Starting phenix.real_space_refine on Sat Nov 16 19:24:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fya_29562/11_2024/8fya_29562.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fya_29562/11_2024/8fya_29562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fya_29562/11_2024/8fya_29562.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fya_29562/11_2024/8fya_29562.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fya_29562/11_2024/8fya_29562.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fya_29562/11_2024/8fya_29562.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.039 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 611 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 57 5.49 5 S 31 5.16 5 C 7056 2.51 5 N 2060 2.21 5 O 2229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11433 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 746 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "B" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2295 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain: "C" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2388 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain breaks: 1 Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 746 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "E" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1865 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 8, 'TRANS': 232} Chain breaks: 1 Chain: "F" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2186 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain: "G" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 573 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "H" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Time building chain proxies: 7.48, per 1000 atoms: 0.65 Number of scatterers: 11433 At special positions: 0 Unit cell: (93.66, 90.315, 142.72, 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 31 16.00 P 57 15.00 O 2229 8.00 N 2060 7.00 C 7056 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 - 3.00 Amino acid : True - 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: 3.08 Conformation dependent library (CDL) restraints added in 1.5 seconds 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2410 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 8 sheets defined 51.2% alpha, 15.4% beta 20 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 4.37 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 20 through 22 No H-bonds generated for 'chain 'A' and resid 20 through 22' Processing helix chain 'A' and resid 36 through 49 removed outlier: 3.823A pdb=" N GLU A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 55 Processing helix chain 'B' and resid 67 through 77 Processing helix chain 'B' and resid 86 through 89 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 102 through 114 removed outlier: 3.982A pdb=" N ASN B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 129 Processing helix chain 'B' and resid 139 through 163 Processing helix chain 'B' and resid 180 through 205 Processing helix chain 'B' and resid 219 through 231 removed outlier: 3.872A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 250 through 265 removed outlier: 4.343A pdb=" N ASP B 265 " --> pdb=" O ASP B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 280 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.871A pdb=" N ARG C 21 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 53 No H-bonds generated for 'chain 'C' and resid 51 through 53' Processing helix chain 'C' and resid 68 through 77 Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.517A pdb=" N ASN C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 130 Processing helix chain 'C' and resid 139 through 163 Processing helix chain 'C' and resid 180 through 205 Processing helix chain 'C' and resid 219 through 231 removed outlier: 3.722A pdb=" N LEU C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.507A pdb=" N LEU C 254 " --> pdb=" O ASP C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 280 removed outlier: 3.539A pdb=" N LEU C 280 " --> pdb=" O LEU C 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 19 Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 36 through 49 Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 68 through 77 Processing helix chain 'E' and resid 86 through 89 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 102 through 114 removed outlier: 3.999A pdb=" N ASN E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 129 removed outlier: 3.581A pdb=" N ARG E 118 " --> pdb=" O ASN E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 205 Processing helix chain 'E' and resid 219 through 231 removed outlier: 3.806A pdb=" N LEU E 228 " --> pdb=" O ASP E 224 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA E 231 " --> pdb=" O ASP E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 245 Processing helix chain 'E' and resid 250 through 265 removed outlier: 4.451A pdb=" N ASP E 265 " --> pdb=" O ASP E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 280 removed outlier: 3.648A pdb=" N LEU E 280 " --> pdb=" O LEU E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 303 Processing helix chain 'F' and resid 51 through 53 No H-bonds generated for 'chain 'F' and resid 51 through 53' Processing helix chain 'F' and resid 68 through 78 Processing helix chain 'F' and resid 102 through 114 removed outlier: 3.881A pdb=" N ASN F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 130 Processing helix chain 'F' and resid 139 through 163 Processing helix chain 'F' and resid 180 through 205 Processing helix chain 'F' and resid 219 through 231 removed outlier: 3.758A pdb=" N LEU F 228 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR F 229 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA F 231 " --> pdb=" O ASP F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 245 Processing helix chain 'F' and resid 250 through 267 Processing helix chain 'F' and resid 267 through 280 removed outlier: 3.868A pdb=" N LEU F 280 " --> pdb=" O LEU F 276 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 5.798A pdb=" N GLU A 25 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL A 32 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA A 27 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N MET A 3 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA A 61 " --> pdb=" O MET A 3 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 56 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 5.461A pdb=" N ILE A 88 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG F 49 " --> pdb=" O ILE A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 289 through 291 removed outlier: 8.105A pdb=" N VAL B 57 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR B 23 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU B 59 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE B 25 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU B 58 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL B 84 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU B 60 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER B 94 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP B 83 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR C 91 " --> pdb=" O TRP C 83 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR C 23 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LEU C 59 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE C 25 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 308 through 310 removed outlier: 3.901A pdb=" N ASN B 308 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA B 30 " --> pdb=" O ASP B 65 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG C 34 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG C 49 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE D 88 " --> pdb=" O ARG C 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 214 through 215 Processing sheet with id=AA6, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.287A pdb=" N VAL D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N MET D 3 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA D 61 " --> pdb=" O MET D 3 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 289 through 291 removed outlier: 7.715A pdb=" N VAL E 57 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N THR E 23 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU E 59 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE E 25 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR F 91 " --> pdb=" O TRP F 83 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR F 23 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU F 59 " --> pdb=" O THR F 23 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE F 25 " --> pdb=" O LEU F 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 308 through 310 removed outlier: 7.598A pdb=" N ILE E 32 " --> pdb=" O SER E 67 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3360 1.34 - 1.45: 2039 1.45 - 1.57: 6193 1.57 - 1.69: 114 1.69 - 1.81: 60 Bond restraints: 11766 Sorted by residual: bond pdb=" CB ILE A 26 " pdb=" CG2 ILE A 26 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" C3' DC G 8 " pdb=" O3' DC G 8 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.36e+00 bond pdb=" C4' DG G 24 " pdb=" O4' DG G 24 " ideal model delta sigma weight residual 1.450 1.431 0.019 2.00e-02 2.50e+03 9.49e-01 bond pdb=" C3' DT H 9 " pdb=" C2' DT H 9 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.00e-02 2.50e+03 8.78e-01 bond pdb=" CA GLN C 87 " pdb=" CB GLN C 87 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.70e-02 3.46e+03 7.95e-01 ... (remaining 11761 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 15632 1.20 - 2.41: 432 2.41 - 3.61: 87 3.61 - 4.81: 12 4.81 - 6.02: 11 Bond angle restraints: 16174 Sorted by residual: angle pdb=" CA GLN C 87 " pdb=" CB GLN C 87 " pdb=" CG GLN C 87 " ideal model delta sigma weight residual 114.10 119.22 -5.12 2.00e+00 2.50e-01 6.55e+00 angle pdb=" CA GLN F 87 " pdb=" CB GLN F 87 " pdb=" CG GLN F 87 " ideal model delta sigma weight residual 114.10 118.53 -4.43 2.00e+00 2.50e-01 4.90e+00 angle pdb=" C ALA E 99 " pdb=" N ARG E 100 " pdb=" CA ARG E 100 " ideal model delta sigma weight residual 121.54 125.35 -3.81 1.91e+00 2.74e-01 3.97e+00 angle pdb=" N VAL E 35 " pdb=" CA VAL E 35 " pdb=" C VAL E 35 " ideal model delta sigma weight residual 109.17 106.16 3.01 1.54e+00 4.22e-01 3.81e+00 angle pdb=" CA GLY B 179 " pdb=" C GLY B 179 " pdb=" N ASP B 180 " ideal model delta sigma weight residual 114.48 116.79 -2.31 1.19e+00 7.06e-01 3.77e+00 ... (remaining 16169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 6645 35.99 - 71.98: 279 71.98 - 107.97: 9 107.97 - 143.96: 0 143.96 - 179.96: 1 Dihedral angle restraints: 6934 sinusoidal: 3177 harmonic: 3757 Sorted by residual: dihedral pdb=" C4' DC G 8 " pdb=" C3' DC G 8 " pdb=" O3' DC G 8 " pdb=" P DT G 9 " ideal model delta sinusoidal sigma weight residual -140.00 39.96 -179.96 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA ARG E 34 " pdb=" C ARG E 34 " pdb=" N VAL E 35 " pdb=" CA VAL E 35 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLU F 19 " pdb=" C GLU F 19 " pdb=" N ASP F 20 " pdb=" CA ASP F 20 " ideal model delta harmonic sigma weight residual -180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 6931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1317 0.037 - 0.074: 375 0.074 - 0.110: 100 0.110 - 0.147: 29 0.147 - 0.184: 2 Chirality restraints: 1823 Sorted by residual: chirality pdb=" CB VAL C 191 " pdb=" CA VAL C 191 " pdb=" CG1 VAL C 191 " pdb=" CG2 VAL C 191 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA ILE B 50 " pdb=" N ILE B 50 " pdb=" C ILE B 50 " pdb=" CB ILE B 50 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CB THR E 113 " pdb=" CA THR E 113 " pdb=" OG1 THR E 113 " pdb=" CG2 THR E 113 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 1820 not shown) Planarity restraints: 1879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 172 " -0.025 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO B 173 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 173 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 173 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 85 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO D 86 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 86 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 86 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 31 " -0.009 2.00e-02 2.50e+03 9.37e-03 1.76e+00 pdb=" CG TYR A 31 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 31 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 31 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 31 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 31 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 31 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 31 " 0.000 2.00e-02 2.50e+03 ... (remaining 1876 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 492 2.72 - 3.26: 11148 3.26 - 3.81: 20453 3.81 - 4.35: 25083 4.35 - 4.90: 41575 Nonbonded interactions: 98751 Sorted by model distance: nonbonded pdb=" OH TYR F 229 " pdb=" OD2 ASP F 275 " model vdw 2.172 3.040 nonbonded pdb=" OH TYR E 229 " pdb=" OD2 ASP E 275 " model vdw 2.174 3.040 nonbonded pdb=" OG1 THR A 7 " pdb=" OG SER A 57 " model vdw 2.201 3.040 nonbonded pdb=" O LEU E 295 " pdb=" OH TYR E 309 " model vdw 2.207 3.040 nonbonded pdb=" O GLY D 17 " pdb=" OG1 THR D 20 " model vdw 2.213 3.040 ... (remaining 98746 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = (chain 'B' and resid 20 through 283) selection = (chain 'C' and resid 20 through 283) selection = (chain 'F' and resid 20 through 283) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.450 Find NCS groups from input model: 0.470 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: 0.010 Load rotamer database and sin/cos tables:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 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 : 0.003 0.042 11766 Z= 0.196 Angle : 0.511 6.016 16174 Z= 0.279 Chirality : 0.040 0.184 1823 Planarity : 0.003 0.047 1879 Dihedral : 16.989 179.956 4524 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.09 % Allowed : 0.00 % Favored : 99.91 % 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: 1.24 (0.24), residues: 1288 helix: 2.15 (0.21), residues: 601 sheet: 0.05 (0.40), residues: 201 loop : -0.49 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 83 HIS 0.010 0.001 HIS B 29 PHE 0.008 0.001 PHE A 35 TYR 0.022 0.001 TYR A 31 ARG 0.008 0.000 ARG F 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 244 time to evaluate : 1.152 Fit side-chains REVERT: A 58 MET cc_start: 0.8838 (ttp) cc_final: 0.8525 (ttp) REVERT: C 257 LEU cc_start: 0.8442 (tt) cc_final: 0.7867 (tp) REVERT: F 254 LEU cc_start: 0.8294 (tt) cc_final: 0.8082 (tt) outliers start: 1 outliers final: 1 residues processed: 244 average time/residue: 1.2958 time to fit residues: 341.0304 Evaluate side-chains 181 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 54 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN C 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11766 Z= 0.293 Angle : 0.575 7.525 16174 Z= 0.313 Chirality : 0.043 0.174 1823 Planarity : 0.004 0.038 1879 Dihedral : 18.489 176.845 2097 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.81 % Allowed : 12.29 % Favored : 84.90 % 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: 1.10 (0.24), residues: 1288 helix: 2.08 (0.21), residues: 608 sheet: -0.21 (0.38), residues: 206 loop : -0.57 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 296 HIS 0.013 0.001 HIS B 29 PHE 0.014 0.001 PHE D 89 TYR 0.016 0.001 TYR A 31 ARG 0.006 0.000 ARG C 258 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 1.227 Fit side-chains REVERT: A 58 MET cc_start: 0.8960 (ttp) cc_final: 0.8756 (ttp) REVERT: C 128 MET cc_start: 0.7473 (mtm) cc_final: 0.7269 (mtm) REVERT: C 257 LEU cc_start: 0.8406 (tt) cc_final: 0.8032 (tp) REVERT: E 31 LYS cc_start: 0.7957 (mtpm) cc_final: 0.7633 (mttp) REVERT: E 289 GLU cc_start: 0.6311 (OUTLIER) cc_final: 0.5147 (pp20) outliers start: 30 outliers final: 14 residues processed: 208 average time/residue: 1.1340 time to fit residues: 256.8278 Evaluate side-chains 183 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 7.9990 chunk 37 optimal weight: 0.2980 chunk 101 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN C 308 ASN D 48 GLN E 29 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11766 Z= 0.212 Angle : 0.519 7.082 16174 Z= 0.283 Chirality : 0.041 0.188 1823 Planarity : 0.003 0.035 1879 Dihedral : 18.439 178.033 2095 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.94 % Allowed : 14.17 % Favored : 81.89 % 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: 1.26 (0.24), residues: 1288 helix: 2.25 (0.21), residues: 610 sheet: -0.16 (0.38), residues: 201 loop : -0.58 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 296 HIS 0.009 0.001 HIS B 29 PHE 0.011 0.001 PHE D 89 TYR 0.013 0.001 TYR D 31 ARG 0.006 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.8999 (ttp) cc_final: 0.8770 (ttp) REVERT: C 257 LEU cc_start: 0.8488 (tt) cc_final: 0.8126 (tp) REVERT: D 23 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8279 (ptm) REVERT: E 31 LYS cc_start: 0.7877 (mtpm) cc_final: 0.7561 (mttp) REVERT: E 33 ASN cc_start: 0.7627 (OUTLIER) cc_final: 0.7385 (m-40) REVERT: E 270 LYS cc_start: 0.7890 (mtpp) cc_final: 0.7639 (mtpt) REVERT: F 138 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6062 (tt) REVERT: F 253 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7715 (tm-30) REVERT: F 277 GLN cc_start: 0.8070 (tt0) cc_final: 0.7867 (tt0) outliers start: 42 outliers final: 17 residues processed: 208 average time/residue: 1.2845 time to fit residues: 289.3070 Evaluate side-chains 196 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN E 29 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11766 Z= 0.306 Angle : 0.557 6.617 16174 Z= 0.301 Chirality : 0.043 0.192 1823 Planarity : 0.004 0.034 1879 Dihedral : 18.666 177.542 2095 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.22 % Allowed : 15.01 % Favored : 80.77 % 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: 1.13 (0.24), residues: 1288 helix: 2.16 (0.21), residues: 610 sheet: -0.42 (0.36), residues: 206 loop : -0.53 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 296 HIS 0.010 0.001 HIS B 29 PHE 0.013 0.001 PHE D 89 TYR 0.010 0.001 TYR B 194 ARG 0.006 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 1.241 Fit side-chains REVERT: A 58 MET cc_start: 0.9038 (ttp) cc_final: 0.8702 (ttp) REVERT: B 33 ASN cc_start: 0.8177 (OUTLIER) cc_final: 0.7917 (m-40) REVERT: C 232 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7522 (pp20) REVERT: C 257 LEU cc_start: 0.8554 (tt) cc_final: 0.8294 (tp) REVERT: D 1 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.6318 (mtm) REVERT: D 23 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8266 (ptm) REVERT: E 31 LYS cc_start: 0.7966 (mtpm) cc_final: 0.7719 (mttm) REVERT: E 33 ASN cc_start: 0.7655 (OUTLIER) cc_final: 0.7395 (m-40) REVERT: E 227 ASP cc_start: 0.8344 (m-30) cc_final: 0.8083 (m-30) REVERT: E 270 LYS cc_start: 0.7915 (mtpp) cc_final: 0.7671 (mtpt) REVERT: E 289 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.5319 (pp20) REVERT: F 138 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6065 (tt) outliers start: 45 outliers final: 22 residues processed: 205 average time/residue: 1.2003 time to fit residues: 267.2982 Evaluate side-chains 193 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 110 optimal weight: 0.0040 chunk 89 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11766 Z= 0.241 Angle : 0.527 6.618 16174 Z= 0.287 Chirality : 0.042 0.176 1823 Planarity : 0.004 0.033 1879 Dihedral : 18.629 177.691 2095 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.03 % Allowed : 16.14 % Favored : 79.83 % 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: 1.21 (0.24), residues: 1288 helix: 2.24 (0.21), residues: 609 sheet: -0.31 (0.36), residues: 206 loop : -0.55 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 296 HIS 0.007 0.001 HIS B 29 PHE 0.011 0.001 PHE D 89 TYR 0.008 0.001 TYR E 229 ARG 0.006 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 181 time to evaluate : 1.137 Fit side-chains REVERT: A 58 MET cc_start: 0.9010 (ttp) cc_final: 0.8646 (ttp) REVERT: A 71 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8134 (mt) REVERT: B 172 ASN cc_start: 0.8710 (t0) cc_final: 0.8366 (t0) REVERT: C 232 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7492 (pp20) REVERT: C 257 LEU cc_start: 0.8497 (tt) cc_final: 0.8254 (tp) REVERT: D 3 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7473 (ttt) REVERT: D 23 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8232 (ptm) REVERT: E 31 LYS cc_start: 0.7918 (mtpm) cc_final: 0.7623 (mttt) REVERT: E 33 ASN cc_start: 0.7643 (OUTLIER) cc_final: 0.7395 (m-40) REVERT: E 227 ASP cc_start: 0.8336 (m-30) cc_final: 0.8063 (m-30) REVERT: E 270 LYS cc_start: 0.7920 (mtpp) cc_final: 0.7668 (mtpt) REVERT: E 289 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.5197 (pp20) outliers start: 43 outliers final: 21 residues processed: 204 average time/residue: 1.2017 time to fit residues: 266.1331 Evaluate side-chains 197 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 48 GLN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11766 Z= 0.349 Angle : 0.581 6.784 16174 Z= 0.313 Chirality : 0.044 0.205 1823 Planarity : 0.004 0.034 1879 Dihedral : 18.768 177.371 2095 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.22 % Allowed : 17.26 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.23), residues: 1288 helix: 2.05 (0.20), residues: 610 sheet: -0.57 (0.35), residues: 211 loop : -0.62 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 296 HIS 0.008 0.001 HIS B 29 PHE 0.013 0.002 PHE D 89 TYR 0.011 0.002 TYR E 229 ARG 0.006 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 1.211 Fit side-chains REVERT: A 58 MET cc_start: 0.9005 (ttp) cc_final: 0.8672 (ttp) REVERT: A 71 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8153 (mt) REVERT: B 33 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7949 (m-40) REVERT: C 232 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7504 (pp20) REVERT: D 23 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8303 (ptm) REVERT: D 35 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: E 31 LYS cc_start: 0.7928 (mtpm) cc_final: 0.7557 (mttp) REVERT: E 33 ASN cc_start: 0.7667 (OUTLIER) cc_final: 0.7369 (m-40) REVERT: E 227 ASP cc_start: 0.8389 (m-30) cc_final: 0.8123 (m-30) REVERT: E 289 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.5360 (pp20) REVERT: F 72 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: F 103 ARG cc_start: 0.7651 (ttp80) cc_final: 0.7421 (ttp-170) REVERT: F 138 LEU cc_start: 0.7274 (tp) cc_final: 0.6970 (tt) outliers start: 45 outliers final: 26 residues processed: 199 average time/residue: 1.2058 time to fit residues: 260.5402 Evaluate side-chains 200 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11766 Z= 0.247 Angle : 0.545 6.966 16174 Z= 0.295 Chirality : 0.042 0.211 1823 Planarity : 0.004 0.044 1879 Dihedral : 18.675 177.331 2095 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.32 % Allowed : 17.73 % Favored : 77.95 % 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: 1.05 (0.24), residues: 1288 helix: 2.12 (0.21), residues: 610 sheet: -0.54 (0.36), residues: 207 loop : -0.59 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 296 HIS 0.006 0.001 HIS B 29 PHE 0.010 0.001 PHE D 89 TYR 0.009 0.001 TYR E 229 ARG 0.010 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 174 time to evaluate : 1.626 Fit side-chains REVERT: A 71 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8136 (mt) REVERT: B 33 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7935 (m-40) REVERT: B 172 ASN cc_start: 0.8715 (t0) cc_final: 0.8365 (t0) REVERT: C 232 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7771 (pp20) REVERT: D 23 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8220 (ptm) REVERT: D 35 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7764 (m-80) REVERT: E 31 LYS cc_start: 0.7864 (mtpm) cc_final: 0.7648 (mtpp) REVERT: E 33 ASN cc_start: 0.7605 (OUTLIER) cc_final: 0.7328 (m-40) REVERT: E 227 ASP cc_start: 0.8339 (m-30) cc_final: 0.8089 (m-30) REVERT: E 289 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.5249 (pp20) REVERT: F 23 THR cc_start: 0.8416 (m) cc_final: 0.8204 (p) REVERT: F 103 ARG cc_start: 0.7675 (ttp80) cc_final: 0.7459 (ttp-170) REVERT: F 138 LEU cc_start: 0.7321 (tp) cc_final: 0.7060 (tt) outliers start: 46 outliers final: 24 residues processed: 200 average time/residue: 1.2137 time to fit residues: 263.6574 Evaluate side-chains 201 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS F 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11766 Z= 0.244 Angle : 0.546 8.145 16174 Z= 0.295 Chirality : 0.042 0.221 1823 Planarity : 0.004 0.033 1879 Dihedral : 18.643 177.181 2095 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.94 % Allowed : 18.20 % Favored : 77.86 % 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: 1.08 (0.24), residues: 1288 helix: 2.16 (0.21), residues: 606 sheet: -0.65 (0.35), residues: 212 loop : -0.49 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 296 HIS 0.006 0.001 HIS B 29 PHE 0.010 0.001 PHE D 89 TYR 0.009 0.001 TYR E 229 ARG 0.006 0.000 ARG F 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 1.221 Fit side-chains REVERT: A 58 MET cc_start: 0.8981 (ttp) cc_final: 0.8524 (ttp) REVERT: A 71 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8117 (mt) REVERT: B 33 ASN cc_start: 0.8174 (OUTLIER) cc_final: 0.7941 (m-40) REVERT: B 172 ASN cc_start: 0.8714 (t0) cc_final: 0.8359 (t0) REVERT: C 232 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7768 (pp20) REVERT: D 3 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7645 (ttt) REVERT: D 23 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8258 (ptm) REVERT: D 35 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7759 (m-80) REVERT: E 31 LYS cc_start: 0.7868 (mtpm) cc_final: 0.7644 (mtmm) REVERT: E 33 ASN cc_start: 0.7602 (OUTLIER) cc_final: 0.7323 (m-40) REVERT: E 227 ASP cc_start: 0.8346 (m-30) cc_final: 0.8092 (m-30) REVERT: E 289 GLU cc_start: 0.6340 (OUTLIER) cc_final: 0.5267 (pp20) REVERT: F 72 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7352 (tt0) REVERT: F 138 LEU cc_start: 0.7349 (tp) cc_final: 0.7097 (tt) outliers start: 42 outliers final: 23 residues processed: 203 average time/residue: 1.2096 time to fit residues: 266.9197 Evaluate side-chains 207 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 0.2980 chunk 113 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11766 Z= 0.263 Angle : 0.558 8.387 16174 Z= 0.300 Chirality : 0.043 0.241 1823 Planarity : 0.004 0.055 1879 Dihedral : 18.657 177.035 2095 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.66 % Allowed : 18.86 % Favored : 77.49 % 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: 1.07 (0.24), residues: 1288 helix: 2.15 (0.21), residues: 605 sheet: -0.67 (0.35), residues: 212 loop : -0.49 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 296 HIS 0.006 0.001 HIS B 29 PHE 0.017 0.001 PHE F 263 TYR 0.009 0.001 TYR A 31 ARG 0.007 0.000 ARG F 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 173 time to evaluate : 1.245 Fit side-chains REVERT: A 23 MET cc_start: 0.8651 (mtp) cc_final: 0.8403 (mtp) REVERT: A 58 MET cc_start: 0.8980 (ttp) cc_final: 0.8538 (ttp) REVERT: B 33 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7941 (m-40) REVERT: B 172 ASN cc_start: 0.8714 (t0) cc_final: 0.8360 (t0) REVERT: C 126 TYR cc_start: 0.7783 (t80) cc_final: 0.7564 (t80) REVERT: C 232 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7743 (pp20) REVERT: D 23 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8229 (ptm) REVERT: D 35 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7766 (m-80) REVERT: E 31 LYS cc_start: 0.7864 (mtpm) cc_final: 0.7641 (mtpp) REVERT: E 33 ASN cc_start: 0.7605 (OUTLIER) cc_final: 0.7321 (m-40) REVERT: E 227 ASP cc_start: 0.8346 (m-30) cc_final: 0.8096 (m-30) REVERT: E 289 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.5380 (pp20) REVERT: F 72 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7355 (tt0) REVERT: F 138 LEU cc_start: 0.7342 (tp) cc_final: 0.7096 (tt) outliers start: 39 outliers final: 26 residues processed: 194 average time/residue: 1.1942 time to fit residues: 251.9098 Evaluate side-chains 202 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 88 optimal weight: 0.0670 chunk 133 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11766 Z= 0.234 Angle : 0.555 8.520 16174 Z= 0.298 Chirality : 0.042 0.238 1823 Planarity : 0.004 0.054 1879 Dihedral : 18.609 176.697 2095 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.56 % Allowed : 19.23 % Favored : 77.20 % 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: 1.11 (0.24), residues: 1288 helix: 2.17 (0.21), residues: 605 sheet: -0.54 (0.36), residues: 207 loop : -0.50 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 296 HIS 0.006 0.001 HIS B 29 PHE 0.011 0.001 PHE F 263 TYR 0.010 0.001 TYR A 31 ARG 0.008 0.001 ARG C 260 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 1.176 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.8613 (mtp) cc_final: 0.8294 (mtp) REVERT: A 58 MET cc_start: 0.8964 (ttp) cc_final: 0.8526 (ttp) REVERT: B 33 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7945 (m-40) REVERT: B 172 ASN cc_start: 0.8709 (t0) cc_final: 0.8360 (t0) REVERT: D 23 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8218 (ptm) REVERT: D 35 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: E 31 LYS cc_start: 0.7855 (mtpm) cc_final: 0.7626 (mtmm) REVERT: E 33 ASN cc_start: 0.7597 (OUTLIER) cc_final: 0.7323 (m-40) REVERT: E 289 GLU cc_start: 0.6323 (OUTLIER) cc_final: 0.5310 (pp20) REVERT: F 72 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7316 (tt0) REVERT: F 138 LEU cc_start: 0.7469 (tp) cc_final: 0.7218 (tt) outliers start: 38 outliers final: 28 residues processed: 192 average time/residue: 1.1401 time to fit residues: 238.6013 Evaluate side-chains 205 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 109 optimal weight: 0.0040 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.159071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.127276 restraints weight = 12179.217| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.78 r_work: 0.3347 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11766 Z= 0.198 Angle : 0.545 7.819 16174 Z= 0.294 Chirality : 0.042 0.238 1823 Planarity : 0.004 0.045 1879 Dihedral : 18.457 176.344 2095 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.19 % Allowed : 20.17 % Favored : 76.64 % 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: 1.16 (0.24), residues: 1288 helix: 2.22 (0.21), residues: 605 sheet: -0.50 (0.36), residues: 207 loop : -0.49 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 296 HIS 0.005 0.001 HIS B 29 PHE 0.011 0.001 PHE F 263 TYR 0.010 0.001 TYR F 126 ARG 0.008 0.000 ARG C 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4528.93 seconds wall clock time: 86 minutes 48.58 seconds (5208.58 seconds total)