Starting phenix.real_space_refine on Fri Feb 16 16:07:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0a_15777/02_2024/8b0a_15777.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0a_15777/02_2024/8b0a_15777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0a_15777/02_2024/8b0a_15777.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0a_15777/02_2024/8b0a_15777.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0a_15777/02_2024/8b0a_15777.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0a_15777/02_2024/8b0a_15777.pdb" } resolution = 3.0 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= 0.003 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 297 5.49 5 S 27 5.16 5 C 9068 2.51 5 N 2914 2.21 5 O 3537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15843 Number of models: 1 Model: "" Number of chains: 11 Chain: "K" Number of atoms: 3671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3671 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 13, 'TRANS': 445} Chain: "A" 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: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 804 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3036 Classifications: {'DNA': 149} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 148} Chain: "J" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3070 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Time building chain proxies: 7.87, per 1000 atoms: 0.50 Number of scatterers: 15843 At special positions: 0 Unit cell: (137.01, 139.595, 107.712, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 297 15.00 O 3537 8.00 N 2914 7.00 C 9068 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: 6.58 Conformation dependent library (CDL) restraints added in 1.7 seconds 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2290 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 12 sheets defined 66.3% alpha, 5.5% beta 148 base pairs and 275 stacking pairs defined. Time for finding SS restraints: 6.73 Creating SS restraints... Processing helix chain 'K' and resid 48 through 63 removed outlier: 4.339A pdb=" N GLU K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 91 Processing helix chain 'K' and resid 103 through 105 No H-bonds generated for 'chain 'K' and resid 103 through 105' Processing helix chain 'K' and resid 106 through 118 Processing helix chain 'K' and resid 129 through 140 removed outlier: 3.801A pdb=" N GLN K 138 " --> pdb=" O ALA K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 159 Processing helix chain 'K' and resid 159 through 165 removed outlier: 3.763A pdb=" N LEU K 163 " --> pdb=" O ASP K 159 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER K 165 " --> pdb=" O SER K 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 181 removed outlier: 3.654A pdb=" N ARG K 178 " --> pdb=" O GLU K 175 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASN K 181 " --> pdb=" O ARG K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 193 Processing helix chain 'K' and resid 209 through 219 Processing helix chain 'K' and resid 221 through 230 removed outlier: 6.174A pdb=" N LYS K 227 " --> pdb=" O ASP K 223 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLU K 228 " --> pdb=" O LEU K 224 " (cutoff:3.500A) Processing helix chain 'K' and resid 231 through 237 removed outlier: 3.981A pdb=" N GLN K 235 " --> pdb=" O GLY K 231 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 241 Processing helix chain 'K' and resid 246 through 255 removed outlier: 3.524A pdb=" N LEU K 250 " --> pdb=" O SER K 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 262 through 267 Processing helix chain 'K' and resid 283 through 294 Processing helix chain 'K' and resid 299 through 304 Processing helix chain 'K' and resid 314 through 324 Processing helix chain 'K' and resid 325 through 328 Processing helix chain 'K' and resid 340 through 345 Processing helix chain 'K' and resid 346 through 362 Processing helix chain 'K' and resid 372 through 387 Processing helix chain 'K' and resid 398 through 410 Processing helix chain 'K' and resid 444 through 453 removed outlier: 3.963A pdb=" N ASP K 448 " --> pdb=" O ASN K 444 " (cutoff:3.500A) Processing helix chain 'K' and resid 474 through 495 removed outlier: 3.833A pdb=" N ILE K 478 " --> pdb=" O THR K 474 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU K 487 " --> pdb=" O ALA K 483 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N MET K 492 " --> pdb=" O GLN K 488 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE K 493 " --> pdb=" O LEU K 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.589A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.646A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.673A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.766A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.510A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.705A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.617A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.691A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.598A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.758A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.733A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.632A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 102 through 119 Processing sheet with id=AA1, first strand: chain 'K' and resid 123 through 125 removed outlier: 6.802A pdb=" N PHE K 98 " --> pdb=" O LEU K 149 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N THR K 151 " --> pdb=" O PHE K 98 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE K 100 " --> pdb=" O THR K 151 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU K 99 " --> pdb=" O VAL K 172 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER K 169 " --> pdb=" O PHE K 197 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N LEU K 199 " --> pdb=" O SER K 169 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU K 171 " --> pdb=" O LEU K 199 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU K 201 " --> pdb=" O LEU K 171 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL K 173 " --> pdb=" O LEU K 201 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE K 68 " --> pdb=" O LEU K 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 275 through 280 removed outlier: 6.575A pdb=" N VAL K 436 " --> pdb=" O ILE K 467 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LEU K 469 " --> pdb=" O VAL K 436 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N PHE K 438 " --> pdb=" O LEU K 469 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N GLY K 471 " --> pdb=" O PHE K 438 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU K 367 " --> pdb=" O ILE K 437 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLU K 391 " --> pdb=" O LEU K 418 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N SER K 420 " --> pdb=" O GLU K 391 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL K 393 " --> pdb=" O SER K 420 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.881A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA6, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.921A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.817A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.710A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.831A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 77 through 78 560 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 379 hydrogen bonds 758 hydrogen bond angles 0 basepair planarities 148 basepair parallelities 275 stacking parallelities Total time for adding SS restraints: 7.17 Time building geometry restraints manager: 7.06 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: 3054 1.33 - 1.45: 5151 1.45 - 1.57: 7895 1.57 - 1.69: 593 1.69 - 1.81: 46 Bond restraints: 16739 Sorted by residual: bond pdb=" O5' DG I 70 " pdb=" C5' DG I 70 " ideal model delta sigma weight residual 1.423 1.361 0.062 3.00e-02 1.11e+03 4.29e+00 bond pdb=" O4' DA I 73 " pdb=" C1' DA I 73 " ideal model delta sigma weight residual 1.414 1.378 0.036 2.00e-02 2.50e+03 3.31e+00 bond pdb=" C4' DT J -16 " pdb=" O4' DT J -16 " ideal model delta sigma weight residual 1.450 1.415 0.035 2.00e-02 2.50e+03 3.07e+00 bond pdb=" C4' DC I -57 " pdb=" O4' DC I -57 " ideal model delta sigma weight residual 1.450 1.416 0.034 2.00e-02 2.50e+03 2.88e+00 bond pdb=" C4' DG I 27 " pdb=" O4' DG I 27 " ideal model delta sigma weight residual 1.450 1.416 0.034 2.00e-02 2.50e+03 2.85e+00 ... (remaining 16734 not shown) Histogram of bond angle deviations from ideal: 97.79 - 105.03: 1158 105.03 - 112.28: 8808 112.28 - 119.53: 5970 119.53 - 126.77: 7105 126.77 - 134.02: 840 Bond angle restraints: 23881 Sorted by residual: angle pdb=" O4' DA I 73 " pdb=" C1' DA I 73 " pdb=" N9 DA I 73 " ideal model delta sigma weight residual 108.40 118.28 -9.88 1.50e+00 4.44e-01 4.34e+01 angle pdb=" C4' DA I 73 " pdb=" O4' DA I 73 " pdb=" C1' DA I 73 " ideal model delta sigma weight residual 109.70 101.82 7.88 1.50e+00 4.44e-01 2.76e+01 angle pdb=" C2' DG I 74 " pdb=" C1' DG I 74 " pdb=" N9 DG I 74 " ideal model delta sigma weight residual 113.50 119.86 -6.36 1.50e+00 4.44e-01 1.80e+01 angle pdb=" C2' DC I -57 " pdb=" C1' DC I -57 " pdb=" N1 DC I -57 " ideal model delta sigma weight residual 113.50 119.32 -5.82 1.50e+00 4.44e-01 1.51e+01 angle pdb=" C2' DT I 64 " pdb=" C1' DT I 64 " pdb=" N1 DT I 64 " ideal model delta sigma weight residual 113.50 119.29 -5.79 1.50e+00 4.44e-01 1.49e+01 ... (remaining 23876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 8144 35.00 - 69.99: 1136 69.99 - 104.99: 32 104.99 - 139.99: 0 139.99 - 174.98: 1 Dihedral angle restraints: 9313 sinusoidal: 5764 harmonic: 3549 Sorted by residual: dihedral pdb=" CA LYS K 307 " pdb=" C LYS K 307 " pdb=" N LYS K 308 " pdb=" CA LYS K 308 " ideal model delta harmonic sigma weight residual -180.00 -151.32 -28.68 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA ALA K 306 " pdb=" C ALA K 306 " pdb=" N LYS K 307 " pdb=" CA LYS K 307 " ideal model delta harmonic sigma weight residual 180.00 151.91 28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA PHE K 409 " pdb=" C PHE K 409 " pdb=" N GLY K 410 " pdb=" CA GLY K 410 " ideal model delta harmonic sigma weight residual 180.00 152.53 27.47 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 9310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2448 0.106 - 0.213: 247 0.213 - 0.319: 12 0.319 - 0.426: 0 0.426 - 0.532: 3 Chirality restraints: 2710 Sorted by residual: chirality pdb=" C1' DA I 73 " pdb=" O4' DA I 73 " pdb=" C2' DA I 73 " pdb=" N9 DA I 73 " both_signs ideal model delta sigma weight residual False 2.42 1.89 0.53 2.00e-01 2.50e+01 7.08e+00 chirality pdb=" C1' DG I 74 " pdb=" O4' DG I 74 " pdb=" C2' DG I 74 " pdb=" N9 DG I 74 " both_signs ideal model delta sigma weight residual False 2.42 1.92 0.50 2.00e-01 2.50e+01 6.20e+00 chirality pdb=" C1' DT I 64 " pdb=" O4' DT I 64 " pdb=" C2' DT I 64 " pdb=" N1 DT I 64 " both_signs ideal model delta sigma weight residual False 2.47 2.02 0.45 2.00e-01 2.50e+01 5.07e+00 ... (remaining 2707 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 74 " -0.085 2.00e-02 2.50e+03 3.58e-02 3.84e+01 pdb=" N9 DG I 74 " 0.082 2.00e-02 2.50e+03 pdb=" C8 DG I 74 " 0.008 2.00e-02 2.50e+03 pdb=" N7 DG I 74 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 74 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 74 " -0.012 2.00e-02 2.50e+03 pdb=" O6 DG I 74 " -0.026 2.00e-02 2.50e+03 pdb=" N1 DG I 74 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DG I 74 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 74 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DG I 74 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DG I 74 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 73 " 0.059 2.00e-02 2.50e+03 2.91e-02 2.32e+01 pdb=" N9 DA I 73 " -0.073 2.00e-02 2.50e+03 pdb=" C8 DA I 73 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DA I 73 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 73 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA I 73 " 0.007 2.00e-02 2.50e+03 pdb=" N6 DA I 73 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DA I 73 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DA I 73 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DA I 73 " -0.011 2.00e-02 2.50e+03 pdb=" C4 DA I 73 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I -57 " 0.058 2.00e-02 2.50e+03 3.20e-02 2.31e+01 pdb=" N1 DC I -57 " -0.073 2.00e-02 2.50e+03 pdb=" C2 DC I -57 " 0.009 2.00e-02 2.50e+03 pdb=" O2 DC I -57 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC I -57 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I -57 " 0.004 2.00e-02 2.50e+03 pdb=" N4 DC I -57 " 0.017 2.00e-02 2.50e+03 pdb=" C5 DC I -57 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DC I -57 " -0.007 2.00e-02 2.50e+03 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4145 2.84 - 3.36: 14086 3.36 - 3.87: 28705 3.87 - 4.39: 34388 4.39 - 4.90: 49476 Nonbonded interactions: 130800 Sorted by model distance: nonbonded pdb=" OH TYR K 289 " pdb=" OE1 GLU K 304 " model vdw 2.331 2.440 nonbonded pdb=" OD1 ASP K 353 " pdb=" OH TYR K 382 " model vdw 2.375 2.440 nonbonded pdb=" OG SER K 226 " pdb=" OE2 GLU K 229 " model vdw 2.404 2.440 nonbonded pdb=" O5' DA I -72 " pdb=" O4 DT J 72 " model vdw 2.447 2.440 nonbonded pdb=" OD1 ASP K 394 " pdb=" N GLY K 395 " model vdw 2.460 2.520 ... (remaining 130795 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 20 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 15 through 118) } ncs_group { reference = (chain 'D' and resid 28 through 121) 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: 1.100 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: 4.350 Check model and map are aligned: 0.210 Set scattering table: 0.150 Process input model: 47.230 Find NCS groups from input model: 0.520 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: 0.000 Load rotamer database and sin/cos tables:10.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 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 0.062 16739 Z= 0.437 Angle : 0.956 9.880 23881 Z= 0.600 Chirality : 0.065 0.532 2710 Planarity : 0.011 0.113 1998 Dihedral : 23.863 174.983 7023 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.42 % Allowed : 2.66 % Favored : 96.93 % Rotamer: Outliers : 0.58 % Allowed : 1.93 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1204 helix: 0.24 (0.17), residues: 767 sheet: 1.14 (0.65), residues: 75 loop : -0.58 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP K 110 HIS 0.006 0.002 HIS B 18 PHE 0.016 0.002 PHE K 162 TYR 0.036 0.004 TYR K 214 ARG 0.026 0.003 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 215 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 73 MET cc_start: 0.7434 (mtp) cc_final: 0.7010 (mmm) REVERT: K 113 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8855 (mp0) REVERT: K 329 ASP cc_start: 0.8945 (m-30) cc_final: 0.8654 (p0) REVERT: K 428 MET cc_start: 0.8954 (mtm) cc_final: 0.8688 (mtm) REVERT: A 59 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8031 (mt-10) REVERT: B 24 ASP cc_start: 0.8910 (t0) cc_final: 0.8665 (t0) REVERT: C 64 GLU cc_start: 0.9086 (tt0) cc_final: 0.8410 (tp30) REVERT: C 92 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8528 (mt-10) REVERT: D 49 THR cc_start: 0.9360 (m) cc_final: 0.9005 (p) REVERT: D 65 ASP cc_start: 0.9550 (t0) cc_final: 0.9219 (t0) REVERT: F 85 ASP cc_start: 0.9237 (m-30) cc_final: 0.8983 (m-30) REVERT: G 64 GLU cc_start: 0.8980 (tt0) cc_final: 0.8347 (tm-30) REVERT: G 90 ASP cc_start: 0.8418 (t70) cc_final: 0.8115 (t0) outliers start: 6 outliers final: 6 residues processed: 221 average time/residue: 1.8234 time to fit residues: 431.5543 Evaluate side-chains 150 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 187 HIS Chi-restraints excluded: chain K residue 293 ILE Chi-restraints excluded: chain K residue 394 ASP Chi-restraints excluded: chain E residue 122 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 84 optimal weight: 0.4980 chunk 131 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 303 ASN B 75 HIS B 93 GLN E 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16739 Z= 0.218 Angle : 0.661 11.653 23881 Z= 0.384 Chirality : 0.040 0.355 2710 Planarity : 0.005 0.061 1998 Dihedral : 28.218 177.121 4620 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.58 % Favored : 98.26 % Rotamer: Outliers : 2.79 % Allowed : 10.50 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.25), residues: 1204 helix: 1.89 (0.19), residues: 787 sheet: 1.87 (0.65), residues: 73 loop : -0.66 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 56 HIS 0.009 0.001 HIS B 18 PHE 0.015 0.001 PHE K 233 TYR 0.021 0.001 TYR K 214 ARG 0.007 0.001 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 176 time to evaluate : 1.304 Fit side-chains revert: symmetry clash REVERT: K 112 GLU cc_start: 0.9138 (tp30) cc_final: 0.8808 (tp30) REVERT: K 329 ASP cc_start: 0.9000 (m-30) cc_final: 0.8722 (p0) REVERT: K 489 LEU cc_start: 0.9132 (pp) cc_final: 0.8871 (pt) REVERT: A 59 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8071 (mt-10) REVERT: A 73 GLU cc_start: 0.9258 (tm-30) cc_final: 0.9040 (tm-30) REVERT: B 20 LYS cc_start: 0.8659 (tppp) cc_final: 0.8355 (tptp) REVERT: B 24 ASP cc_start: 0.8810 (t0) cc_final: 0.8596 (t0) REVERT: C 64 GLU cc_start: 0.8994 (tt0) cc_final: 0.8362 (tp30) REVERT: C 90 ASP cc_start: 0.8855 (t0) cc_final: 0.8293 (t0) REVERT: D 65 ASP cc_start: 0.9395 (t0) cc_final: 0.9079 (t0) REVERT: E 59 GLU cc_start: 0.8186 (pm20) cc_final: 0.7798 (pm20) REVERT: G 64 GLU cc_start: 0.8993 (tt0) cc_final: 0.8520 (tm-30) REVERT: G 90 ASP cc_start: 0.8414 (t70) cc_final: 0.8122 (t70) REVERT: G 101 THR cc_start: 0.9220 (t) cc_final: 0.8986 (p) outliers start: 29 outliers final: 7 residues processed: 188 average time/residue: 1.6294 time to fit residues: 332.1725 Evaluate side-chains 144 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 137 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 123 CYS Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain K residue 187 HIS Chi-restraints excluded: chain K residue 239 ASP Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain H residue 84 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 109 optimal weight: 0.0770 chunk 89 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN G 73 ASN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16739 Z= 0.298 Angle : 0.632 9.241 23881 Z= 0.360 Chirality : 0.038 0.294 2710 Planarity : 0.004 0.045 1998 Dihedral : 28.409 178.053 4608 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.99 % Favored : 97.84 % Rotamer: Outliers : 2.70 % Allowed : 13.58 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.25), residues: 1204 helix: 2.07 (0.19), residues: 786 sheet: 1.68 (0.64), residues: 75 loop : -0.88 (0.30), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 168 HIS 0.006 0.001 HIS B 18 PHE 0.011 0.001 PHE K 417 TYR 0.032 0.002 TYR K 214 ARG 0.007 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 157 time to evaluate : 1.386 Fit side-chains revert: symmetry clash REVERT: K 112 GLU cc_start: 0.9313 (tp30) cc_final: 0.9099 (tp30) REVERT: K 113 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8502 (mp0) REVERT: K 329 ASP cc_start: 0.8957 (m-30) cc_final: 0.8629 (p0) REVERT: A 59 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8281 (pt0) REVERT: A 105 GLU cc_start: 0.8912 (tp30) cc_final: 0.8640 (tp30) REVERT: B 20 LYS cc_start: 0.8833 (tppp) cc_final: 0.8600 (tptp) REVERT: C 64 GLU cc_start: 0.9006 (tt0) cc_final: 0.8411 (tp30) REVERT: C 90 ASP cc_start: 0.8941 (t0) cc_final: 0.8674 (t0) REVERT: D 49 THR cc_start: 0.9427 (m) cc_final: 0.9176 (p) REVERT: D 65 ASP cc_start: 0.9404 (t0) cc_final: 0.9124 (t0) REVERT: D 102 GLU cc_start: 0.8639 (pm20) cc_final: 0.8160 (pm20) REVERT: E 59 GLU cc_start: 0.8669 (pm20) cc_final: 0.8405 (pm20) REVERT: E 73 GLU cc_start: 0.8835 (tp30) cc_final: 0.8475 (tt0) REVERT: F 25 ASN cc_start: 0.8691 (p0) cc_final: 0.8022 (p0) REVERT: F 85 ASP cc_start: 0.9275 (m-30) cc_final: 0.8868 (m-30) REVERT: G 64 GLU cc_start: 0.9001 (tt0) cc_final: 0.8522 (tm-30) REVERT: G 101 THR cc_start: 0.9172 (t) cc_final: 0.8956 (p) outliers start: 28 outliers final: 10 residues processed: 175 average time/residue: 1.7719 time to fit residues: 333.5138 Evaluate side-chains 151 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain K residue 187 HIS Chi-restraints excluded: chain K residue 239 ASP Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain H residue 84 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 18 HIS G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 16739 Z= 0.372 Angle : 0.652 10.693 23881 Z= 0.369 Chirality : 0.039 0.224 2710 Planarity : 0.004 0.054 1998 Dihedral : 28.443 177.147 4608 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.08 % Favored : 97.76 % Rotamer: Outliers : 2.79 % Allowed : 16.18 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.25), residues: 1204 helix: 2.09 (0.19), residues: 781 sheet: 1.49 (0.63), residues: 75 loop : -0.81 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 168 HIS 0.004 0.001 HIS K 280 PHE 0.010 0.001 PHE B 61 TYR 0.018 0.001 TYR K 214 ARG 0.007 0.000 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 146 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: K 112 GLU cc_start: 0.9372 (tp30) cc_final: 0.9080 (tp30) REVERT: K 113 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8558 (mp0) REVERT: K 282 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7960 (ptm) REVERT: K 310 LYS cc_start: 0.9076 (mptt) cc_final: 0.8690 (mmmt) REVERT: K 329 ASP cc_start: 0.8953 (m-30) cc_final: 0.8575 (p0) REVERT: A 105 GLU cc_start: 0.8862 (tp30) cc_final: 0.8588 (tp30) REVERT: B 40 ARG cc_start: 0.9415 (OUTLIER) cc_final: 0.8306 (ttp-170) REVERT: C 64 GLU cc_start: 0.9014 (tt0) cc_final: 0.8402 (tp30) REVERT: C 90 ASP cc_start: 0.9165 (t0) cc_final: 0.8432 (t0) REVERT: D 49 THR cc_start: 0.9466 (m) cc_final: 0.9263 (p) REVERT: D 65 ASP cc_start: 0.9442 (t0) cc_final: 0.9185 (t0) REVERT: F 23 ARG cc_start: 0.8738 (mtm-85) cc_final: 0.8498 (mtm-85) REVERT: F 85 ASP cc_start: 0.9244 (m-30) cc_final: 0.8881 (m-30) REVERT: G 64 GLU cc_start: 0.9001 (tt0) cc_final: 0.8536 (tm-30) outliers start: 29 outliers final: 10 residues processed: 168 average time/residue: 1.7347 time to fit residues: 314.2936 Evaluate side-chains 149 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain K residue 239 ASP Chi-restraints excluded: chain K residue 282 MET Chi-restraints excluded: chain K residue 448 ASP Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain H residue 84 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 119 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 71 optimal weight: 0.4980 chunk 125 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16739 Z= 0.206 Angle : 0.597 12.358 23881 Z= 0.336 Chirality : 0.035 0.250 2710 Planarity : 0.004 0.057 1998 Dihedral : 28.268 175.939 4606 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.08 % Favored : 97.76 % Rotamer: Outliers : 2.60 % Allowed : 16.67 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.25), residues: 1204 helix: 2.38 (0.19), residues: 784 sheet: 1.53 (0.63), residues: 75 loop : -0.86 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 168 HIS 0.004 0.001 HIS K 187 PHE 0.011 0.001 PHE K 219 TYR 0.013 0.001 TYR K 214 ARG 0.006 0.000 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 1.564 Fit side-chains revert: symmetry clash REVERT: K 112 GLU cc_start: 0.9370 (tp30) cc_final: 0.9085 (tp30) REVERT: K 113 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8535 (mp0) REVERT: K 282 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7996 (ptm) REVERT: K 310 LYS cc_start: 0.9027 (mptt) cc_final: 0.8691 (mmpt) REVERT: K 372 MET cc_start: 0.8431 (mtm) cc_final: 0.7830 (mpt) REVERT: A 105 GLU cc_start: 0.8902 (tp30) cc_final: 0.8580 (tp30) REVERT: C 64 GLU cc_start: 0.8979 (tt0) cc_final: 0.8450 (tp30) REVERT: C 79 ILE cc_start: 0.9114 (pt) cc_final: 0.8850 (pp) REVERT: C 90 ASP cc_start: 0.9075 (t0) cc_final: 0.8454 (t0) REVERT: D 65 ASP cc_start: 0.9391 (t0) cc_final: 0.9145 (t0) REVERT: E 73 GLU cc_start: 0.8877 (tp30) cc_final: 0.8387 (tt0) REVERT: F 85 ASP cc_start: 0.9279 (m-30) cc_final: 0.8890 (m-30) REVERT: G 64 GLU cc_start: 0.8994 (tt0) cc_final: 0.8565 (tm-30) outliers start: 27 outliers final: 11 residues processed: 169 average time/residue: 1.7284 time to fit residues: 315.5384 Evaluate side-chains 154 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain K residue 135 CYS Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain K residue 239 ASP Chi-restraints excluded: chain K residue 282 MET Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 84 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 450 GLN K 498 HIS B 18 HIS B 25 ASN E 68 GLN G 110 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16739 Z= 0.175 Angle : 0.583 12.227 23881 Z= 0.326 Chirality : 0.034 0.229 2710 Planarity : 0.004 0.059 1998 Dihedral : 28.203 175.542 4606 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.08 % Favored : 97.76 % Rotamer: Outliers : 2.12 % Allowed : 17.82 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.25), residues: 1204 helix: 2.48 (0.19), residues: 782 sheet: 1.53 (0.71), residues: 63 loop : -0.78 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 168 HIS 0.009 0.001 HIS K 187 PHE 0.012 0.001 PHE K 219 TYR 0.012 0.001 TYR F 88 ARG 0.006 0.000 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 152 time to evaluate : 1.343 Fit side-chains revert: symmetry clash REVERT: K 113 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8586 (mp0) REVERT: K 282 MET cc_start: 0.8262 (mtp) cc_final: 0.7925 (ptm) REVERT: K 310 LYS cc_start: 0.8993 (mptt) cc_final: 0.8662 (mmpt) REVERT: K 372 MET cc_start: 0.8443 (mtm) cc_final: 0.7942 (mpt) REVERT: A 105 GLU cc_start: 0.8897 (tp30) cc_final: 0.8597 (tp30) REVERT: C 64 GLU cc_start: 0.8983 (tt0) cc_final: 0.8453 (tp30) REVERT: C 79 ILE cc_start: 0.9017 (pt) cc_final: 0.8775 (pp) REVERT: C 90 ASP cc_start: 0.9088 (t0) cc_final: 0.8458 (t0) REVERT: D 65 ASP cc_start: 0.9344 (t0) cc_final: 0.9109 (t0) REVERT: E 73 GLU cc_start: 0.8829 (tp30) cc_final: 0.8268 (tt0) REVERT: E 120 MET cc_start: 0.9020 (mtp) cc_final: 0.8807 (mtm) REVERT: F 85 ASP cc_start: 0.9267 (m-30) cc_final: 0.8891 (m-30) REVERT: G 64 GLU cc_start: 0.8973 (tt0) cc_final: 0.8632 (tm-30) outliers start: 22 outliers final: 6 residues processed: 168 average time/residue: 1.7216 time to fit residues: 311.7852 Evaluate side-chains 145 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 138 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain K residue 135 CYS Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain K residue 239 ASP Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 86 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 10.0000 chunk 15 optimal weight: 0.2980 chunk 79 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 86 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 450 GLN B 18 HIS C 73 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 110 ASN H 81 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16739 Z= 0.160 Angle : 0.576 10.643 23881 Z= 0.321 Chirality : 0.034 0.306 2710 Planarity : 0.003 0.062 1998 Dihedral : 28.084 175.292 4606 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.74 % Favored : 98.09 % Rotamer: Outliers : 1.45 % Allowed : 19.08 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.25), residues: 1204 helix: 2.63 (0.19), residues: 766 sheet: 1.45 (0.71), residues: 64 loop : -0.59 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 110 HIS 0.005 0.001 HIS D 106 PHE 0.006 0.001 PHE D 67 TYR 0.018 0.001 TYR K 214 ARG 0.010 0.000 ARG H 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 160 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 113 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8552 (mp0) REVERT: K 282 MET cc_start: 0.8347 (mtp) cc_final: 0.8011 (ptm) REVERT: K 372 MET cc_start: 0.8475 (mtm) cc_final: 0.7994 (mpt) REVERT: A 79 LYS cc_start: 0.9142 (tttm) cc_final: 0.8441 (mmmt) REVERT: A 105 GLU cc_start: 0.8901 (tp30) cc_final: 0.8623 (tp30) REVERT: C 64 GLU cc_start: 0.8967 (tt0) cc_final: 0.8503 (tp30) REVERT: C 79 ILE cc_start: 0.8870 (pt) cc_final: 0.8616 (pp) REVERT: C 90 ASP cc_start: 0.9000 (t0) cc_final: 0.8195 (t0) REVERT: D 65 ASP cc_start: 0.9280 (t0) cc_final: 0.8934 (t0) REVERT: E 120 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8706 (mtm) REVERT: F 85 ASP cc_start: 0.9255 (m-30) cc_final: 0.8945 (m-30) REVERT: G 64 GLU cc_start: 0.8940 (tt0) cc_final: 0.8613 (tm-30) REVERT: G 90 ASP cc_start: 0.8402 (t70) cc_final: 0.8185 (t0) outliers start: 15 outliers final: 5 residues processed: 168 average time/residue: 1.5760 time to fit residues: 287.1212 Evaluate side-chains 146 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 139 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain K residue 123 CYS Chi-restraints excluded: chain K residue 135 CYS Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain K residue 239 ASP Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 450 GLN B 18 HIS E 68 GLN G 38 ASN G 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16739 Z= 0.216 Angle : 0.602 12.512 23881 Z= 0.333 Chirality : 0.034 0.266 2710 Planarity : 0.004 0.051 1998 Dihedral : 28.183 174.559 4606 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.99 % Favored : 97.84 % Rotamer: Outliers : 1.64 % Allowed : 19.85 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.25), residues: 1204 helix: 2.57 (0.19), residues: 772 sheet: 1.24 (0.67), residues: 69 loop : -0.72 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 168 HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE B 61 TYR 0.013 0.001 TYR F 88 ARG 0.007 0.000 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 113 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8621 (mp0) REVERT: K 282 MET cc_start: 0.8355 (mtp) cc_final: 0.8039 (ptm) REVERT: K 372 MET cc_start: 0.8551 (mtm) cc_final: 0.8001 (mpt) REVERT: A 105 GLU cc_start: 0.8874 (tp30) cc_final: 0.8609 (tp30) REVERT: C 64 GLU cc_start: 0.8994 (tt0) cc_final: 0.8464 (tp30) REVERT: C 79 ILE cc_start: 0.9061 (pt) cc_final: 0.8795 (pp) REVERT: C 90 ASP cc_start: 0.9090 (t0) cc_final: 0.8523 (t0) REVERT: D 65 ASP cc_start: 0.9351 (t0) cc_final: 0.9120 (t0) REVERT: E 120 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8811 (mtm) REVERT: F 85 ASP cc_start: 0.9280 (m-30) cc_final: 0.8907 (m-30) REVERT: G 64 GLU cc_start: 0.8982 (tt0) cc_final: 0.8628 (tm-30) outliers start: 17 outliers final: 8 residues processed: 154 average time/residue: 1.7127 time to fit residues: 285.0772 Evaluate side-chains 144 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain K residue 123 CYS Chi-restraints excluded: chain K residue 135 CYS Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain K residue 239 ASP Chi-restraints excluded: chain K residue 428 MET Chi-restraints excluded: chain K residue 448 ASP Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 102 optimal weight: 0.0370 chunk 39 optimal weight: 30.0000 chunk 117 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 overall best weight: 3.8068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 450 GLN A 68 GLN B 18 HIS D 81 ASN E 68 GLN G 110 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16739 Z= 0.265 Angle : 0.630 12.750 23881 Z= 0.347 Chirality : 0.036 0.243 2710 Planarity : 0.004 0.057 1998 Dihedral : 28.227 174.060 4606 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.16 % Favored : 97.67 % Rotamer: Outliers : 2.02 % Allowed : 19.46 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.25), residues: 1204 helix: 2.46 (0.19), residues: 781 sheet: 1.33 (0.69), residues: 66 loop : -0.88 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 168 HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE K 219 TYR 0.011 0.001 TYR K 214 ARG 0.007 0.000 ARG F 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 113 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8509 (mp0) REVERT: K 282 MET cc_start: 0.8384 (mtp) cc_final: 0.8055 (ptm) REVERT: K 372 MET cc_start: 0.8586 (mtm) cc_final: 0.8011 (mpt) REVERT: A 59 GLU cc_start: 0.8697 (pt0) cc_final: 0.8117 (pm20) REVERT: A 105 GLU cc_start: 0.8851 (tp30) cc_final: 0.8582 (tp30) REVERT: C 64 GLU cc_start: 0.9014 (tt0) cc_final: 0.8468 (tp30) REVERT: C 79 ILE cc_start: 0.9179 (pt) cc_final: 0.8920 (pp) REVERT: C 90 ASP cc_start: 0.9195 (t0) cc_final: 0.8774 (t0) REVERT: D 65 ASP cc_start: 0.9392 (t0) cc_final: 0.9149 (t0) REVERT: D 102 GLU cc_start: 0.8867 (pm20) cc_final: 0.8543 (pm20) REVERT: E 120 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8864 (mtm) REVERT: F 85 ASP cc_start: 0.9209 (m-30) cc_final: 0.8819 (m-30) REVERT: G 64 GLU cc_start: 0.8995 (tt0) cc_final: 0.8578 (tm-30) REVERT: H 99 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8890 (mp) outliers start: 21 outliers final: 12 residues processed: 151 average time/residue: 1.6382 time to fit residues: 267.7090 Evaluate side-chains 146 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain K residue 123 CYS Chi-restraints excluded: chain K residue 135 CYS Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain K residue 239 ASP Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 450 GLN B 18 HIS G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16739 Z= 0.229 Angle : 0.625 11.345 23881 Z= 0.343 Chirality : 0.035 0.246 2710 Planarity : 0.004 0.053 1998 Dihedral : 28.202 173.979 4606 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.16 % Favored : 97.67 % Rotamer: Outliers : 1.64 % Allowed : 19.85 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.25), residues: 1204 helix: 2.51 (0.19), residues: 778 sheet: 1.31 (0.69), residues: 66 loop : -0.93 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 168 HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE B 61 TYR 0.013 0.001 TYR F 88 ARG 0.008 0.000 ARG H 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 113 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.8617 (mp0) REVERT: K 282 MET cc_start: 0.8373 (mtp) cc_final: 0.8039 (ptm) REVERT: K 372 MET cc_start: 0.8590 (mtm) cc_final: 0.8028 (mpt) REVERT: A 59 GLU cc_start: 0.8634 (pt0) cc_final: 0.8092 (pm20) REVERT: A 105 GLU cc_start: 0.8853 (tp30) cc_final: 0.8579 (tp30) REVERT: C 64 GLU cc_start: 0.8995 (tt0) cc_final: 0.8444 (tp30) REVERT: C 79 ILE cc_start: 0.9125 (pt) cc_final: 0.8855 (pp) REVERT: C 90 ASP cc_start: 0.9219 (t0) cc_final: 0.8798 (t0) REVERT: D 65 ASP cc_start: 0.9389 (t0) cc_final: 0.9168 (t0) REVERT: E 120 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8852 (mtm) REVERT: F 85 ASP cc_start: 0.9233 (m-30) cc_final: 0.8848 (m-30) REVERT: G 64 GLU cc_start: 0.8988 (tt0) cc_final: 0.8567 (tm-30) outliers start: 17 outliers final: 9 residues processed: 146 average time/residue: 1.7564 time to fit residues: 276.3776 Evaluate side-chains 139 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain K residue 123 CYS Chi-restraints excluded: chain K residue 135 CYS Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain K residue 239 ASP Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 115 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 14 optimal weight: 0.2980 chunk 21 optimal weight: 20.0000 chunk 101 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 208 ASN K 450 GLN B 18 HIS E 68 GLN G 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.055981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.036593 restraints weight = 74351.397| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 3.05 r_work: 0.2522 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16739 Z= 0.167 Angle : 0.604 11.144 23881 Z= 0.330 Chirality : 0.034 0.243 2710 Planarity : 0.004 0.055 1998 Dihedral : 28.068 174.098 4606 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.91 % Favored : 97.92 % Rotamer: Outliers : 1.45 % Allowed : 20.04 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.25), residues: 1204 helix: 2.65 (0.19), residues: 766 sheet: 1.39 (0.68), residues: 66 loop : -0.66 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 110 HIS 0.007 0.001 HIS B 75 PHE 0.007 0.001 PHE D 67 TYR 0.012 0.001 TYR K 214 ARG 0.008 0.000 ARG F 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5492.81 seconds wall clock time: 97 minutes 46.09 seconds (5866.09 seconds total)