Starting phenix.real_space_refine (version: dev) on Fri Feb 24 13:12:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scz_25043/02_2023/7scz_25043.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scz_25043/02_2023/7scz_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_25043/02_2023/7scz_25043.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scz_25043/02_2023/7scz_25043.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scz_25043/02_2023/7scz_25043.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scz_25043/02_2023/7scz_25043.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 10.39, per 1000 atoms: 0.45 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: 20.93 Conformation dependent library (CDL) restraints added in 1.2 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: 11.83 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: 10.30 Time building geometry restraints manager: 21.50 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: 7319 35.32 - 70.64: 1401 70.64 - 105.96: 39 105.96 - 141.28: 1 141.28 - 176.60: 3 Dihedral angle restraints: 8763 sinusoidal: 6024 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 8760 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 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. 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.300 Extract box with map and model: 6.110 Check model and map are aligned: 0.330 Process input model: 83.950 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.210 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 27.471 176.605 5601 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 % 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 *********************** 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 : 1.455 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 outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.7689 time to fit residues: 303.9121 Evaluate side-chains 194 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.322 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6093 ------------------------------------------------------------------------------- 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: 0.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN K 476 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 13590 Z= 0.236 Angle : 0.720 5.320 19596 Z= 0.442 Chirality : 0.042 0.411 2232 Planarity : 0.005 0.043 1456 Dihedral : 31.736 172.282 3893 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer Outliers : 1.96 % 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: 2.01 (0.28), residues: 832 helix: 1.98 (0.21), residues: 582 sheet: -1.69 (1.32), residues: 11 loop : -0.08 (0.35), residues: 239 *********************** 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 222 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 208 time to evaluate : 1.382 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 outliers start: 14 outliers final: 10 residues processed: 219 average time/residue: 0.6215 time to fit residues: 185.4979 Evaluate side-chains 194 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 184 time to evaluate : 1.367 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2550 time to fit residues: 6.2664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN E 68 GLN F 75 HIS H 82 HIS H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 13590 Z= 0.321 Angle : 0.669 5.016 19596 Z= 0.411 Chirality : 0.045 0.372 2232 Planarity : 0.004 0.046 1456 Dihedral : 31.572 170.862 3893 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.28), residues: 832 helix: 2.21 (0.21), residues: 578 sheet: -1.87 (1.34), residues: 11 loop : -0.39 (0.35), residues: 243 *********************** 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 208 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 192 time to evaluate : 1.461 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 outliers start: 16 outliers final: 12 residues processed: 199 average time/residue: 0.6206 time to fit residues: 170.5707 Evaluate side-chains 188 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 176 time to evaluate : 1.611 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2597 time to fit residues: 7.3002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 104 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.7713 moved from start: 0.5015 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= 0.195 Angle : 0.615 6.325 19596 Z= 0.378 Chirality : 0.039 0.363 2232 Planarity : 0.003 0.044 1456 Dihedral : 31.368 171.497 3893 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.28), residues: 832 helix: 2.62 (0.21), residues: 581 sheet: -1.65 (1.39), residues: 11 loop : -0.24 (0.36), residues: 240 *********************** 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 191 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 188 time to evaluate : 1.259 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 outliers start: 3 outliers final: 3 residues processed: 189 average time/residue: 0.5861 time to fit residues: 154.4979 Evaluate side-chains 181 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 178 time to evaluate : 1.414 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2683 time to fit residues: 3.1451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.7980 chunk 59 optimal weight: 0.4980 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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: 0.7757 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 13590 Z= 0.266 Angle : 0.617 4.870 19596 Z= 0.380 Chirality : 0.042 0.358 2232 Planarity : 0.004 0.048 1456 Dihedral : 31.271 171.864 3893 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.29), residues: 832 helix: 2.66 (0.21), residues: 578 sheet: -1.66 (1.42), residues: 11 loop : -0.25 (0.37), residues: 243 *********************** 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 185 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 179 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 181 average time/residue: 0.6306 time to fit residues: 157.7224 Evaluate side-chains 176 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 173 time to evaluate : 1.441 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2599 time to fit residues: 3.1669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 0.2980 chunk 25 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 86 optimal weight: 0.2980 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: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN E 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 13590 Z= 0.244 Angle : 0.611 5.155 19596 Z= 0.376 Chirality : 0.041 0.357 2232 Planarity : 0.003 0.047 1456 Dihedral : 31.232 172.400 3893 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 0.70 % 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: 2.68 (0.29), residues: 832 helix: 2.67 (0.21), residues: 578 sheet: -1.33 (1.51), residues: 11 loop : -0.32 (0.37), residues: 243 *********************** 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 182 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 177 time to evaluate : 1.389 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 outliers start: 5 outliers final: 5 residues processed: 179 average time/residue: 0.6303 time to fit residues: 154.2305 Evaluate side-chains 180 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 175 time to evaluate : 1.462 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.2520 time to fit residues: 3.9471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 63 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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: 0.7753 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 13590 Z= 0.246 Angle : 0.609 5.436 19596 Z= 0.374 Chirality : 0.041 0.356 2232 Planarity : 0.003 0.047 1456 Dihedral : 31.179 172.968 3893 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.29), residues: 832 helix: 2.72 (0.21), residues: 577 sheet: -1.15 (1.67), residues: 11 loop : -0.30 (0.38), residues: 244 *********************** 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 181 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 177 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 178 average time/residue: 0.6658 time to fit residues: 163.2384 Evaluate side-chains 176 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 173 time to evaluate : 1.528 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4647 time to fit residues: 3.6054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 20.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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: 0.7747 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 13590 Z= 0.236 Angle : 0.612 8.869 19596 Z= 0.374 Chirality : 0.041 0.357 2232 Planarity : 0.003 0.048 1456 Dihedral : 31.072 173.300 3893 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 0.70 % 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: 2.77 (0.29), residues: 832 helix: 2.75 (0.21), residues: 578 sheet: -1.43 (1.58), residues: 11 loop : -0.33 (0.38), residues: 243 *********************** 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 183 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 178 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 178 average time/residue: 0.6281 time to fit residues: 153.8460 Evaluate side-chains 176 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 173 time to evaluate : 1.782 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3260 time to fit residues: 3.7940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 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: 1.9990 chunk 87 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 0.4980 chunk 63 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.7692 moved from start: 0.5912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 13590 Z= 0.182 Angle : 0.594 8.003 19596 Z= 0.363 Chirality : 0.038 0.356 2232 Planarity : 0.003 0.045 1456 Dihedral : 30.903 173.052 3893 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 0.00 % 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: 3.09 (0.29), residues: 832 helix: 2.94 (0.21), residues: 582 sheet: -1.42 (1.53), residues: 11 loop : -0.11 (0.39), residues: 239 *********************** 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 184 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.5847 time to fit residues: 148.0515 Evaluate side-chains 176 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.434 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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: 0.7754 moved from start: 0.5975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 13590 Z= 0.277 Angle : 0.620 8.972 19596 Z= 0.377 Chirality : 0.042 0.355 2232 Planarity : 0.004 0.049 1456 Dihedral : 30.919 173.894 3893 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 0.14 % 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: 2.75 (0.21), residues: 579 sheet: -1.54 (1.51), residues: 11 loop : -0.27 (0.38), residues: 242 ********************** 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 175 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 174 average time/residue: 0.6205 time to fit residues: 148.1724 Evaluate side-chains 172 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 1.467 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2646 time to fit residues: 2.1433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.093282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.065944 restraints weight = 70122.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.068820 restraints weight = 24767.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.070635 restraints weight = 14700.779| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.6037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 13590 Z= 0.252 Angle : 0.618 9.185 19596 Z= 0.375 Chirality : 0.041 0.353 2232 Planarity : 0.003 0.047 1456 Dihedral : 30.934 173.808 3893 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 0.00 % 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: 2.68 (0.21), residues: 579 sheet: -1.67 (1.55), residues: 11 loop : -0.29 (0.38), residues: 242 =============================================================================== Job complete usr+sys time: 5979.74 seconds wall clock time: 105 minutes 42.53 seconds (6342.53 seconds total)