Starting phenix.real_space_refine on Sat Mar 16 14:56:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7joa_22409/03_2024/7joa_22409.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7joa_22409/03_2024/7joa_22409.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/7joa_22409/03_2024/7joa_22409.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7joa_22409/03_2024/7joa_22409.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7joa_22409/03_2024/7joa_22409.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7joa_22409/03_2024/7joa_22409.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 PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "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 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 64": "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 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 222": "NH1" <-> "NH2" Residue "K PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" 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" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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 23.933 65.763 50.961 1.00 90.89 S ATOM 13975 SG CYS K 385 24.055 69.257 48.730 1.00 83.30 S ATOM 14020 SG CYS K 392 23.001 70.170 51.751 1.00 87.81 S Time building chain proxies: 7.42, per 1000 atoms: 0.49 Number of scatterers: 14994 At special positions: 0 Unit cell: (150.15, 110.11, 116.48, 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: 6.94 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=" SG CYS K 385 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 392 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 378 " 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 63.2% alpha, 7.4% beta 138 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 7.18 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.659A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.526A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.609A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.774A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 4.119A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.529A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.848A 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 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.616A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.535A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.979A 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: 3.643A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.898A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.587A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 removed outlier: 4.105A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.967A 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: 3.949A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.581A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.702A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.779A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.188A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.587A 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 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.617A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.535A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.979A 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: 3.642A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.898A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.585A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 4.104A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 185 removed outlier: 3.797A pdb=" N ARG K 161 " --> pdb=" O LEU K 157 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS K 162 " --> pdb=" O ARG K 158 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP K 163 " --> pdb=" O LEU K 159 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU K 166 " --> pdb=" O LYS K 162 " (cutoff:3.500A) removed outlier: 5.206A 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: 3.705A pdb=" N GLU K 276 " --> pdb=" O GLU K 272 " (cutoff:3.500A) Processing helix chain 'K' and resid 319 through 325 removed outlier: 4.399A pdb=" N GLU K 324 " --> pdb=" O SER K 321 " (cutoff:3.500A) Processing helix chain 'K' and resid 332 through 342 removed outlier: 4.377A pdb=" N VAL K 336 " --> pdb=" O LEU K 332 " (cutoff:3.500A) removed outlier: 3.601A 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: 3.847A pdb=" N VAL K 423 " --> pdb=" O CYS K 419 " (cutoff:3.500A) Processing helix chain 'K' and resid 436 through 443 removed outlier: 4.038A 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 removed outlier: 3.525A pdb=" N PHE K 455 " --> pdb=" O LYS K 451 " (cutoff:3.500A) Processing helix chain 'K' and resid 482 through 499 Processing helix chain 'K' and resid 500 through 505 removed outlier: 5.995A pdb=" N ILE K 503 " --> pdb=" O GLY K 500 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.193A 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 removed outlier: 3.598A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 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: 8.193A 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: 6.953A 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: 7.526A 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 removed outlier: 3.500A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 8.045A 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: 4.626A pdb=" N MET K 215 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE K 212 " --> pdb=" O ASP K 307 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE K 309 " --> pdb=" O PHE K 212 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL K 214 " --> pdb=" O ILE K 309 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA K 311 " --> pdb=" O VAL K 214 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N PHE K 216 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLU K 313 " --> pdb=" O PHE K 216 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU K 218 " --> pdb=" O GLU K 313 " (cutoff:3.500A) removed outlier: 3.905A 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: 4.626A pdb=" N MET K 215 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE K 212 " --> pdb=" O ASP K 307 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE K 309 " --> pdb=" O PHE K 212 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL K 214 " --> pdb=" O ILE K 309 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA K 311 " --> pdb=" O VAL K 214 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N PHE K 216 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLU K 313 " --> pdb=" O PHE K 216 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU K 218 " --> pdb=" O GLU K 313 " (cutoff:3.500A) removed outlier: 7.730A 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 253 507 hydrogen bonds defined for protein. 1470 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 356 hydrogen bonds 712 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 7.51 Time building geometry restraints manager: 7.46 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: 2781 1.33 - 1.45: 4959 1.45 - 1.57: 7503 1.57 - 1.69: 578 1.69 - 1.81: 40 Bond restraints: 15861 Sorted by residual: bond pdb=" CA GLN A 55 " pdb=" C GLN A 55 " ideal model delta sigma weight residual 1.524 1.471 0.052 2.25e-02 1.98e+03 5.37e+00 bond pdb=" C4' DG J -49 " pdb=" C3' DG J -49 " ideal model delta sigma weight residual 1.523 1.496 0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C3' DG I 27 " pdb=" O3' DG I 27 " ideal model delta sigma weight residual 1.422 1.381 0.041 3.00e-02 1.11e+03 1.87e+00 bond pdb=" CG ARG F 39 " pdb=" CD ARG F 39 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.84e+00 bond pdb=" CB VAL F 43 " pdb=" CG2 VAL F 43 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.79e+00 ... (remaining 15856 not shown) Histogram of bond angle deviations from ideal: 98.21 - 105.36: 1398 105.36 - 112.51: 8810 112.51 - 119.66: 5273 119.66 - 126.81: 6341 126.81 - 133.96: 812 Bond angle restraints: 22634 Sorted by residual: angle pdb=" N TRP K 431 " pdb=" CA TRP K 431 " pdb=" CB TRP K 431 " ideal model delta sigma weight residual 110.28 116.47 -6.19 1.55e+00 4.16e-01 1.60e+01 angle pdb=" C TYR A 54 " pdb=" N GLN A 55 " pdb=" CA GLN A 55 " ideal model delta sigma weight residual 122.55 114.52 8.03 2.03e+00 2.43e-01 1.57e+01 angle pdb=" C PHE E 104 " pdb=" N GLU E 105 " pdb=" CA GLU E 105 " ideal model delta sigma weight residual 120.29 115.67 4.62 1.42e+00 4.96e-01 1.06e+01 angle pdb=" CB MET A 90 " pdb=" CG MET A 90 " pdb=" SD MET A 90 " ideal model delta sigma weight residual 112.70 120.60 -7.90 3.00e+00 1.11e-01 6.93e+00 angle pdb=" C ARG K 461 " pdb=" N THR K 462 " pdb=" CA THR K 462 " ideal model delta sigma weight residual 122.38 117.80 4.58 1.81e+00 3.05e-01 6.39e+00 ... (remaining 22629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.59: 7315 33.59 - 67.18: 1493 67.18 - 100.77: 34 100.77 - 134.35: 0 134.35 - 167.94: 1 Dihedral angle restraints: 8843 sinusoidal: 5568 harmonic: 3275 Sorted by residual: dihedral pdb=" CA ASN K 377 " pdb=" C ASN K 377 " pdb=" N HIS K 378 " pdb=" CA HIS K 378 " ideal model delta harmonic sigma weight residual -180.00 -159.69 -20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA HIS D 49 " pdb=" C HIS D 49 " pdb=" N PRO D 50 " pdb=" CA PRO D 50 " ideal model delta harmonic sigma weight residual 180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA HIS H 49 " pdb=" C HIS H 49 " pdb=" N PRO H 50 " pdb=" CA PRO H 50 " ideal model delta harmonic sigma weight residual -180.00 -159.75 -20.25 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 8840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2318 0.073 - 0.146: 223 0.146 - 0.219: 5 0.219 - 0.292: 0 0.292 - 0.365: 1 Chirality restraints: 2547 Sorted by residual: chirality pdb=" CB ILE K 427 " pdb=" CA ILE K 427 " pdb=" CG1 ILE K 427 " pdb=" CG2 ILE K 427 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB ILE K 269 " pdb=" CA ILE K 269 " pdb=" CG1 ILE K 269 " pdb=" CG2 ILE K 269 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CA PHE E 104 " pdb=" N PHE E 104 " pdb=" C PHE E 104 " pdb=" CB PHE E 104 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.62e-01 ... (remaining 2544 not shown) Planarity restraints: 1861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP K 431 " 0.041 2.00e-02 2.50e+03 4.25e-02 4.52e+01 pdb=" CG TRP K 431 " -0.111 2.00e-02 2.50e+03 pdb=" CD1 TRP K 431 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP K 431 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP K 431 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP K 431 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP K 431 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 431 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 431 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP K 431 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA K 454 " 0.016 2.00e-02 2.50e+03 3.10e-02 9.64e+00 pdb=" C ALA K 454 " -0.054 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 446 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.06e+00 pdb=" C SER K 446 " -0.052 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 ... (remaining 1858 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1970 2.74 - 3.28: 13642 3.28 - 3.82: 26254 3.82 - 4.36: 30171 4.36 - 4.90: 45898 Nonbonded interactions: 117935 Sorted by model distance: nonbonded pdb=" OE1 GLU C 92 " pdb=" NH1 ARG K 241 " model vdw 2.206 2.520 nonbonded pdb=" O ARG E 129 " pdb=" NH1 ARG E 129 " model vdw 2.232 2.520 nonbonded pdb=" OE2 GLU K 494 " pdb=" ND2 ASN K 498 " model vdw 2.241 2.520 nonbonded pdb=" NH2 ARG K 394 " pdb=" OD1 ASP K 437 " model vdw 2.249 2.520 nonbonded pdb=" O ILE C 78 " pdb=" OG SER D 55 " model vdw 2.252 2.440 ... (remaining 117930 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: 15.690 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: 16.110 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 48.850 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 0.009 0.052 15861 Z= 0.521 Angle : 0.780 8.033 22634 Z= 0.464 Chirality : 0.045 0.365 2547 Planarity : 0.006 0.054 1861 Dihedral : 25.945 167.942 6725 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -0.33 (0.24), residues: 1107 helix: 0.88 (0.20), residues: 655 sheet: -0.47 (0.64), residues: 57 loop : -2.08 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.111 0.008 TRP K 431 HIS 0.004 0.001 HIS E 39 PHE 0.029 0.003 PHE E 104 TYR 0.017 0.002 TYR K 468 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 240 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.688 Fit side-chains revert: symmetry clash REVERT: B 68 ASP cc_start: 0.8067 (m-30) cc_final: 0.7862 (m-30) REVERT: G 74 LYS cc_start: 0.7759 (mtmm) cc_final: 0.7246 (mmmt) REVERT: G 110 ASN cc_start: 0.8076 (t0) cc_final: 0.7854 (t0) REVERT: H 88 THR cc_start: 0.8962 (t) cc_final: 0.8630 (m) REVERT: H 90 THR cc_start: 0.8640 (m) cc_final: 0.8432 (p) REVERT: K 273 GLU cc_start: 0.3902 (mm-30) cc_final: 0.3206 (mm-30) REVERT: K 428 PHE cc_start: 0.6931 (m-10) cc_final: 0.6671 (m-10) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.4367 time to fit residues: 134.1539 Evaluate side-chains 133 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.334 ------------------------------------------------------------------------------- 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: 8.9990 chunk 102 optimal weight: 3.9990 chunk 56 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 0.1980 chunk 40 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 25 ASN C 38 ASN F 25 ASN F 75 HIS G 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2249 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= 0.174 Angle : 0.549 6.567 22634 Z= 0.326 Chirality : 0.035 0.125 2547 Planarity : 0.004 0.050 1861 Dihedral : 28.797 169.861 4411 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.44 % Allowed : 6.40 % Favored : 92.16 % 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: 1.36 (0.25), residues: 1107 helix: 2.40 (0.20), residues: 654 sheet: 0.08 (0.66), residues: 59 loop : -1.70 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP K 431 HIS 0.003 0.001 HIS H 49 PHE 0.018 0.002 PHE K 488 TYR 0.015 0.001 TYR K 346 ARG 0.005 0.000 ARG K 364 *********************** 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 169 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 155 time to evaluate : 1.311 Fit side-chains REVERT: C 61 GLU cc_start: 0.7594 (tp30) cc_final: 0.7254 (mm-30) REVERT: C 95 LYS cc_start: 0.8954 (ttmm) cc_final: 0.8461 (tttm) REVERT: G 74 LYS cc_start: 0.7750 (mtmm) cc_final: 0.7291 (mmmt) REVERT: G 95 LYS cc_start: 0.8997 (ttpt) cc_final: 0.8496 (tttm) REVERT: G 110 ASN cc_start: 0.8103 (t0) cc_final: 0.7898 (t0) REVERT: K 183 GLN cc_start: 0.6698 (mt0) cc_final: 0.6372 (tm-30) REVERT: K 273 GLU cc_start: 0.3653 (mm-30) cc_final: 0.3017 (mm-30) REVERT: K 428 PHE cc_start: 0.6843 (m-10) cc_final: 0.6624 (m-10) outliers start: 14 outliers final: 11 residues processed: 162 average time/residue: 0.3748 time to fit residues: 82.1313 Evaluate side-chains 133 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 230 GLU Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.0980 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN K 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15861 Z= 0.256 Angle : 0.588 10.691 22634 Z= 0.342 Chirality : 0.037 0.136 2547 Planarity : 0.004 0.047 1861 Dihedral : 28.992 174.604 4411 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.86 % Allowed : 8.57 % Favored : 89.58 % 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: 1.42 (0.25), residues: 1107 helix: 2.44 (0.20), residues: 660 sheet: 0.30 (0.64), residues: 59 loop : -1.75 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP K 431 HIS 0.004 0.001 HIS K 429 PHE 0.024 0.003 PHE G 25 TYR 0.014 0.002 TYR G 57 ARG 0.006 0.001 ARG K 364 *********************** 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 148 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 1.263 Fit side-chains REVERT: C 61 GLU cc_start: 0.7708 (tp30) cc_final: 0.7446 (mm-30) REVERT: C 74 LYS cc_start: 0.8270 (mtpt) cc_final: 0.8055 (mtmt) REVERT: C 95 LYS cc_start: 0.8996 (ttmm) cc_final: 0.8548 (tttm) REVERT: E 56 LYS cc_start: 0.8778 (ttmm) cc_final: 0.8515 (tttp) REVERT: G 74 LYS cc_start: 0.7987 (mtmm) cc_final: 0.7509 (mmmt) REVERT: G 95 LYS cc_start: 0.9024 (ttpt) cc_final: 0.8537 (tttm) REVERT: G 110 ASN cc_start: 0.8142 (t0) cc_final: 0.7906 (t0) REVERT: K 183 GLN cc_start: 0.6529 (mt0) cc_final: 0.6280 (tm-30) REVERT: K 273 GLU cc_start: 0.3528 (mm-30) cc_final: 0.3013 (mm-30) REVERT: K 482 ASP cc_start: 0.2846 (t0) cc_final: 0.1950 (m-30) REVERT: K 496 GLU cc_start: 0.2458 (mm-30) cc_final: 0.1341 (mm-30) outliers start: 18 outliers final: 12 residues processed: 142 average time/residue: 0.3671 time to fit residues: 70.4272 Evaluate side-chains 134 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 213 ASP Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15861 Z= 0.202 Angle : 0.537 8.651 22634 Z= 0.317 Chirality : 0.035 0.129 2547 Planarity : 0.004 0.037 1861 Dihedral : 28.785 175.126 4411 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.75 % Allowed : 10.11 % Favored : 88.13 % 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: 1.66 (0.25), residues: 1107 helix: 2.59 (0.20), residues: 661 sheet: 0.66 (0.70), residues: 52 loop : -1.58 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 431 HIS 0.002 0.001 HIS K 250 PHE 0.013 0.002 PHE C 25 TYR 0.011 0.001 TYR K 346 ARG 0.004 0.000 ARG K 483 *********************** 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 148 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 1.257 Fit side-chains REVERT: A 56 LYS cc_start: 0.8805 (ttmm) cc_final: 0.8502 (tttp) REVERT: C 61 GLU cc_start: 0.7712 (tp30) cc_final: 0.7428 (mm-30) REVERT: C 95 LYS cc_start: 0.9022 (ttmm) cc_final: 0.8610 (tttm) REVERT: E 56 LYS cc_start: 0.8780 (ttmm) cc_final: 0.8507 (tttp) REVERT: G 74 LYS cc_start: 0.8071 (mtmm) cc_final: 0.7551 (mmmt) REVERT: G 95 LYS cc_start: 0.9066 (ttpt) cc_final: 0.8561 (tttm) REVERT: G 110 ASN cc_start: 0.8140 (t0) cc_final: 0.7902 (t0) REVERT: K 183 GLN cc_start: 0.6520 (mt0) cc_final: 0.6257 (tm-30) REVERT: K 273 GLU cc_start: 0.3605 (mm-30) cc_final: 0.3310 (mm-30) REVERT: K 396 GLU cc_start: 0.5878 (mp0) cc_final: 0.5675 (mp0) REVERT: K 464 LYS cc_start: 0.5005 (tptp) cc_final: 0.4275 (tttm) REVERT: K 482 ASP cc_start: 0.3203 (t0) cc_final: 0.2356 (m-30) REVERT: K 496 GLU cc_start: 0.2632 (mm-30) cc_final: 0.1580 (mm-30) outliers start: 17 outliers final: 14 residues processed: 141 average time/residue: 0.3546 time to fit residues: 67.7770 Evaluate side-chains 135 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 279 ASP Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 15861 Z= 0.346 Angle : 0.629 10.847 22634 Z= 0.363 Chirality : 0.039 0.144 2547 Planarity : 0.005 0.041 1861 Dihedral : 28.982 177.767 4411 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.75 % Allowed : 11.46 % Favored : 86.79 % 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: 1.39 (0.25), residues: 1107 helix: 2.24 (0.20), residues: 669 sheet: 0.62 (0.65), residues: 52 loop : -1.51 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP K 431 HIS 0.005 0.001 HIS E 39 PHE 0.022 0.002 PHE C 25 TYR 0.014 0.002 TYR K 346 ARG 0.008 0.001 ARG K 364 *********************** 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 140 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.239 Fit side-chains REVERT: A 56 LYS cc_start: 0.8839 (ttmm) cc_final: 0.8575 (tttp) REVERT: C 36 LYS cc_start: 0.8593 (mttt) cc_final: 0.8362 (mttp) REVERT: C 61 GLU cc_start: 0.7726 (tp30) cc_final: 0.7446 (mm-30) REVERT: C 95 LYS cc_start: 0.9040 (ttmm) cc_final: 0.8601 (tttm) REVERT: E 56 LYS cc_start: 0.8837 (ttmm) cc_final: 0.8579 (tttp) REVERT: G 74 LYS cc_start: 0.8169 (mtmm) cc_final: 0.7720 (mmmt) REVERT: G 95 LYS cc_start: 0.9076 (ttpt) cc_final: 0.8563 (tttm) REVERT: G 110 ASN cc_start: 0.8109 (t0) cc_final: 0.7877 (t0) REVERT: K 177 ARG cc_start: 0.6562 (mtt90) cc_final: 0.6317 (ttm-80) REVERT: K 183 GLN cc_start: 0.6538 (mt0) cc_final: 0.6222 (tm-30) REVERT: K 273 GLU cc_start: 0.3765 (mm-30) cc_final: 0.3311 (mm-30) REVERT: K 396 GLU cc_start: 0.5944 (mp0) cc_final: 0.5697 (mp0) REVERT: K 482 ASP cc_start: 0.2738 (t0) cc_final: 0.1891 (m-30) outliers start: 17 outliers final: 14 residues processed: 133 average time/residue: 0.3643 time to fit residues: 65.6221 Evaluate side-chains 132 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 213 ASP Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 0.0980 chunk 130 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 68 optimal weight: 0.4980 chunk 125 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN E 68 GLN E 76 GLN G 38 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3838 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= 0.158 Angle : 0.516 10.171 22634 Z= 0.307 Chirality : 0.034 0.123 2547 Planarity : 0.004 0.036 1861 Dihedral : 28.620 175.958 4411 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.44 % Allowed : 11.87 % 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: 1.86 (0.25), residues: 1107 helix: 2.59 (0.20), residues: 669 sheet: 0.90 (0.65), residues: 52 loop : -1.29 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 431 HIS 0.002 0.000 HIS K 250 PHE 0.008 0.001 PHE K 449 TYR 0.010 0.001 TYR K 468 ARG 0.007 0.000 ARG K 364 *********************** 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 138 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 1.175 Fit side-chains REVERT: A 56 LYS cc_start: 0.8776 (ttmm) cc_final: 0.8500 (tttp) REVERT: C 36 LYS cc_start: 0.8577 (mttt) cc_final: 0.8365 (mttp) REVERT: C 61 GLU cc_start: 0.7642 (tp30) cc_final: 0.7356 (mm-30) REVERT: C 95 LYS cc_start: 0.9060 (ttmm) cc_final: 0.8609 (tttm) REVERT: D 63 ASN cc_start: 0.7869 (t0) cc_final: 0.7646 (m-40) REVERT: G 42 ARG cc_start: 0.8852 (ptm-80) cc_final: 0.8504 (mtm110) REVERT: G 74 LYS cc_start: 0.8038 (mtmm) cc_final: 0.7392 (mmmt) REVERT: G 95 LYS cc_start: 0.9005 (ttpt) cc_final: 0.8524 (tttm) REVERT: G 110 ASN cc_start: 0.8102 (t0) cc_final: 0.7891 (t0) REVERT: K 183 GLN cc_start: 0.6469 (mt0) cc_final: 0.6132 (tm-30) REVERT: K 273 GLU cc_start: 0.3745 (mm-30) cc_final: 0.3361 (mt-10) REVERT: K 322 THR cc_start: 0.8014 (OUTLIER) cc_final: 0.7632 (p) REVERT: K 482 ASP cc_start: 0.3023 (t0) cc_final: 0.2248 (m-30) outliers start: 14 outliers final: 10 residues processed: 133 average time/residue: 0.3730 time to fit residues: 67.0677 Evaluate side-chains 127 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain K residue 322 THR Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.0980 chunk 74 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 109 optimal weight: 0.5980 chunk 72 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 15861 Z= 0.357 Angle : 0.631 9.662 22634 Z= 0.364 Chirality : 0.040 0.151 2547 Planarity : 0.005 0.039 1861 Dihedral : 28.923 178.900 4411 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.75 % Allowed : 13.11 % Favored : 85.14 % 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: 1.57 (0.25), residues: 1107 helix: 2.29 (0.20), residues: 671 sheet: 0.94 (0.64), residues: 52 loop : -1.33 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP K 431 HIS 0.005 0.001 HIS E 39 PHE 0.019 0.002 PHE C 25 TYR 0.014 0.002 TYR F 51 ARG 0.009 0.001 ARG K 364 *********************** 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 137 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 1.170 Fit side-chains REVERT: A 56 LYS cc_start: 0.8853 (ttmm) cc_final: 0.8565 (tttp) REVERT: C 36 LYS cc_start: 0.8595 (mttt) cc_final: 0.8381 (mttp) REVERT: C 61 GLU cc_start: 0.7732 (tp30) cc_final: 0.7459 (mm-30) REVERT: C 95 LYS cc_start: 0.9072 (ttmm) cc_final: 0.8597 (tttm) REVERT: G 42 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8046 (ptm-80) REVERT: G 74 LYS cc_start: 0.8219 (mtmm) cc_final: 0.7741 (mmmt) REVERT: G 95 LYS cc_start: 0.9079 (ttpt) cc_final: 0.8555 (tttm) REVERT: G 110 ASN cc_start: 0.8138 (t0) cc_final: 0.7889 (t0) REVERT: K 183 GLN cc_start: 0.6448 (mt0) cc_final: 0.6153 (tm-30) REVERT: K 273 GLU cc_start: 0.4009 (mm-30) cc_final: 0.3790 (mt-10) REVERT: K 482 ASP cc_start: 0.2782 (t0) cc_final: 0.1954 (m-30) outliers start: 17 outliers final: 12 residues processed: 130 average time/residue: 0.3696 time to fit residues: 65.3875 Evaluate side-chains 129 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 88 THR 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 G residue 114 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 213 ASP Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3994 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= 0.190 Angle : 0.572 9.187 22634 Z= 0.338 Chirality : 0.037 0.208 2547 Planarity : 0.004 0.039 1861 Dihedral : 28.808 177.144 4411 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.44 % Allowed : 13.73 % 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: 1.74 (0.25), residues: 1107 helix: 2.43 (0.20), residues: 671 sheet: 1.11 (0.65), residues: 52 loop : -1.27 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP K 431 HIS 0.004 0.001 HIS E 39 PHE 0.009 0.002 PHE C 25 TYR 0.009 0.001 TYR F 51 ARG 0.010 0.000 ARG K 364 *********************** 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 133 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 1.299 Fit side-chains REVERT: C 36 LYS cc_start: 0.8616 (mttt) cc_final: 0.8405 (mttp) REVERT: C 42 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8465 (mtm110) REVERT: C 61 GLU cc_start: 0.7665 (tp30) cc_final: 0.7386 (mm-30) REVERT: C 95 LYS cc_start: 0.9069 (ttmm) cc_final: 0.8604 (tttm) REVERT: G 42 ARG cc_start: 0.8872 (ptm-80) cc_final: 0.8493 (mtm110) REVERT: G 74 LYS cc_start: 0.8176 (mtmm) cc_final: 0.7643 (mmmt) REVERT: G 95 LYS cc_start: 0.9051 (ttpt) cc_final: 0.8555 (tttm) REVERT: G 110 ASN cc_start: 0.8097 (t0) cc_final: 0.7847 (t0) REVERT: H 33 ARG cc_start: 0.7135 (ptt180) cc_final: 0.6904 (ptt180) REVERT: K 183 GLN cc_start: 0.6396 (mt0) cc_final: 0.6124 (tm-30) REVERT: K 273 GLU cc_start: 0.4260 (mm-30) cc_final: 0.4051 (mt-10) REVERT: K 482 ASP cc_start: 0.2950 (t0) cc_final: 0.2154 (m-30) outliers start: 14 outliers final: 9 residues processed: 129 average time/residue: 0.3766 time to fit residues: 65.2710 Evaluate side-chains 127 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 124 optimal weight: 0.0770 chunk 72 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 120 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- 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: 0.8110 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15861 Z= 0.213 Angle : 0.555 8.639 22634 Z= 0.327 Chirality : 0.035 0.133 2547 Planarity : 0.004 0.038 1861 Dihedral : 28.706 177.224 4411 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.34 % Allowed : 14.04 % Favored : 84.62 % 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: 1.91 (0.25), residues: 1107 helix: 2.56 (0.20), residues: 671 sheet: 1.17 (0.65), residues: 52 loop : -1.19 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP K 431 HIS 0.002 0.001 HIS K 250 PHE 0.013 0.002 PHE C 25 TYR 0.010 0.001 TYR K 346 ARG 0.008 0.000 ARG K 364 *********************** 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 134 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 1.519 Fit side-chains REVERT: C 36 LYS cc_start: 0.8597 (mttt) cc_final: 0.8397 (mttp) REVERT: C 42 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8450 (mtm110) REVERT: C 61 GLU cc_start: 0.7706 (tp30) cc_final: 0.7435 (mm-30) REVERT: C 95 LYS cc_start: 0.9102 (ttmm) cc_final: 0.8620 (tttm) REVERT: G 42 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8102 (ptm-80) REVERT: G 74 LYS cc_start: 0.8150 (mtmm) cc_final: 0.7621 (mmmt) REVERT: G 95 LYS cc_start: 0.9077 (ttpt) cc_final: 0.8551 (tttm) REVERT: G 110 ASN cc_start: 0.8116 (t0) cc_final: 0.7862 (t0) REVERT: H 33 ARG cc_start: 0.7187 (ptt180) cc_final: 0.6962 (ptt180) REVERT: K 183 GLN cc_start: 0.6391 (mt0) cc_final: 0.6079 (tm-30) REVERT: K 354 ASP cc_start: 0.3945 (t0) cc_final: 0.2845 (p0) REVERT: K 482 ASP cc_start: 0.2955 (t0) cc_final: 0.2187 (m-30) outliers start: 13 outliers final: 10 residues processed: 131 average time/residue: 0.3612 time to fit residues: 63.7190 Evaluate side-chains 128 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 457 LEU 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: 0.8980 chunk 89 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 15861 Z= 0.368 Angle : 0.640 8.542 22634 Z= 0.369 Chirality : 0.040 0.170 2547 Planarity : 0.005 0.035 1861 Dihedral : 28.969 179.455 4411 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.24 % Allowed : 14.65 % Favored : 84.11 % 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: 1.51 (0.25), residues: 1107 helix: 2.25 (0.20), residues: 672 sheet: 1.08 (0.65), residues: 52 loop : -1.38 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.005 TRP K 431 HIS 0.005 0.001 HIS E 39 PHE 0.020 0.002 PHE C 25 TYR 0.014 0.002 TYR K 346 ARG 0.008 0.001 ARG K 364 ********************** 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 127 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.212 Fit side-chains REVERT: C 36 LYS cc_start: 0.8596 (mttt) cc_final: 0.8380 (mttp) REVERT: C 42 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8702 (mtm180) REVERT: C 61 GLU cc_start: 0.7738 (tp30) cc_final: 0.7464 (mm-30) REVERT: C 95 LYS cc_start: 0.9079 (ttmm) cc_final: 0.8593 (tttm) REVERT: G 42 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8019 (ptm-80) REVERT: G 74 LYS cc_start: 0.8221 (mtmm) cc_final: 0.7780 (mmmt) REVERT: G 95 LYS cc_start: 0.9092 (ttpt) cc_final: 0.8536 (tttm) REVERT: G 110 ASN cc_start: 0.8143 (t0) cc_final: 0.7873 (t0) REVERT: K 183 GLN cc_start: 0.6397 (mt0) cc_final: 0.5997 (tm-30) REVERT: K 482 ASP cc_start: 0.2782 (t0) cc_final: 0.1877 (m-30) outliers start: 12 outliers final: 10 residues processed: 124 average time/residue: 0.3655 time to fit residues: 61.1489 Evaluate side-chains 125 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 4.9990 chunk 32 optimal weight: 0.0570 chunk 98 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 110 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.146586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106644 restraints weight = 23755.097| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.40 r_work: 0.2991 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4212 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= 0.172 Angle : 0.528 8.784 22634 Z= 0.314 Chirality : 0.034 0.141 2547 Planarity : 0.004 0.037 1861 Dihedral : 28.605 176.817 4411 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.24 % Allowed : 14.76 % Favored : 84.00 % 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: 1.94 (0.25), residues: 1107 helix: 2.65 (0.20), residues: 666 sheet: 1.26 (0.66), residues: 52 loop : -1.27 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP K 431 HIS 0.002 0.000 HIS K 250 PHE 0.010 0.001 PHE K 428 TYR 0.008 0.001 TYR K 468 ARG 0.008 0.000 ARG K 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2673.80 seconds wall clock time: 51 minutes 14.15 seconds (3074.15 seconds total)