Starting phenix.real_space_refine on Sat Mar 16 12:09:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d1z_30551/03_2024/7d1z_30551.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d1z_30551/03_2024/7d1z_30551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d1z_30551/03_2024/7d1z_30551.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d1z_30551/03_2024/7d1z_30551.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d1z_30551/03_2024/7d1z_30551.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d1z_30551/03_2024/7d1z_30551.pdb" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1358 atoms to isotropic. 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 288 5.49 5 S 20 5.16 5 C 7463 2.51 5 N 2499 2.21 5 O 3057 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 72": "OD1" <-> "OD2" Residue "G ASP 90": "OD1" <-> "OD2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 51": "OD1" <-> "OD2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "K ARG 188": "NH1" <-> "NH2" Residue "K ARG 189": "NH1" <-> "NH2" Residue "K ARG 192": "NH1" <-> "NH2" Residue "K GLU 201": "OE1" <-> "OE2" Residue "K ASP 207": "OD1" <-> "OD2" Residue "K GLU 216": "OE1" <-> "OE2" Residue "K TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 285": "OD1" <-> "OD2" Residue "K GLU 289": "OE1" <-> "OE2" Residue "K ASP 311": "OD1" <-> "OD2" Residue "K TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 338": "OD1" <-> "OD2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13327 Number of models: 1 Model: "" Number of chains: 11 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: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1330 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 3, 'TRANS': 162} Chain: "F" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 699 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 7.62, per 1000 atoms: 0.57 Number of scatterers: 13327 At special positions: 0 Unit cell: (118.65, 99.75, 123.9, 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 20 16.00 P 288 15.00 O 3057 8.00 N 2499 7.00 C 7463 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: 7.19 Conformation dependent library (CDL) restraints added in 1.4 seconds 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 15 sheets defined 64.5% alpha, 5.6% beta 138 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 6.12 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.805A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.544A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.399A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.557A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (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 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.409A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.632A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'K' and resid 194 through 211 Processing helix chain 'K' and resid 254 through 264 removed outlier: 3.805A pdb=" N GLU K 259 " --> pdb=" O ALA K 255 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA K 260 " --> pdb=" O LYS K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 347 Processing helix chain 'K' and resid 348 through 352 removed outlier: 3.729A pdb=" N LYS K 351 " --> pdb=" O PRO K 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.595A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.784A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.876A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.807A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.863A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.199A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 218 through 223 removed outlier: 3.735A pdb=" N GLY K 227 " --> pdb=" O ILE K 223 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU K 330 " --> pdb=" O ALA K 232 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 240 through 244 removed outlier: 3.693A pdb=" N ASP K 240 " --> pdb=" O ALA K 322 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU K 320 " --> pdb=" O VAL K 242 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE K 321 " --> pdb=" O GLN K 306 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN K 306 " --> pdb=" O ILE K 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 248 through 250 removed outlier: 3.849A pdb=" N CYS K 283 " --> pdb=" O ILE K 250 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 276 through 277 Processing sheet with id=AB6, first strand: chain 'K' and resid 310 through 312 removed outlier: 3.966A pdb=" N VAL K 315 " --> pdb=" O ILE K 312 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 356 hydrogen bonds 712 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 5.45 Time building geometry restraints manager: 7.61 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: 2477 1.33 - 1.45: 4477 1.45 - 1.57: 6590 1.57 - 1.69: 576 1.69 - 1.81: 32 Bond restraints: 14152 Sorted by residual: bond pdb=" CA ALA F 76 " pdb=" C ALA F 76 " ideal model delta sigma weight residual 1.523 1.491 0.033 1.80e-02 3.09e+03 3.26e+00 bond pdb=" C LEU E 61 " pdb=" N ILE E 62 " ideal model delta sigma weight residual 1.334 1.315 0.019 1.29e-02 6.01e+03 2.08e+00 bond pdb=" CB ARG A 131 " pdb=" CG ARG A 131 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" CB ARG D 79 " pdb=" CG ARG D 79 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.60e+00 bond pdb=" CB THR C 59 " pdb=" CG2 THR C 59 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 ... (remaining 14147 not shown) Histogram of bond angle deviations from ideal: 80.88 - 91.50: 2 91.50 - 102.12: 331 102.12 - 112.74: 9026 112.74 - 123.36: 9604 123.36 - 133.97: 1376 Bond angle restraints: 20339 Sorted by residual: angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" OP1 DG J 21 " ideal model delta sigma weight residual 108.00 80.88 27.12 3.00e+00 1.11e-01 8.17e+01 angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 113.71 106.59 7.12 9.50e-01 1.11e+00 5.61e+01 angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" OP2 DG J 21 " ideal model delta sigma weight residual 108.00 87.24 20.76 3.00e+00 1.11e-01 4.79e+01 angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" O5' DG J 21 " ideal model delta sigma weight residual 104.00 97.98 6.02 1.50e+00 4.44e-01 1.61e+01 angle pdb=" C HIS F 75 " pdb=" N ALA F 76 " pdb=" CA ALA F 76 " ideal model delta sigma weight residual 122.31 114.58 7.73 2.00e+00 2.50e-01 1.49e+01 ... (remaining 20334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.83: 6034 31.83 - 63.67: 1699 63.67 - 95.50: 49 95.50 - 127.34: 0 127.34 - 159.17: 2 Dihedral angle restraints: 7784 sinusoidal: 5097 harmonic: 2687 Sorted by residual: dihedral pdb=" CA ALA G 12 " pdb=" C ALA G 12 " pdb=" N LYS G 13 " pdb=" CA LYS G 13 " ideal model delta harmonic sigma weight residual 180.00 -157.79 -22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual -180.00 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 60.83 159.17 1 3.50e+01 8.16e-04 1.52e+01 ... (remaining 7781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.410: 2296 0.410 - 0.819: 0 0.819 - 1.229: 0 1.229 - 1.639: 0 1.639 - 2.048: 1 Chirality restraints: 2297 Sorted by residual: chirality pdb=" P DG J 21 " pdb=" OP1 DG J 21 " pdb=" OP2 DG J 21 " pdb=" O5' DG J 21 " both_signs ideal model delta sigma weight residual True 2.35 0.30 2.05 2.00e-01 2.50e+01 1.05e+02 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA VAL A 117 " pdb=" N VAL A 117 " pdb=" C VAL A 117 " pdb=" CB VAL A 117 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 2294 not shown) Planarity restraints: 1578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " 0.028 2.00e-02 2.50e+03 1.22e-02 4.09e+00 pdb=" N9 DA I -35 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 28 " 0.027 2.00e-02 2.50e+03 1.12e-02 3.76e+00 pdb=" N9 DG I 28 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DG I 28 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 28 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG I 28 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 28 " 0.006 2.00e-02 2.50e+03 pdb=" O6 DG I 28 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 28 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 28 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 28 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 28 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " 0.026 2.00e-02 2.50e+03 1.09e-02 3.57e+00 pdb=" N9 DG I 26 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " -0.002 2.00e-02 2.50e+03 ... (remaining 1575 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 453 2.67 - 3.23: 11697 3.23 - 3.79: 25151 3.79 - 4.34: 32751 4.34 - 4.90: 46742 Nonbonded interactions: 116794 Sorted by model distance: nonbonded pdb=" O ALA K 255 " pdb=" OH TYR K 274 " model vdw 2.118 2.440 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.179 2.520 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.194 2.440 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.247 2.440 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.254 2.440 ... (remaining 116789 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 22 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 118) } ncs_group { reference = (chain 'D' and resid 33 through 124) 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 2.110 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 44.910 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 : 0.007 0.047 14152 Z= 0.440 Angle : 0.731 27.121 20339 Z= 0.423 Chirality : 0.058 2.048 2297 Planarity : 0.003 0.035 1578 Dihedral : 28.096 159.170 6056 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.24), residues: 911 helix: -0.32 (0.19), residues: 582 sheet: -3.86 (0.67), residues: 28 loop : -3.32 (0.28), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 349 HIS 0.006 0.001 HIS K 299 PHE 0.018 0.002 PHE K 275 TYR 0.015 0.002 TYR G 50 ARG 0.005 0.000 ARG G 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.097 Fit side-chains REVERT: A 59 GLU cc_start: 0.8147 (pp20) cc_final: 0.7642 (pp20) REVERT: B 88 TYR cc_start: 0.9097 (m-10) cc_final: 0.8748 (m-80) REVERT: C 75 LYS cc_start: 0.8629 (mttp) cc_final: 0.8408 (mtpt) REVERT: D 43 LYS cc_start: 0.8950 (mttt) cc_final: 0.8716 (mttm) REVERT: D 116 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8440 (ttmm) REVERT: E 50 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7909 (mt-10) REVERT: H 46 LYS cc_start: 0.9042 (mmtt) cc_final: 0.8561 (mmtm) REVERT: H 116 LYS cc_start: 0.8901 (tttt) cc_final: 0.8639 (ttmt) REVERT: K 288 ARG cc_start: 0.5444 (ttp80) cc_final: 0.5186 (ttp80) REVERT: K 334 TYR cc_start: 0.7132 (p90) cc_final: 0.6896 (p90) REVERT: F 31 LYS cc_start: 0.9004 (tttt) cc_final: 0.8697 (tttm) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.3880 time to fit residues: 100.0873 Evaluate side-chains 158 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 30.0000 chunk 87 optimal weight: 6.9990 chunk 48 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 0.3980 chunk 90 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS B 93 GLN D 82 HIS D 84 ASN D 95 GLN E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 84 ASN K 347 HIS F 75 HIS F 93 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14152 Z= 0.168 Angle : 0.619 26.938 20339 Z= 0.350 Chirality : 0.054 2.036 2297 Planarity : 0.003 0.030 1578 Dihedral : 30.599 160.726 4211 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.90 % Allowed : 12.53 % Favored : 86.56 % 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: 0.45 (0.27), residues: 911 helix: 1.69 (0.20), residues: 589 sheet: -3.19 (0.64), residues: 43 loop : -2.25 (0.32), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 349 HIS 0.004 0.001 HIS K 299 PHE 0.011 0.001 PHE E 67 TYR 0.013 0.001 TYR K 274 ARG 0.011 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 175 time to evaluate : 0.985 Fit side-chains REVERT: A 59 GLU cc_start: 0.8101 (pp20) cc_final: 0.7417 (pp20) REVERT: A 77 ASP cc_start: 0.8025 (t0) cc_final: 0.7674 (t0) REVERT: B 88 TYR cc_start: 0.8949 (m-10) cc_final: 0.8662 (m-80) REVERT: C 56 GLU cc_start: 0.8057 (tt0) cc_final: 0.7679 (tt0) REVERT: C 75 LYS cc_start: 0.8547 (mttp) cc_final: 0.8318 (mtpt) REVERT: D 43 LYS cc_start: 0.8882 (mttt) cc_final: 0.8674 (mttm) REVERT: E 52 ARG cc_start: 0.7765 (ttm110) cc_final: 0.7565 (mtp-110) REVERT: H 86 ARG cc_start: 0.8204 (mmt90) cc_final: 0.7750 (mmt90) REVERT: H 116 LYS cc_start: 0.8873 (tttt) cc_final: 0.8591 (ttmt) REVERT: H 121 TYR cc_start: 0.9196 (t80) cc_final: 0.8920 (t80) REVERT: K 218 MET cc_start: 0.3584 (mpp) cc_final: 0.2948 (mtm) REVERT: F 31 LYS cc_start: 0.8831 (tttt) cc_final: 0.8595 (tttm) REVERT: F 79 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8718 (mtpp) outliers start: 7 outliers final: 2 residues processed: 178 average time/residue: 0.3273 time to fit residues: 77.8793 Evaluate side-chains 158 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain K residue 320 LEU Chi-restraints excluded: chain F residue 79 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 0.0470 chunk 87 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 114 optimal weight: 0.5980 chunk 93 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 overall best weight: 3.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 49 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14152 Z= 0.334 Angle : 0.655 27.109 20339 Z= 0.364 Chirality : 0.056 2.027 2297 Planarity : 0.004 0.028 1578 Dihedral : 30.802 160.363 4211 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.55 % Allowed : 15.50 % Favored : 82.95 % 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: 0.94 (0.28), residues: 911 helix: 2.04 (0.21), residues: 587 sheet: -3.13 (0.64), residues: 43 loop : -1.92 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 349 HIS 0.004 0.001 HIS C 31 PHE 0.012 0.002 PHE G 25 TYR 0.014 0.001 TYR K 274 ARG 0.004 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 160 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8115 (t0) cc_final: 0.7906 (t0) REVERT: B 53 GLU cc_start: 0.7892 (tp30) cc_final: 0.7687 (tp30) REVERT: B 88 TYR cc_start: 0.9004 (m-10) cc_final: 0.8694 (m-80) REVERT: C 56 GLU cc_start: 0.8068 (tt0) cc_final: 0.7728 (tt0) REVERT: D 71 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7350 (tm-30) REVERT: H 116 LYS cc_start: 0.8868 (tttt) cc_final: 0.8590 (ttmt) REVERT: K 208 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.6001 (tm-30) REVERT: F 31 LYS cc_start: 0.8949 (tttt) cc_final: 0.8691 (tttm) REVERT: F 79 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8839 (mtpp) outliers start: 12 outliers final: 8 residues processed: 164 average time/residue: 0.3249 time to fit residues: 71.4581 Evaluate side-chains 162 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 152 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain F residue 79 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 50.0000 chunk 30 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14152 Z= 0.174 Angle : 0.610 27.165 20339 Z= 0.341 Chirality : 0.054 2.029 2297 Planarity : 0.003 0.032 1578 Dihedral : 30.527 161.717 4211 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.42 % Allowed : 16.15 % Favored : 82.43 % 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: 1.53 (0.28), residues: 911 helix: 2.40 (0.21), residues: 590 sheet: -2.87 (0.67), residues: 46 loop : -1.46 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 349 HIS 0.004 0.001 HIS K 299 PHE 0.011 0.001 PHE E 67 TYR 0.015 0.001 TYR H 40 ARG 0.006 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 173 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7996 (t0) cc_final: 0.7614 (t0) REVERT: B 88 TYR cc_start: 0.8947 (m-10) cc_final: 0.8743 (m-80) REVERT: C 56 GLU cc_start: 0.8079 (tt0) cc_final: 0.7736 (tt0) REVERT: D 71 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7314 (tm-30) REVERT: H 37 TYR cc_start: 0.9351 (m-80) cc_final: 0.9077 (m-80) REVERT: H 76 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7579 (mm-30) REVERT: H 86 ARG cc_start: 0.8257 (mmt90) cc_final: 0.7763 (mmt90) REVERT: H 116 LYS cc_start: 0.8832 (tttt) cc_final: 0.8549 (ttmt) REVERT: H 121 TYR cc_start: 0.9177 (t80) cc_final: 0.8884 (t80) REVERT: K 208 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.6075 (tm-30) REVERT: F 31 LYS cc_start: 0.8915 (tttt) cc_final: 0.8665 (tttm) REVERT: F 79 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8656 (mtpp) outliers start: 11 outliers final: 7 residues processed: 178 average time/residue: 0.3135 time to fit residues: 75.7019 Evaluate side-chains 170 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 161 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain F residue 79 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 0.0670 chunk 95 optimal weight: 40.0000 chunk 77 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 overall best weight: 2.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14152 Z= 0.275 Angle : 0.634 27.144 20339 Z= 0.351 Chirality : 0.055 2.022 2297 Planarity : 0.004 0.031 1578 Dihedral : 30.619 160.924 4211 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.33 % Allowed : 16.67 % Favored : 81.01 % 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: 1.62 (0.28), residues: 911 helix: 2.44 (0.21), residues: 587 sheet: -2.61 (0.71), residues: 46 loop : -1.36 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 349 HIS 0.004 0.001 HIS C 31 PHE 0.010 0.002 PHE E 67 TYR 0.014 0.001 TYR K 274 ARG 0.006 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 153 time to evaluate : 1.110 Fit side-chains REVERT: A 77 ASP cc_start: 0.8070 (t0) cc_final: 0.7648 (t0) REVERT: B 88 TYR cc_start: 0.9038 (m-10) cc_final: 0.8667 (m-80) REVERT: C 56 GLU cc_start: 0.8088 (tt0) cc_final: 0.7742 (tt0) REVERT: D 71 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7360 (tm-30) REVERT: H 37 TYR cc_start: 0.9387 (m-80) cc_final: 0.9114 (m-80) REVERT: H 86 ARG cc_start: 0.8276 (mmt90) cc_final: 0.7806 (mmt90) REVERT: H 116 LYS cc_start: 0.8823 (tttt) cc_final: 0.8580 (ttpt) REVERT: H 121 TYR cc_start: 0.9198 (t80) cc_final: 0.8952 (t80) REVERT: K 208 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.5953 (tm-30) REVERT: F 31 LYS cc_start: 0.8956 (tttt) cc_final: 0.8705 (tttm) REVERT: F 79 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8732 (mtpp) outliers start: 18 outliers final: 13 residues processed: 165 average time/residue: 0.3266 time to fit residues: 73.1218 Evaluate side-chains 171 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 156 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 221 ASP Chi-restraints excluded: chain F residue 79 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14152 Z= 0.352 Angle : 0.659 27.122 20339 Z= 0.363 Chirality : 0.056 2.023 2297 Planarity : 0.004 0.027 1578 Dihedral : 30.738 161.365 4211 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.71 % Allowed : 17.18 % Favored : 80.10 % 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: 1.54 (0.28), residues: 911 helix: 2.35 (0.21), residues: 585 sheet: -2.54 (0.71), residues: 46 loop : -1.31 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 349 HIS 0.004 0.001 HIS H 49 PHE 0.011 0.002 PHE C 25 TYR 0.015 0.001 TYR H 40 ARG 0.003 0.000 ARG K 188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 1.170 Fit side-chains REVERT: A 42 ARG cc_start: 0.7697 (mtp85) cc_final: 0.7494 (ptp-110) REVERT: A 77 ASP cc_start: 0.8149 (t0) cc_final: 0.7865 (t0) REVERT: B 53 GLU cc_start: 0.7902 (tp30) cc_final: 0.7701 (tp30) REVERT: B 88 TYR cc_start: 0.9024 (m-10) cc_final: 0.8603 (m-80) REVERT: C 36 LYS cc_start: 0.8900 (mttp) cc_final: 0.8685 (mttp) REVERT: C 56 GLU cc_start: 0.8061 (tt0) cc_final: 0.7742 (tt0) REVERT: D 86 ARG cc_start: 0.8534 (mmt90) cc_final: 0.8275 (mmt90) REVERT: E 50 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7871 (mt-10) REVERT: H 86 ARG cc_start: 0.8300 (mmt90) cc_final: 0.7845 (mmt90) REVERT: H 116 LYS cc_start: 0.8840 (tttt) cc_final: 0.8558 (ttmt) REVERT: K 208 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5896 (tm-30) REVERT: F 31 LYS cc_start: 0.8986 (tttt) cc_final: 0.8716 (tttm) REVERT: F 79 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8833 (mtpp) outliers start: 21 outliers final: 16 residues processed: 167 average time/residue: 0.3215 time to fit residues: 72.9329 Evaluate side-chains 168 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 221 ASP Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 79 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 94 optimal weight: 30.0000 chunk 62 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14152 Z= 0.206 Angle : 0.629 27.032 20339 Z= 0.347 Chirality : 0.055 2.030 2297 Planarity : 0.003 0.029 1578 Dihedral : 30.674 161.583 4211 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.58 % Allowed : 17.31 % Favored : 80.10 % 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: 1.65 (0.28), residues: 911 helix: 2.43 (0.21), residues: 585 sheet: -2.53 (0.72), residues: 46 loop : -1.24 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 349 HIS 0.003 0.001 HIS C 31 PHE 0.010 0.001 PHE E 67 TYR 0.016 0.001 TYR H 40 ARG 0.003 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 1.059 Fit side-chains REVERT: A 42 ARG cc_start: 0.7684 (mtp85) cc_final: 0.7470 (ptp-110) REVERT: A 77 ASP cc_start: 0.8063 (t0) cc_final: 0.7811 (t0) REVERT: B 84 MET cc_start: 0.8656 (mmm) cc_final: 0.8368 (tpt) REVERT: C 56 GLU cc_start: 0.8032 (tt0) cc_final: 0.7720 (tt0) REVERT: D 71 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7398 (tm-30) REVERT: D 86 ARG cc_start: 0.8512 (mmt90) cc_final: 0.8275 (mmt90) REVERT: H 37 TYR cc_start: 0.9397 (m-80) cc_final: 0.9139 (m-80) REVERT: H 86 ARG cc_start: 0.8283 (mmt90) cc_final: 0.7829 (mmt90) REVERT: H 116 LYS cc_start: 0.8813 (tttt) cc_final: 0.8569 (ttpt) REVERT: H 121 TYR cc_start: 0.9188 (t80) cc_final: 0.8933 (t80) REVERT: K 208 GLU cc_start: 0.6269 (OUTLIER) cc_final: 0.5895 (tm-30) REVERT: F 31 LYS cc_start: 0.8938 (tttt) cc_final: 0.8705 (tttm) REVERT: F 79 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8746 (mtpp) outliers start: 20 outliers final: 17 residues processed: 161 average time/residue: 0.3042 time to fit residues: 66.8054 Evaluate side-chains 165 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 221 ASP Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 79 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 101 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14152 Z= 0.282 Angle : 0.642 27.067 20339 Z= 0.353 Chirality : 0.055 2.024 2297 Planarity : 0.004 0.030 1578 Dihedral : 30.597 161.390 4211 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.84 % Allowed : 17.70 % Favored : 79.46 % 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: 1.68 (0.28), residues: 911 helix: 2.46 (0.21), residues: 585 sheet: -2.55 (0.72), residues: 46 loop : -1.24 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 349 HIS 0.004 0.001 HIS C 31 PHE 0.011 0.002 PHE E 67 TYR 0.028 0.002 TYR B 88 ARG 0.010 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 1.048 Fit side-chains REVERT: A 77 ASP cc_start: 0.8068 (t0) cc_final: 0.7647 (t0) REVERT: C 36 LYS cc_start: 0.8836 (mttp) cc_final: 0.8427 (mttp) REVERT: C 56 GLU cc_start: 0.8068 (tt0) cc_final: 0.7728 (tt0) REVERT: D 86 ARG cc_start: 0.8536 (mmt90) cc_final: 0.8320 (mmt90) REVERT: H 86 ARG cc_start: 0.8298 (mmt90) cc_final: 0.7845 (mmt90) REVERT: H 116 LYS cc_start: 0.8821 (tttt) cc_final: 0.8571 (ttpt) REVERT: H 121 TYR cc_start: 0.9201 (t80) cc_final: 0.8944 (t80) REVERT: K 208 GLU cc_start: 0.6273 (OUTLIER) cc_final: 0.5911 (tm-30) REVERT: F 31 LYS cc_start: 0.8960 (tttt) cc_final: 0.8721 (tttm) REVERT: F 79 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8803 (mtpp) outliers start: 22 outliers final: 20 residues processed: 165 average time/residue: 0.3124 time to fit residues: 70.2564 Evaluate side-chains 172 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 221 ASP Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 79 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 40.0000 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 94 optimal weight: 50.0000 chunk 98 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14152 Z= 0.258 Angle : 0.641 27.135 20339 Z= 0.352 Chirality : 0.055 2.022 2297 Planarity : 0.004 0.032 1578 Dihedral : 30.594 161.472 4211 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.71 % Allowed : 18.09 % Favored : 79.20 % 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: 1.72 (0.28), residues: 911 helix: 2.49 (0.21), residues: 585 sheet: -2.53 (0.73), residues: 46 loop : -1.23 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 349 HIS 0.003 0.001 HIS C 31 PHE 0.011 0.002 PHE E 67 TYR 0.047 0.002 TYR B 88 ARG 0.008 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 149 time to evaluate : 1.133 Fit side-chains REVERT: A 77 ASP cc_start: 0.8063 (t0) cc_final: 0.7643 (t0) REVERT: C 36 LYS cc_start: 0.8828 (mttp) cc_final: 0.8447 (mttp) REVERT: C 56 GLU cc_start: 0.8066 (tt0) cc_final: 0.7731 (tt0) REVERT: D 86 ARG cc_start: 0.8526 (mmt90) cc_final: 0.8317 (mmt90) REVERT: H 86 ARG cc_start: 0.8290 (mmt90) cc_final: 0.7837 (mmt90) REVERT: H 116 LYS cc_start: 0.8817 (tttt) cc_final: 0.8569 (ttpt) REVERT: H 121 TYR cc_start: 0.9198 (t80) cc_final: 0.8942 (t80) REVERT: K 208 GLU cc_start: 0.6271 (OUTLIER) cc_final: 0.5912 (tm-30) REVERT: F 31 LYS cc_start: 0.8958 (tttt) cc_final: 0.8722 (tttm) REVERT: F 79 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8803 (mtpp) outliers start: 21 outliers final: 19 residues processed: 162 average time/residue: 0.3118 time to fit residues: 68.8332 Evaluate side-chains 170 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 149 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 221 ASP Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 79 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 106 optimal weight: 50.0000 chunk 92 optimal weight: 9.9990 chunk 9 optimal weight: 0.0070 chunk 71 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14152 Z= 0.189 Angle : 0.630 27.194 20339 Z= 0.347 Chirality : 0.055 2.023 2297 Planarity : 0.004 0.040 1578 Dihedral : 30.586 161.644 4211 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.58 % Allowed : 18.60 % Favored : 78.81 % 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: 1.75 (0.28), residues: 911 helix: 2.52 (0.21), residues: 585 sheet: -2.50 (0.74), residues: 46 loop : -1.21 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 349 HIS 0.003 0.001 HIS K 299 PHE 0.011 0.001 PHE E 67 TYR 0.061 0.002 TYR B 88 ARG 0.007 0.000 ARG E 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 1.078 Fit side-chains REVERT: C 36 LYS cc_start: 0.8816 (mttp) cc_final: 0.8471 (mttp) REVERT: C 56 GLU cc_start: 0.8041 (tt0) cc_final: 0.7711 (tt0) REVERT: H 37 TYR cc_start: 0.9396 (m-80) cc_final: 0.9102 (m-80) REVERT: H 86 ARG cc_start: 0.8268 (mmt90) cc_final: 0.7871 (mmt90) REVERT: H 116 LYS cc_start: 0.8805 (tttt) cc_final: 0.8558 (ttpt) REVERT: H 121 TYR cc_start: 0.9188 (t80) cc_final: 0.8935 (t80) REVERT: K 208 GLU cc_start: 0.6273 (OUTLIER) cc_final: 0.5910 (tm-30) REVERT: F 31 LYS cc_start: 0.8947 (tttt) cc_final: 0.8714 (tttm) REVERT: F 79 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8738 (mtpp) outliers start: 20 outliers final: 18 residues processed: 164 average time/residue: 0.2971 time to fit residues: 66.9203 Evaluate side-chains 166 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 221 ASP Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 79 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 94 optimal weight: 40.0000 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS G 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.148794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.089253 restraints weight = 20709.998| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.91 r_work: 0.2881 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14152 Z= 0.302 Angle : 0.646 27.147 20339 Z= 0.354 Chirality : 0.055 2.019 2297 Planarity : 0.004 0.034 1578 Dihedral : 30.566 161.786 4211 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.84 % Allowed : 18.35 % Favored : 78.81 % 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: 1.68 (0.28), residues: 911 helix: 2.45 (0.21), residues: 585 sheet: -2.50 (0.74), residues: 46 loop : -1.22 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 349 HIS 0.003 0.001 HIS C 31 PHE 0.010 0.002 PHE E 67 TYR 0.059 0.002 TYR B 88 ARG 0.008 0.000 ARG D 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2560.49 seconds wall clock time: 46 minutes 47.40 seconds (2807.40 seconds total)