Starting phenix.real_space_refine on Tue Mar 19 03:20:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scz_25043/03_2024/7scz_25043.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scz_25043/03_2024/7scz_25043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scz_25043/03_2024/7scz_25043.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scz_25043/03_2024/7scz_25043.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scz_25043/03_2024/7scz_25043.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scz_25043/03_2024/7scz_25043.pdb" } resolution = 3.5 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= 0.006 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 294 5.49 5 S 19 5.16 5 C 7110 2.51 5 N 2388 2.21 5 O 2959 1.98 5 H 10435 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "G ASP 90": "OD1" <-> "OD2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 387": "OD1" <-> "OD2" Residue "K GLU 407": "OE1" <-> "OE2" Residue "K GLU 435": "OE1" <-> "OE2" Residue "K GLU 437": "OE1" <-> "OE2" Residue "K GLU 448": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23205 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 4682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4682 Classifications: {'DNA': 147} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 4646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4646 Classifications: {'DNA': 147} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 146} Chain: "A" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1271 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1733 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1461 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1684 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1459 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1667 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1450 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "K" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1536 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Time building chain proxies: 9.97, per 1000 atoms: 0.43 Number of scatterers: 23205 At special positions: 0 Unit cell: (89.46, 121.41, 120.345, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 19 16.00 P 294 15.00 O 2959 8.00 N 2388 7.00 C 7110 6.00 H 10435 1.00 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: 21.97 Conformation dependent library (CDL) restraints added in 1.4 seconds 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1588 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 11 sheets defined 70.7% alpha, 3.9% beta 146 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 12.87 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.793A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.988A 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 removed outlier: 3.642A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.501A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (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 123 removed outlier: 3.644A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (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 131 removed outlier: 3.633A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.880A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.142A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.665A 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 90 through 97 Processing helix chain 'G' and resid 112 through 116 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 122 Processing helix chain 'K' and resid 404 through 415 Processing helix chain 'K' and resid 433 through 439 Processing helix chain 'K' and resid 440 through 449 Processing helix chain 'K' and resid 457 through 465 removed outlier: 3.766A pdb=" N ASP K 461 " --> pdb=" O ASP K 457 " (cutoff:3.500A) Processing helix chain 'K' and resid 468 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.967A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.647A 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 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.649A 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: 6.725A 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 418 through 420 removed outlier: 6.351A pdb=" N CYS K 429 " --> pdb=" O VAL K 454 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 374 hydrogen bonds 748 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 9.60 Time building geometry restraints manager: 22.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.88 - 1.07: 2390 1.07 - 1.26: 9404 1.26 - 1.45: 5394 1.45 - 1.63: 6804 1.63 - 1.82: 33 Bond restraints: 24025 Sorted by residual: bond pdb=" N LEU K 478 " pdb=" H LEU K 478 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N SER K 479 " pdb=" H SER K 479 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" C6 DC J 69 " pdb=" H6 DC J 69 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NH1 ARG G 88 " pdb="HH11 ARG G 88 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" C6 DC I -58 " pdb=" H6 DC I -58 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 24020 not shown) Histogram of bond angle deviations from ideal: 77.72 - 89.29: 3 89.29 - 100.85: 190 100.85 - 112.42: 26746 112.42 - 123.99: 14950 123.99 - 135.55: 1694 Bond angle restraints: 43583 Sorted by residual: angle pdb=" C ARG F 17 " pdb=" CA ARG F 17 " pdb=" HA ARG F 17 " ideal model delta sigma weight residual 109.00 77.72 31.28 3.00e+00 1.11e-01 1.09e+02 angle pdb=" N ARG F 17 " pdb=" CA ARG F 17 " pdb=" HA ARG F 17 " ideal model delta sigma weight residual 110.00 79.30 30.70 3.00e+00 1.11e-01 1.05e+02 angle pdb=" CB ARG F 17 " pdb=" CA ARG F 17 " pdb=" HA ARG F 17 " ideal model delta sigma weight residual 109.00 79.95 29.05 3.00e+00 1.11e-01 9.38e+01 angle pdb=" N ARG F 17 " pdb=" CA ARG F 17 " pdb=" C ARG F 17 " ideal model delta sigma weight residual 109.52 123.02 -13.50 1.55e+00 4.16e-01 7.58e+01 angle pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 110.00 120.05 -10.05 1.50e+00 4.44e-01 4.49e+01 ... (remaining 43578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 8370 35.32 - 70.64: 1611 70.64 - 105.96: 39 105.96 - 141.28: 1 141.28 - 176.60: 3 Dihedral angle restraints: 10024 sinusoidal: 7285 harmonic: 2739 Sorted by residual: dihedral pdb=" C ARG F 17 " pdb=" N ARG F 17 " pdb=" CA ARG F 17 " pdb=" CB ARG F 17 " ideal model delta harmonic sigma weight residual -122.60 -142.09 19.49 0 2.50e+00 1.60e-01 6.08e+01 dihedral pdb=" N ARG F 17 " pdb=" C ARG F 17 " pdb=" CA ARG F 17 " pdb=" CB ARG F 17 " ideal model delta harmonic sigma weight residual 122.80 141.32 -18.52 0 2.50e+00 1.60e-01 5.49e+01 dihedral pdb=" CA SER K 431 " pdb=" C SER K 431 " pdb=" N THR K 432 " pdb=" CA THR K 432 " ideal model delta harmonic sigma weight residual 180.00 152.38 27.62 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 10021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 2105 0.163 - 0.326: 114 0.326 - 0.489: 12 0.489 - 0.652: 0 0.652 - 0.815: 1 Chirality restraints: 2232 Sorted by residual: chirality pdb=" CA ARG F 17 " pdb=" N ARG F 17 " pdb=" C ARG F 17 " pdb=" CB ARG F 17 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.81 2.00e-01 2.50e+01 1.66e+01 chirality pdb=" C3' DG I -44 " pdb=" C4' DG I -44 " pdb=" O3' DG I -44 " pdb=" C2' DG I -44 " both_signs ideal model delta sigma weight residual False -2.66 -2.26 -0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CB THR B 82 " pdb=" CA THR B 82 " pdb=" OG1 THR B 82 " pdb=" CG2 THR B 82 " both_signs ideal model delta sigma weight residual False 2.55 2.17 0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 2229 not shown) Planarity restraints: 2501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT J 38 " -0.301 2.00e-02 2.50e+03 1.63e-01 7.98e+02 pdb=" N1 DT J 38 " -0.094 2.00e-02 2.50e+03 pdb=" C2 DT J 38 " 0.051 2.00e-02 2.50e+03 pdb=" O2 DT J 38 " 0.285 2.00e-02 2.50e+03 pdb=" N3 DT J 38 " -0.035 2.00e-02 2.50e+03 pdb=" C4 DT J 38 " -0.100 2.00e-02 2.50e+03 pdb=" O4 DT J 38 " -0.257 2.00e-02 2.50e+03 pdb=" C5 DT J 38 " 0.035 2.00e-02 2.50e+03 pdb=" C7 DT J 38 " 0.193 2.00e-02 2.50e+03 pdb=" C6 DT J 38 " 0.028 2.00e-02 2.50e+03 pdb=" H3 DT J 38 " 0.087 2.00e-02 2.50e+03 pdb=" H6 DT J 38 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 47 " -0.369 2.00e-02 2.50e+03 1.34e-01 6.26e+02 pdb=" N9 DG J 47 " 0.012 2.00e-02 2.50e+03 pdb=" C8 DG J 47 " 0.096 2.00e-02 2.50e+03 pdb=" N7 DG J 47 " 0.103 2.00e-02 2.50e+03 pdb=" C5 DG J 47 " 0.057 2.00e-02 2.50e+03 pdb=" C6 DG J 47 " -0.034 2.00e-02 2.50e+03 pdb=" O6 DG J 47 " -0.218 2.00e-02 2.50e+03 pdb=" N1 DG J 47 " 0.021 2.00e-02 2.50e+03 pdb=" C2 DG J 47 " 0.077 2.00e-02 2.50e+03 pdb=" N2 DG J 47 " 0.084 2.00e-02 2.50e+03 pdb=" N3 DG J 47 " 0.091 2.00e-02 2.50e+03 pdb=" C4 DG J 47 " 0.080 2.00e-02 2.50e+03 pdb=" H8 DG J 47 " 0.085 2.00e-02 2.50e+03 pdb=" H1 DG J 47 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT J 55 " 0.349 2.00e-02 2.50e+03 1.42e-01 6.07e+02 pdb=" N1 DT J 55 " -0.040 2.00e-02 2.50e+03 pdb=" C2 DT J 55 " -0.108 2.00e-02 2.50e+03 pdb=" O2 DT J 55 " -0.200 2.00e-02 2.50e+03 pdb=" N3 DT J 55 " -0.026 2.00e-02 2.50e+03 pdb=" C4 DT J 55 " 0.045 2.00e-02 2.50e+03 pdb=" O4 DT J 55 " 0.211 2.00e-02 2.50e+03 pdb=" C5 DT J 55 " -0.050 2.00e-02 2.50e+03 pdb=" C7 DT J 55 " -0.093 2.00e-02 2.50e+03 pdb=" C6 DT J 55 " -0.064 2.00e-02 2.50e+03 pdb=" H3 DT J 55 " 0.035 2.00e-02 2.50e+03 pdb=" H6 DT J 55 " -0.059 2.00e-02 2.50e+03 ... (remaining 2498 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1155 2.18 - 2.79: 36628 2.79 - 3.39: 62947 3.39 - 4.00: 89620 4.00 - 4.60: 128365 Nonbonded interactions: 318715 Sorted by model distance: nonbonded pdb=" OP1 DA I 28 " pdb=" HG1 THR B 80 " model vdw 1.578 1.850 nonbonded pdb=" OP1 DG J 28 " pdb=" HG1 THR F 80 " model vdw 1.611 1.850 nonbonded pdb=" HG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 1.617 1.850 nonbonded pdb=" OD2 ASP D 68 " pdb=" HH TYR F 98 " model vdw 1.621 1.850 nonbonded pdb=" HG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 1.628 1.850 ... (remaining 318710 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 101) } ncs_group { reference = (chain 'C' and resid 15 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 123) 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 group one per residue 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.270 Extract box with map and model: 4.750 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 87.040 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.100 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 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 : 0.014 0.065 13590 Z= 0.752 Angle : 1.915 13.497 19596 Z= 1.269 Chirality : 0.088 0.815 2232 Planarity : 0.035 0.172 1456 Dihedral : 27.439 176.605 5861 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 0.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.13 % 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: 0.09 (0.26), residues: 832 helix: 0.25 (0.19), residues: 580 sheet: -0.58 (1.52), residues: 6 loop : -0.05 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.027 TRP K 481 HIS 0.014 0.004 HIS D 49 PHE 0.049 0.012 PHE D 70 TYR 0.124 0.021 TYR C 57 ARG 0.011 0.001 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.8343 (t0) cc_final: 0.8024 (t0) REVERT: B 98 TYR cc_start: 0.8484 (m-10) cc_final: 0.8269 (m-10) REVERT: C 40 SER cc_start: 0.7653 (p) cc_final: 0.7293 (p) REVERT: C 90 ASP cc_start: 0.6952 (t70) cc_final: 0.6673 (t70) REVERT: D 89 ILE cc_start: 0.9265 (mt) cc_final: 0.8900 (mt) REVERT: E 97 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6935 (mt-10) REVERT: G 61 GLU cc_start: 0.8342 (tp30) cc_final: 0.8060 (tp30) REVERT: H 88 THR cc_start: 0.9138 (m) cc_final: 0.8860 (p) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.7505 time to fit residues: 295.9959 Evaluate side-chains 195 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 476 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13590 Z= 0.236 Angle : 0.714 5.213 19596 Z= 0.438 Chirality : 0.042 0.406 2232 Planarity : 0.005 0.045 1456 Dihedral : 31.310 171.366 4153 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.96 % Allowed : 12.01 % Favored : 86.03 % Cbeta Deviations : 0.13 % 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: 2.03 (0.28), residues: 832 helix: 1.98 (0.21), residues: 584 sheet: -1.78 (1.32), residues: 11 loop : -0.04 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP K 481 HIS 0.008 0.001 HIS F 75 PHE 0.019 0.001 PHE A 67 TYR 0.012 0.001 TYR F 98 ARG 0.004 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 210 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.8400 (t0) cc_final: 0.8121 (t0) REVERT: E 73 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7499 (tm-30) REVERT: E 90 MET cc_start: 0.8071 (mmp) cc_final: 0.7829 (mmt) outliers start: 14 outliers final: 10 residues processed: 221 average time/residue: 0.6058 time to fit residues: 182.7947 Evaluate side-chains 196 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 186 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 80 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 0.0970 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 106 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN H 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13590 Z= 0.280 Angle : 0.652 5.073 19596 Z= 0.402 Chirality : 0.043 0.371 2232 Planarity : 0.004 0.049 1456 Dihedral : 31.035 170.822 4153 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.49 % Allowed : 13.41 % Favored : 83.10 % 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: 2.38 (0.28), residues: 832 helix: 2.38 (0.21), residues: 581 sheet: -1.80 (1.39), residues: 11 loop : -0.26 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 481 HIS 0.006 0.001 HIS F 75 PHE 0.015 0.001 PHE K 458 TYR 0.012 0.001 TYR G 57 ARG 0.011 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 189 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.8427 (t0) cc_final: 0.8171 (t0) REVERT: D 42 TYR cc_start: 0.7942 (t80) cc_final: 0.7591 (t80) outliers start: 25 outliers final: 23 residues processed: 203 average time/residue: 0.5928 time to fit residues: 166.9491 Evaluate side-chains 202 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 179 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 104 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13590 Z= 0.269 Angle : 0.637 8.638 19596 Z= 0.390 Chirality : 0.042 0.364 2232 Planarity : 0.004 0.050 1456 Dihedral : 30.858 171.761 4153 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.21 % Allowed : 15.92 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.28), residues: 832 helix: 2.44 (0.21), residues: 578 sheet: -1.67 (1.39), residues: 11 loop : -0.32 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP K 481 HIS 0.005 0.001 HIS F 75 PHE 0.016 0.001 PHE K 458 TYR 0.011 0.001 TYR G 57 ARG 0.004 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 193 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.8425 (t0) cc_final: 0.8192 (t0) outliers start: 23 outliers final: 20 residues processed: 206 average time/residue: 0.5821 time to fit residues: 167.0253 Evaluate side-chains 208 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 188 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 72 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 0.0870 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13590 Z= 0.202 Angle : 0.602 4.902 19596 Z= 0.372 Chirality : 0.039 0.359 2232 Planarity : 0.003 0.047 1456 Dihedral : 30.620 171.393 4153 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.51 % Allowed : 17.18 % Favored : 80.31 % 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: 2.80 (0.29), residues: 832 helix: 2.76 (0.21), residues: 578 sheet: -1.71 (1.40), residues: 11 loop : -0.23 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 481 HIS 0.005 0.001 HIS F 75 PHE 0.011 0.001 PHE K 458 TYR 0.015 0.001 TYR D 40 ARG 0.003 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 191 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 93 GLU cc_start: 0.7399 (mp0) cc_final: 0.7144 (mp0) outliers start: 18 outliers final: 17 residues processed: 202 average time/residue: 0.5822 time to fit residues: 163.0046 Evaluate side-chains 200 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 183 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 104 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 13590 Z= 0.353 Angle : 0.644 4.985 19596 Z= 0.395 Chirality : 0.046 0.357 2232 Planarity : 0.004 0.051 1456 Dihedral : 30.659 172.550 4153 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.35 % Allowed : 17.74 % Favored : 78.91 % 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: 2.37 (0.28), residues: 832 helix: 2.45 (0.21), residues: 578 sheet: -1.48 (1.50), residues: 11 loop : -0.45 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 481 HIS 0.004 0.001 HIS F 75 PHE 0.014 0.002 PHE C 25 TYR 0.013 0.002 TYR G 57 ARG 0.005 0.001 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 178 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 80 THR cc_start: 0.9005 (m) cc_final: 0.8760 (p) outliers start: 24 outliers final: 23 residues processed: 192 average time/residue: 0.5922 time to fit residues: 156.9766 Evaluate side-chains 197 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 174 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 59 optimal weight: 0.3980 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13590 Z= 0.201 Angle : 0.602 5.317 19596 Z= 0.371 Chirality : 0.039 0.356 2232 Planarity : 0.003 0.049 1456 Dihedral : 30.518 172.290 4153 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.96 % Allowed : 18.72 % Favored : 79.33 % 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: 2.79 (0.29), residues: 832 helix: 2.73 (0.21), residues: 581 sheet: -1.35 (1.54), residues: 11 loop : -0.25 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 481 HIS 0.002 0.000 HIS F 75 PHE 0.014 0.001 PHE K 458 TYR 0.009 0.001 TYR C 57 ARG 0.002 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 93 GLU cc_start: 0.7397 (mp0) cc_final: 0.7146 (mp0) outliers start: 14 outliers final: 13 residues processed: 192 average time/residue: 0.5888 time to fit residues: 154.9163 Evaluate side-chains 192 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 179 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13590 Z= 0.276 Angle : 0.619 6.735 19596 Z= 0.380 Chirality : 0.042 0.355 2232 Planarity : 0.004 0.051 1456 Dihedral : 30.476 173.110 4153 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.37 % Allowed : 18.58 % Favored : 79.05 % 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: 2.66 (0.29), residues: 832 helix: 2.67 (0.21), residues: 579 sheet: -1.33 (1.61), residues: 11 loop : -0.38 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 481 HIS 0.003 0.001 HIS F 75 PHE 0.014 0.001 PHE K 458 TYR 0.011 0.001 TYR G 57 ARG 0.004 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 176 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 93 GLU cc_start: 0.7427 (mp0) cc_final: 0.7213 (mp0) outliers start: 17 outliers final: 15 residues processed: 185 average time/residue: 0.5914 time to fit residues: 149.8551 Evaluate side-chains 190 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 175 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 0.0070 chunk 99 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.5866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13590 Z= 0.200 Angle : 0.604 8.345 19596 Z= 0.370 Chirality : 0.039 0.356 2232 Planarity : 0.003 0.049 1456 Dihedral : 30.381 173.179 4153 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.23 % Allowed : 18.99 % Favored : 78.77 % 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: 2.83 (0.29), residues: 832 helix: 2.78 (0.21), residues: 582 sheet: -1.31 (1.59), residues: 11 loop : -0.32 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 481 HIS 0.002 0.001 HIS F 75 PHE 0.017 0.001 PHE K 458 TYR 0.007 0.001 TYR C 57 ARG 0.003 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 182 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 93 GLU cc_start: 0.7389 (mp0) cc_final: 0.7161 (mp0) outliers start: 16 outliers final: 13 residues processed: 190 average time/residue: 0.5989 time to fit residues: 156.9961 Evaluate side-chains 192 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 179 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 30.0000 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13590 Z= 0.257 Angle : 0.622 8.919 19596 Z= 0.378 Chirality : 0.042 0.355 2232 Planarity : 0.004 0.051 1456 Dihedral : 30.373 173.614 4153 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.68 % Allowed : 19.69 % Favored : 78.63 % 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: 2.70 (0.29), residues: 832 helix: 2.71 (0.21), residues: 579 sheet: -1.25 (1.55), residues: 11 loop : -0.40 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 481 HIS 0.003 0.001 HIS F 75 PHE 0.017 0.001 PHE K 458 TYR 0.010 0.001 TYR G 57 ARG 0.003 0.000 ARG B 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 176 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 93 GLU cc_start: 0.7407 (mp0) cc_final: 0.7193 (mp0) outliers start: 12 outliers final: 12 residues processed: 184 average time/residue: 0.6053 time to fit residues: 152.3103 Evaluate side-chains 185 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 173 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.092701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.065313 restraints weight = 70257.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.068171 restraints weight = 24757.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.069968 restraints weight = 14733.487| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.6027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13590 Z= 0.270 Angle : 0.626 9.150 19596 Z= 0.381 Chirality : 0.042 0.352 2232 Planarity : 0.004 0.051 1456 Dihedral : 30.384 173.790 4153 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.82 % Allowed : 19.83 % Favored : 78.35 % 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: 2.54 (0.29), residues: 832 helix: 2.58 (0.21), residues: 579 sheet: -1.55 (1.53), residues: 11 loop : -0.44 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 481 HIS 0.003 0.001 HIS B 75 PHE 0.018 0.001 PHE K 458 TYR 0.010 0.001 TYR G 57 ARG 0.003 0.000 ARG B 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6129.58 seconds wall clock time: 108 minutes 1.24 seconds (6481.24 seconds total)