Starting phenix.real_space_refine on Sun Dec 10 22:41:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0a_15777/12_2023/8b0a_15777.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0a_15777/12_2023/8b0a_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_15777/12_2023/8b0a_15777.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0a_15777/12_2023/8b0a_15777.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0a_15777/12_2023/8b0a_15777.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0a_15777/12_2023/8b0a_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 10.06, per 1000 atoms: 0.63 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: 7.71 Conformation dependent library (CDL) restraints added in 1.9 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: 7.81 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: 8.08 Time building geometry restraints manager: 8.20 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.340 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 53.450 Find NCS groups from input model: 0.550 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:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.650 ------------------------------------------------------------------------------- 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 : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 221 average time/residue: 1.8292 time to fit residues: 433.0256 Evaluate side-chains 145 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 139 time to evaluate : 1.403 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.3863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 131 optimal weight: 10.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 D 46 HIS E 93 GLN H 81 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16739 Z= 0.205 Angle : 0.667 12.554 23881 Z= 0.383 Chirality : 0.039 0.340 2710 Planarity : 0.005 0.059 1998 Dihedral : 28.344 177.563 4606 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.58 % Favored : 98.26 % Rotamer: Outliers : 2.79 % Allowed : 11.27 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.25), residues: 1204 helix: 1.96 (0.19), residues: 785 sheet: 1.90 (0.65), residues: 74 loop : -0.64 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 56 HIS 0.008 0.001 HIS B 18 PHE 0.012 0.001 PHE K 233 TYR 0.021 0.001 TYR K 214 ARG 0.008 0.001 ARG B 23 *********************** 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 204 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 175 time to evaluate : 1.454 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 7 residues processed: 189 average time/residue: 1.6907 time to fit residues: 345.7895 Evaluate side-chains 139 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 1.254 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.1262 time to fit residues: 1.9737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 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: 3.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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: 0.8773 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16739 Z= 0.336 Angle : 0.655 11.168 23881 Z= 0.372 Chirality : 0.039 0.301 2710 Planarity : 0.004 0.047 1998 Dihedral : 28.425 178.028 4606 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.08 % Favored : 97.76 % Rotamer: Outliers : 3.18 % Allowed : 14.07 % Favored : 82.76 % 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: 1.83 (0.25), residues: 1204 helix: 2.04 (0.19), residues: 787 sheet: 1.62 (0.63), residues: 75 loop : -0.89 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 168 HIS 0.009 0.001 HIS D 46 PHE 0.011 0.001 PHE B 61 TYR 0.032 0.002 TYR K 214 ARG 0.006 0.000 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 184 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 151 time to evaluate : 1.377 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 11 residues processed: 173 average time/residue: 1.7510 time to fit residues: 326.2367 Evaluate side-chains 146 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 1.389 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 2 average time/residue: 0.2040 time to fit residues: 2.2733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 14 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 109 ASN A 68 GLN B 18 HIS G 73 ASN G 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16739 Z= 0.249 Angle : 0.609 10.894 23881 Z= 0.346 Chirality : 0.037 0.213 2710 Planarity : 0.004 0.057 1998 Dihedral : 28.283 177.303 4606 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.49 % Favored : 97.34 % Rotamer: Outliers : 3.08 % Allowed : 15.70 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.25), residues: 1204 helix: 2.24 (0.19), residues: 785 sheet: 1.53 (0.63), residues: 75 loop : -0.85 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 168 HIS 0.006 0.001 HIS D 46 PHE 0.010 0.001 PHE K 225 TYR 0.024 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 183 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 151 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 13 residues processed: 172 average time/residue: 1.7965 time to fit residues: 332.7850 Evaluate side-chains 147 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 1.295 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 4 average time/residue: 0.9862 time to fit residues: 6.0647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 2 optimal weight: 30.0000 chunk 104 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 71 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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: 0.8771 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16739 Z= 0.283 Angle : 0.621 10.561 23881 Z= 0.350 Chirality : 0.037 0.215 2710 Planarity : 0.004 0.059 1998 Dihedral : 28.367 175.685 4606 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.66 % Favored : 97.18 % Rotamer: Outliers : 3.08 % Allowed : 16.67 % Favored : 80.25 % 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: 2.05 (0.25), residues: 1204 helix: 2.27 (0.19), residues: 786 sheet: 1.45 (0.63), residues: 75 loop : -0.88 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 168 HIS 0.009 0.001 HIS K 187 PHE 0.010 0.001 PHE K 219 TYR 0.011 0.001 TYR K 214 ARG 0.006 0.000 ARG F 23 *********************** 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 174 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 16 residues processed: 164 average time/residue: 1.8240 time to fit residues: 322.3700 Evaluate side-chains 150 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 1.364 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 5 average time/residue: 0.4744 time to fit residues: 4.6152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 498 HIS B 18 HIS B 25 ASN G 110 ASN H 46 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16739 Z= 0.271 Angle : 0.617 11.506 23881 Z= 0.347 Chirality : 0.036 0.215 2710 Planarity : 0.004 0.061 1998 Dihedral : 28.307 175.194 4606 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.66 % Favored : 97.18 % Rotamer: Outliers : 2.99 % Allowed : 17.15 % Favored : 79.87 % 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: 2.04 (0.25), residues: 1204 helix: 2.31 (0.19), residues: 782 sheet: 1.35 (0.69), residues: 65 loop : -0.90 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 168 HIS 0.014 0.001 HIS K 187 PHE 0.008 0.001 PHE B 61 TYR 0.013 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 171 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 140 time to evaluate : 1.469 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 18 residues processed: 163 average time/residue: 1.7545 time to fit residues: 309.0203 Evaluate side-chains 149 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 1.344 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 13 residues processed: 6 average time/residue: 0.6950 time to fit residues: 6.5374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 30.0000 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS C 73 ASN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16739 Z= 0.188 Angle : 0.601 10.581 23881 Z= 0.337 Chirality : 0.034 0.279 2710 Planarity : 0.004 0.062 1998 Dihedral : 28.211 174.766 4606 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.33 % Favored : 97.51 % Rotamer: Outliers : 1.83 % Allowed : 18.88 % Favored : 79.29 % 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: 2.16 (0.25), residues: 1204 helix: 2.42 (0.20), residues: 781 sheet: 1.39 (0.72), residues: 63 loop : -0.88 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 110 HIS 0.008 0.001 HIS K 187 PHE 0.006 0.001 PHE B 61 TYR 0.017 0.001 TYR K 214 ARG 0.006 0.000 ARG H 30 *********************** 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 165 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 1.344 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 161 average time/residue: 1.7957 time to fit residues: 311.2426 Evaluate side-chains 146 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 1.611 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.7423 time to fit residues: 4.2861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 187 HIS B 18 HIS E 68 GLN G 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16739 Z= 0.249 Angle : 0.626 10.687 23881 Z= 0.348 Chirality : 0.036 0.278 2710 Planarity : 0.004 0.058 1998 Dihedral : 28.279 174.602 4606 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.33 % Favored : 97.51 % Rotamer: Outliers : 2.12 % Allowed : 19.46 % Favored : 78.42 % 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: 2.10 (0.25), residues: 1204 helix: 2.37 (0.20), residues: 782 sheet: 1.46 (0.72), residues: 63 loop : -0.91 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 168 HIS 0.006 0.001 HIS K 187 PHE 0.007 0.001 PHE B 61 TYR 0.015 0.001 TYR F 88 ARG 0.008 0.000 ARG H 76 *********************** 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 164 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 1.308 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 159 average time/residue: 1.6996 time to fit residues: 291.9520 Evaluate side-chains 148 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.478 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 4 average time/residue: 0.1695 time to fit residues: 2.9214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 56 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 overall best weight: 5.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS E 68 GLN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16739 Z= 0.338 Angle : 0.669 11.464 23881 Z= 0.371 Chirality : 0.038 0.260 2710 Planarity : 0.004 0.057 1998 Dihedral : 28.376 174.027 4606 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.07 % Favored : 96.76 % Rotamer: Outliers : 1.64 % Allowed : 20.52 % Favored : 77.84 % 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: 1.92 (0.25), residues: 1204 helix: 2.24 (0.19), residues: 782 sheet: 1.42 (0.72), residues: 63 loop : -1.01 (0.30), 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 0.009 0.001 PHE H 62 TYR 0.022 0.001 TYR F 88 ARG 0.008 0.000 ARG H 76 *********************** 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 147 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 1.461 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 143 average time/residue: 1.7849 time to fit residues: 274.9994 Evaluate side-chains 140 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 1.365 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.3072 time to fit residues: 2.0960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 65 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS E 68 GLN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16739 Z= 0.212 Angle : 0.639 10.906 23881 Z= 0.352 Chirality : 0.035 0.266 2710 Planarity : 0.004 0.059 1998 Dihedral : 28.235 174.093 4606 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.41 % Favored : 97.43 % Rotamer: Outliers : 1.45 % Allowed : 20.52 % Favored : 78.03 % 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: 2.10 (0.25), residues: 1204 helix: 2.41 (0.20), residues: 781 sheet: 1.40 (0.71), residues: 63 loop : -0.99 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 110 HIS 0.006 0.001 HIS B 75 PHE 0.007 0.001 PHE D 67 TYR 0.020 0.001 TYR F 88 ARG 0.013 0.000 ARG F 23 ********************** 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 155 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 1.414 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 152 average time/residue: 1.7553 time to fit residues: 287.8043 Evaluate side-chains 145 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 1.373 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 3 average time/residue: 0.6397 time to fit residues: 3.9629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 106 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.0170 chunk 101 optimal weight: 0.9980 overall best weight: 1.1220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 207 GLN ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.055145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.035723 restraints weight = 74281.263| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 3.02 r_work: 0.2493 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16739 Z= 0.179 Angle : 0.629 10.875 23881 Z= 0.345 Chirality : 0.034 0.266 2710 Planarity : 0.004 0.059 1998 Dihedral : 28.180 174.298 4606 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.24 % Favored : 97.59 % Rotamer: Outliers : 1.35 % Allowed : 21.19 % Favored : 77.46 % 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: 2.28 (0.25), residues: 1204 helix: 2.56 (0.20), residues: 771 sheet: 1.25 (0.70), residues: 64 loop : -0.79 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 F 88 ARG 0.008 0.000 ARG H 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5375.51 seconds wall clock time: 95 minutes 54.56 seconds (5754.56 seconds total)