-01 1.73e+00 1.08e+01 angle pdb=" CA GLY D 53 " pdb=" C GLY D 53 " pdb=" N ILE D 54 " ideal model delta sigma weight residual 115.27 117.71 -2.44 7.60e-01 1.73e+00 1.03e+01 angle pdb=" N ARG K 222 " pdb=" CA ARG K 222 " pdb=" C ARG K 222 " ideal model delta sigma weight residual 111.02 114.33 -3.31 1.25e+00 6.40e-01 7.00e+00 angle pdb=" CB MET F 84 " pdb=" CG MET F 84 " pdb=" SD MET F 84 " ideal model delta sigma weight residual 112.70 104.77 7.93 3.00e+00 1.11e-01 6.99e+00 angle pdb=" C ARG D 33 " pdb=" CA ARG D 33 " pdb=" CB ARG D 33 " ideal model delta sigma weight residual 109.80 114.06 -4.26 1.70e+00 3.46e-01 6.29e+00 ... (remaining 22629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.52: 7314 33.52 - 67.04: 1488 67.04 - 100.56: 40 100.56 - 134.08: 0 134.08 - 167.60: 1 Dihedral angle restraints: 8843 sinusoidal: 5568 harmonic: 3275 Sorted by residual: dihedral pdb=" CA ARG H 33 " pdb=" C ARG H 33 " pdb=" N LYS H 34 " pdb=" CA LYS H 34 " ideal model delta harmonic sigma weight residual 180.00 -155.78 -24.22 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA ARG D 33 " pdb=" C ARG D 33 " pdb=" N LYS D 34 " pdb=" CA LYS D 34 " ideal model delta harmonic sigma weight residual -180.00 -155.79 -24.21 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 52.40 167.60 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 8840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1386 0.029 - 0.059: 777 0.059 - 0.088: 279 0.088 - 0.117: 80 0.117 - 0.147: 25 Chirality restraints: 2547 Sorted by residual: chirality pdb=" CB ILE H 54 " pdb=" CA ILE H 54 " pdb=" CG1 ILE H 54 " pdb=" CG2 ILE H 54 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CB ILE D 54 " pdb=" CA ILE D 54 " pdb=" CG1 ILE D 54 " pdb=" CG2 ILE D 54 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA PRO H 50 " pdb=" N PRO H 50 " pdb=" C PRO H 50 " pdb=" CB PRO H 50 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 2544 not shown) Planarity restraints: 1861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER K 446 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" C SER K 446 " -0.055 2.00e-02 2.50e+03 pdb=" O SER K 446 " 0.020 2.00e-02 2.50e+03 pdb=" N SER K 447 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA K 454 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.54e+00 pdb=" C ALA K 454 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA K 454 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE K 455 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER K 447 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.61e+00 pdb=" C SER K 447 " 0.051 2.00e-02 2.50e+03 pdb=" O SER K 447 " -0.019 2.00e-02 2.50e+03 pdb=" N CYS K 448 " -0.017 2.00e-02 2.50e+03 ... (remaining 1858 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2251 2.76 - 3.29: 13369 3.29 - 3.83: 26368 3.83 - 4.36: 30229 4.36 - 4.90: 45966 Nonbonded interactions: 118183 Sorted by model distance: nonbonded pdb=" OE1 GLU C 64 " pdb=" NH2 ARG K 222 " model vdw 2.222 2.520 nonbonded pdb=" OH TYR K 421 " pdb=" NE2 HIS K 467 " model vdw 2.237 2.520 nonbonded pdb=" OE1 GLU C 92 " pdb=" NH1 ARG K 241 " model vdw 2.255 2.520 nonbonded pdb=" NH2 ARG F 19 " pdb=" OP1 DA J -22 " model vdw 2.276 2.520 nonbonded pdb=" O ARG E 129 " pdb=" NH1 ARG E 129 " model vdw 2.289 2.520 ... (remaining 118178 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 7.430 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 52.930 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 0.008 0.047 15861 Z= 0.466 Angle : 0.738 7.933 22634 Z= 0.442 Chirality : 0.042 0.147 2547 Planarity : 0.005 0.067 1861 Dihedral : 25.947 167.599 6725 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.41 % Allowed : 0.72 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.34 (0.25), residues: 1107 helix: 1.48 (0.20), residues: 646 sheet: -0.28 (0.64), residues: 57 loop : -1.83 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 363 HIS 0.004 0.001 HIS E 39 PHE 0.023 0.002 PHE K 266 TYR 0.023 0.002 TYR K 346 ARG 0.010 0.001 ARG K 443 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 231 time to evaluate : 1.414 Fit side-chains REVERT: D 68 ASP cc_start: 0.8115 (t0) cc_final: 0.7913 (t0) REVERT: E 73 GLU cc_start: 0.8100 (tt0) cc_final: 0.7667 (tt0) REVERT: E 90 MET cc_start: 0.7432 (mmp) cc_final: 0.7134 (mmm) REVERT: F 68 ASP cc_start: 0.7764 (m-30) cc_final: 0.7555 (m-30) REVERT: F 91 LYS cc_start: 0.8420 (ttmt) cc_final: 0.8156 (ttmm) REVERT: G 99 LYS cc_start: 0.8417 (mmtm) cc_final: 0.8073 (mmtt) REVERT: K 173 LYS cc_start: 0.5271 (mtmm) cc_final: 0.5067 (mtmt) REVERT: K 269 ILE cc_start: 0.6058 (mt) cc_final: 0.5368 (tt) outliers start: 4 outliers final: 0 residues processed: 232 average time/residue: 0.4121 time to fit residues: 124.4133 Evaluate side-chains 134 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 0.0570 chunk 40 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS D 63 ASN E 68 GLN F 25 ASN G 38 ASN H 47 GLN K 339 ASN K 429 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15861 Z= 0.178 Angle : 0.553 6.549 22634 Z= 0.325 Chirality : 0.035 0.126 2547 Planarity : 0.004 0.055 1861 Dihedral : 28.564 171.005 4411 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.44 % Allowed : 8.57 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.72 (0.26), residues: 1107 helix: 2.52 (0.21), residues: 660 sheet: 0.34 (0.65), residues: 59 loop : -1.29 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 363 HIS 0.004 0.001 HIS F 18 PHE 0.021 0.002 PHE K 455 TYR 0.016 0.002 TYR K 373 ARG 0.006 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 152 time to evaluate : 1.412 Fit side-chains revert: symmetry clash REVERT: D 33 ARG cc_start: 0.6982 (ppt170) cc_final: 0.6713 (ptt180) REVERT: D 63 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.7961 (m-40) REVERT: D 68 ASP cc_start: 0.8326 (t0) cc_final: 0.8116 (t70) REVERT: E 73 GLU cc_start: 0.7961 (tt0) cc_final: 0.7752 (tt0) REVERT: F 91 LYS cc_start: 0.8393 (ttmt) cc_final: 0.8185 (tttt) REVERT: G 99 LYS cc_start: 0.8482 (mmtm) cc_final: 0.8225 (mmmt) REVERT: K 173 LYS cc_start: 0.5154 (mtmm) cc_final: 0.4853 (mtmt) REVERT: K 353 LYS cc_start: 0.3452 (mmpt) cc_final: 0.2905 (pttm) REVERT: K 430 MET cc_start: 0.6370 (mmp) cc_final: 0.5984 (mmm) REVERT: K 487 GLU cc_start: 0.4433 (mt-10) cc_final: 0.4088 (mt-10) REVERT: K 496 GLU cc_start: 0.5701 (mm-30) cc_final: 0.4723 (tp30) outliers start: 14 outliers final: 6 residues processed: 157 average time/residue: 0.3669 time to fit residues: 78.0949 Evaluate side-chains 126 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 119 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 481 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 109 optimal weight: 0.0970 chunk 121 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN E 76 GLN G 38 ASN G 104 GLN K 499 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15861 Z= 0.270 Angle : 0.587 5.164 22634 Z= 0.345 Chirality : 0.037 0.155 2547 Planarity : 0.004 0.047 1861 Dihedral : 28.895 175.297 4411 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.65 % Allowed : 10.42 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.62 (0.25), residues: 1107 helix: 2.43 (0.20), residues: 660 sheet: 0.22 (0.67), residues: 61 loop : -1.30 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 363 HIS 0.006 0.001 HIS E 39 PHE 0.022 0.002 PHE G 25 TYR 0.014 0.002 TYR H 83 ARG 0.006 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 1.377 Fit side-chains revert: symmetry clash REVERT: D 63 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8406 (t0) REVERT: D 68 ASP cc_start: 0.8482 (t0) cc_final: 0.8134 (t0) REVERT: F 91 LYS cc_start: 0.8493 (ttmt) cc_final: 0.8164 (ttmm) REVERT: G 99 LYS cc_start: 0.8551 (mmtm) cc_final: 0.8289 (mmmt) REVERT: K 173 LYS cc_start: 0.5246 (mtmm) cc_final: 0.4956 (mtmt) REVERT: K 180 ARG cc_start: 0.4530 (tpm170) cc_final: 0.3726 (mtm-85) REVERT: K 373 TYR cc_start: 0.6542 (t80) cc_final: 0.6303 (t80) REVERT: K 430 MET cc_start: 0.6264 (mmp) cc_final: 0.6018 (mmm) REVERT: K 496 GLU cc_start: 0.6023 (mm-30) cc_final: 0.5747 (tp30) outliers start: 16 outliers final: 11 residues processed: 136 average time/residue: 0.3651 time to fit residues: 67.8553 Evaluate side-chains 130 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 472 LYS Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 499 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 123 optimal weight: 30.0000 chunk 130 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15861 Z= 0.279 Angle : 0.580 5.276 22634 Z= 0.342 Chirality : 0.037 0.150 2547 Planarity : 0.004 0.042 1861 Dihedral : 28.847 175.460 4411 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.17 % Allowed : 11.15 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.25), residues: 1107 helix: 2.29 (0.20), residues: 663 sheet: 0.34 (0.68), residues: 60 loop : -1.32 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 363 HIS 0.006 0.001 HIS E 39 PHE 0.023 0.002 PHE K 455 TYR 0.014 0.002 TYR H 83 ARG 0.008 0.001 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 1.300 Fit side-chains REVERT: F 91 LYS cc_start: 0.8496 (ttmt) cc_final: 0.8160 (ttmm) REVERT: G 99 LYS cc_start: 0.8604 (mmtm) cc_final: 0.8319 (mmmt) REVERT: K 154 LEU cc_start: 0.3147 (OUTLIER) cc_final: 0.2783 (tt) REVERT: K 483 ARG cc_start: 0.6050 (ttm110) cc_final: 0.5499 (ptm160) REVERT: K 496 GLU cc_start: 0.6100 (mm-30) cc_final: 0.5685 (tp30) outliers start: 21 outliers final: 11 residues processed: 140 average time/residue: 0.3577 time to fit residues: 68.5821 Evaluate side-chains 126 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 423 VAL Chi-restraints excluded: chain K residue 446 SER Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 481 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15861 Z= 0.307 Angle : 0.600 7.625 22634 Z= 0.351 Chirality : 0.038 0.143 2547 Planarity : 0.005 0.040 1861 Dihedral : 28.949 175.266 4411 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.37 % Allowed : 11.97 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.25), residues: 1107 helix: 2.23 (0.20), residues: 664 sheet: 0.99 (0.68), residues: 54 loop : -1.37 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 363 HIS 0.006 0.001 HIS E 39 PHE 0.020 0.002 PHE C 25 TYR 0.012 0.002 TYR H 83 ARG 0.008 0.001 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 1.342 Fit side-chains revert: symmetry clash REVERT: F 91 LYS cc_start: 0.8481 (ttmt) cc_final: 0.8160 (ttmm) REVERT: G 64 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7248 (tt0) REVERT: G 99 LYS cc_start: 0.8636 (mmtm) cc_final: 0.8335 (mmmt) REVERT: H 35 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7808 (mt-10) REVERT: K 154 LEU cc_start: 0.3054 (OUTLIER) cc_final: 0.2684 (tt) REVERT: K 180 ARG cc_start: 0.4756 (tpm170) cc_final: 0.3859 (mtm-85) REVERT: K 483 ARG cc_start: 0.6174 (ttm110) cc_final: 0.5332 (ptm160) outliers start: 23 outliers final: 15 residues processed: 135 average time/residue: 0.3519 time to fit residues: 65.0324 Evaluate side-chains 129 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 423 VAL Chi-restraints excluded: chain K residue 446 SER Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 481 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 25 optimal weight: 0.0060 chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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: 0.8059 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15861 Z= 0.174 Angle : 0.541 6.453 22634 Z= 0.323 Chirality : 0.035 0.128 2547 Planarity : 0.004 0.073 1861 Dihedral : 28.825 175.400 4411 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.44 % Allowed : 13.00 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.78 (0.25), residues: 1107 helix: 2.51 (0.20), residues: 659 sheet: 1.11 (0.70), residues: 54 loop : -1.23 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 431 HIS 0.004 0.001 HIS F 18 PHE 0.036 0.002 PHE K 455 TYR 0.009 0.001 TYR F 51 ARG 0.008 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: F 91 LYS cc_start: 0.8443 (ttmt) cc_final: 0.8115 (ttmm) REVERT: G 64 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7290 (tt0) REVERT: G 99 LYS cc_start: 0.8613 (mmtm) cc_final: 0.8324 (mmmt) REVERT: H 35 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7773 (mt-10) REVERT: K 154 LEU cc_start: 0.2949 (OUTLIER) cc_final: 0.2612 (tt) REVERT: K 180 ARG cc_start: 0.4670 (tpm170) cc_final: 0.3848 (mtm180) REVERT: K 430 MET cc_start: 0.6527 (mmp) cc_final: 0.6144 (mmm) REVERT: K 496 GLU cc_start: 0.6159 (mm-30) cc_final: 0.5921 (tp30) outliers start: 14 outliers final: 9 residues processed: 127 average time/residue: 0.3495 time to fit residues: 60.7746 Evaluate side-chains 122 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 420 SER Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 481 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 413 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 15861 Z= 0.335 Angle : 0.608 6.103 22634 Z= 0.355 Chirality : 0.039 0.151 2547 Planarity : 0.005 0.059 1861 Dihedral : 28.983 174.858 4411 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.17 % Allowed : 13.00 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.48 (0.25), residues: 1107 helix: 2.26 (0.20), residues: 660 sheet: 0.99 (0.69), residues: 54 loop : -1.34 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 363 HIS 0.006 0.001 HIS E 39 PHE 0.028 0.002 PHE K 455 TYR 0.011 0.002 TYR F 51 ARG 0.011 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 1.405 Fit side-chains REVERT: D 31 ARG cc_start: 0.4492 (ttt180) cc_final: 0.3856 (ttp-110) REVERT: F 91 LYS cc_start: 0.8489 (ttmt) cc_final: 0.8149 (ttmm) REVERT: G 42 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.7468 (ptm-80) REVERT: G 64 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7251 (tt0) REVERT: G 99 LYS cc_start: 0.8625 (mmtm) cc_final: 0.8306 (mmmt) REVERT: H 35 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7788 (mt-10) REVERT: K 154 LEU cc_start: 0.2923 (OUTLIER) cc_final: 0.2664 (tt) REVERT: K 180 ARG cc_start: 0.4689 (tpm170) cc_final: 0.3770 (mtm-85) REVERT: K 430 MET cc_start: 0.6318 (mmp) cc_final: 0.6116 (mmm) outliers start: 21 outliers final: 12 residues processed: 128 average time/residue: 0.3646 time to fit residues: 63.7228 Evaluate side-chains 125 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 420 SER Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 481 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.8085 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15861 Z= 0.225 Angle : 0.567 6.861 22634 Z= 0.336 Chirality : 0.036 0.146 2547 Planarity : 0.004 0.065 1861 Dihedral : 28.895 175.016 4411 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.65 % Allowed : 14.14 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.58 (0.25), residues: 1107 helix: 2.37 (0.20), residues: 659 sheet: 0.95 (0.69), residues: 55 loop : -1.35 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 363 HIS 0.005 0.001 HIS E 39 PHE 0.026 0.002 PHE K 455 TYR 0.010 0.001 TYR F 51 ARG 0.012 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.408 Fit side-chains REVERT: D 31 ARG cc_start: 0.4544 (ttt180) cc_final: 0.3846 (ttp-110) REVERT: F 91 LYS cc_start: 0.8460 (ttmt) cc_final: 0.8132 (ttmm) REVERT: G 64 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7286 (tt0) REVERT: G 99 LYS cc_start: 0.8631 (mmtm) cc_final: 0.8277 (mmmt) REVERT: H 35 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7787 (mt-10) REVERT: K 154 LEU cc_start: 0.2771 (OUTLIER) cc_final: 0.2516 (tt) REVERT: K 180 ARG cc_start: 0.4658 (tpm170) cc_final: 0.3770 (mtm-85) REVERT: K 483 ARG cc_start: 0.6135 (ttm110) cc_final: 0.5285 (ptm160) outliers start: 16 outliers final: 13 residues processed: 129 average time/residue: 0.3812 time to fit residues: 66.3789 Evaluate side-chains 129 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 420 SER Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 503 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.5980 chunk 121 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 120 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.8073 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15861 Z= 0.179 Angle : 0.550 6.968 22634 Z= 0.328 Chirality : 0.035 0.179 2547 Planarity : 0.004 0.075 1861 Dihedral : 28.872 174.871 4411 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.75 % Allowed : 14.04 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.70 (0.25), residues: 1107 helix: 2.48 (0.20), residues: 659 sheet: 0.97 (0.69), residues: 55 loop : -1.32 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 363 HIS 0.005 0.001 HIS E 39 PHE 0.016 0.002 PHE K 455 TYR 0.010 0.001 TYR F 51 ARG 0.013 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 1.389 Fit side-chains REVERT: D 31 ARG cc_start: 0.4529 (ttt180) cc_final: 0.3845 (ttp-110) REVERT: F 91 LYS cc_start: 0.8444 (ttmt) cc_final: 0.8111 (ttmm) REVERT: G 42 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.7475 (ptm-80) REVERT: G 64 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7277 (tt0) REVERT: G 99 LYS cc_start: 0.8622 (mmtm) cc_final: 0.8270 (mmmt) REVERT: H 35 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7784 (mt-10) REVERT: K 154 LEU cc_start: 0.2751 (OUTLIER) cc_final: 0.2502 (tt) REVERT: K 180 ARG cc_start: 0.4696 (tpm170) cc_final: 0.3827 (mtm-85) outliers start: 17 outliers final: 12 residues processed: 127 average time/residue: 0.4041 time to fit residues: 69.6588 Evaluate side-chains 128 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 503 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 123 optimal weight: 0.0870 chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 65 optimal weight: 0.0970 chunk 85 optimal weight: 7.9990 overall best weight: 1.6360 ------------------------------------------------------------------------------- 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: 0.8090 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15861 Z= 0.268 Angle : 0.580 9.252 22634 Z= 0.342 Chirality : 0.037 0.160 2547 Planarity : 0.004 0.065 1861 Dihedral : 28.867 174.392 4411 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.44 % Allowed : 14.34 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.25), residues: 1107 helix: 2.39 (0.20), residues: 659 sheet: 0.96 (0.70), residues: 55 loop : -1.36 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 318 HIS 0.005 0.001 HIS E 39 PHE 0.025 0.002 PHE K 455 TYR 0.011 0.001 TYR F 51 ARG 0.014 0.001 ARG A 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 1.298 Fit side-chains REVERT: D 31 ARG cc_start: 0.4399 (ttt180) cc_final: 0.3795 (ttp-110) REVERT: F 91 LYS cc_start: 0.8469 (ttmt) cc_final: 0.8149 (ttmm) REVERT: G 42 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.7473 (ptm-80) REVERT: G 64 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7279 (tt0) REVERT: G 99 LYS cc_start: 0.8633 (mmtm) cc_final: 0.8337 (mmmt) REVERT: H 35 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7790 (mt-10) REVERT: K 154 LEU cc_start: 0.2770 (OUTLIER) cc_final: 0.2517 (tt) REVERT: K 180 ARG cc_start: 0.4732 (tpm170) cc_final: 0.3840 (mtm-85) REVERT: K 430 MET cc_start: 0.6396 (mmp) cc_final: 0.6054 (mmm) REVERT: K 440 TRP cc_start: 0.4585 (m100) cc_final: 0.4258 (m100) REVERT: K 483 ARG cc_start: 0.6170 (ttm110) cc_final: 0.5315 (ptm160) outliers start: 14 outliers final: 10 residues processed: 128 average time/residue: 0.3841 time to fit residues: 66.3615 Evaluate side-chains 127 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 481 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 110 optimal weight: 0.0170 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.150096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.111931 restraints weight = 22075.423| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.28 r_work: 0.2884 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15861 Z= 0.179 Angle : 0.555 8.121 22634 Z= 0.330 Chirality : 0.035 0.157 2547 Planarity : 0.004 0.067 1861 Dihedral : 28.850 174.370 4411 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.55 % Allowed : 14.55 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 (0.25), residues: 1107 helix: 2.51 (0.20), residues: 659 sheet: 1.00 (0.70), residues: 55 loop : -1.32 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 363 HIS 0.004 0.001 HIS E 39 PHE 0.032 0.002 PHE K 455 TYR 0.011 0.001 TYR F 51 ARG 0.012 0.000 ARG A 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2740.06 seconds wall clock time: 50 minutes 20.64 seconds (3020.64 seconds total)