Starting phenix.real_space_refine on Sun Feb 18 22:28:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scy_25042/02_2024/7scy_25042.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scy_25042/02_2024/7scy_25042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scy_25042/02_2024/7scy_25042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scy_25042/02_2024/7scy_25042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scy_25042/02_2024/7scy_25042.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scy_25042/02_2024/7scy_25042.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 10436 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 "A GLU 105": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 90": "OD1" <-> "OD2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "K ASP 387": "OD1" <-> "OD2" Residue "K GLU 445": "OE1" <-> "OE2" Residue "K GLU 448": "OE1" <-> "OE2" Residue "K ASP 457": "OD1" <-> "OD2" Residue "K PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23206 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: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1537 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Time building chain proxies: 9.74, per 1000 atoms: 0.42 Number of scatterers: 23206 At special positions: 0 Unit cell: (123.54, 117.15, 109.695, 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 10436 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: 21.10 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: 42 helices and 11 sheets defined 72.1% alpha, 3.2% beta 145 base pairs and 234 stacking pairs defined. Time for finding SS restraints: 12.13 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.825A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.932A 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: 3.810A 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 45 through 73 removed outlier: 3.991A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.598A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 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 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.738A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.841A 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: 3.711A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (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: 4.305A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (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 123 Processing helix chain 'K' and resid 404 through 415 Processing helix chain 'K' and resid 422 through 426 Processing helix chain 'K' and resid 432 through 439 removed outlier: 4.195A pdb=" N VAL K 436 " --> pdb=" O THR K 432 " (cutoff:3.500A) Processing helix chain 'K' and resid 440 through 449 Processing helix chain 'K' and resid 456 through 463 removed outlier: 3.697A pdb=" N GLN K 460 " --> pdb=" O GLU K 456 " (cutoff:3.500A) Processing helix chain 'K' and resid 468 through 476 removed outlier: 3.906A pdb=" N LEU K 474 " --> pdb=" O GLN K 470 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.924A 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: 6.729A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.669A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.639A 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: 6.649A 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 419 through 420 removed outlier: 5.710A pdb=" N ILE K 395 " --> pdb=" O THR K 420 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU K 396 " --> pdb=" O ILE K 430 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 372 hydrogen bonds 744 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 234 stacking parallelities Total time for adding SS restraints: 9.96 Time building geometry restraints manager: 21.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 2339 1.02 - 1.22: 8147 1.22 - 1.42: 6386 1.42 - 1.62: 7121 1.62 - 1.82: 33 Bond restraints: 24026 Sorted by residual: bond pdb=" C8 DG I 10 " pdb=" H8 DG I 10 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" C8 DA J -5 " pdb=" H8 DA J -5 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" C6 DT I -29 " pdb=" H6 DT I -29 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.62e+01 bond pdb=" N ALA E 91 " pdb=" H ALA E 91 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" C6 DT I 33 " pdb=" H6 DT I 33 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.61e+01 ... (remaining 24021 not shown) Histogram of bond angle deviations from ideal: 74.40 - 86.67: 3 86.67 - 98.95: 44 98.95 - 111.22: 24256 111.22 - 123.49: 17198 123.49 - 135.76: 2084 Bond angle restraints: 43585 Sorted by residual: angle pdb=" N ARG F 17 " pdb=" CA ARG F 17 " pdb=" C ARG F 17 " ideal model delta sigma weight residual 110.61 125.19 -14.58 1.25e+00 6.40e-01 1.36e+02 angle pdb=" C ARG F 17 " pdb=" CA ARG F 17 " pdb=" HA ARG F 17 " ideal model delta sigma weight residual 109.00 74.40 34.60 3.00e+00 1.11e-01 1.33e+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 77.76 32.24 3.00e+00 1.11e-01 1.15e+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 84.22 24.78 3.00e+00 1.11e-01 6.83e+01 angle pdb=" O3' DT J -47 " pdb=" C3' DT J -47 " pdb=" C2' DT J -47 " ideal model delta sigma weight residual 111.50 121.91 -10.41 1.50e+00 4.44e-01 4.82e+01 ... (remaining 43580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 8346 35.20 - 70.39: 1622 70.39 - 105.59: 54 105.59 - 140.78: 0 140.78 - 175.98: 3 Dihedral angle restraints: 10025 sinusoidal: 7285 harmonic: 2740 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 -139.87 17.27 0 2.50e+00 1.60e-01 4.77e+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 122.80 138.75 -15.95 0 2.50e+00 1.60e-01 4.07e+01 dihedral pdb=" CA TYR H 37 " pdb=" C TYR H 37 " pdb=" N SER H 38 " pdb=" CA SER H 38 " ideal model delta harmonic sigma weight residual 180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 10022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 2053 0.148 - 0.296: 165 0.296 - 0.444: 13 0.444 - 0.592: 0 0.592 - 0.739: 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 1.77 0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" C4' DT I -67 " pdb=" C5' DT I -67 " pdb=" O4' DT I -67 " pdb=" C3' DT I -67 " both_signs ideal model delta sigma weight residual False -2.53 -2.08 -0.44 2.00e-01 2.50e+01 4.89e+00 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 4.00e+00 ... (remaining 2229 not shown) Planarity restraints: 2501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT J -39 " -0.444 2.00e-02 2.50e+03 1.92e-01 1.11e+03 pdb=" N1 DT J -39 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DT J -39 " 0.131 2.00e-02 2.50e+03 pdb=" O2 DT J -39 " 0.277 2.00e-02 2.50e+03 pdb=" N3 DT J -39 " 0.076 2.00e-02 2.50e+03 pdb=" C4 DT J -39 " -0.070 2.00e-02 2.50e+03 pdb=" O4 DT J -39 " -0.315 2.00e-02 2.50e+03 pdb=" C5 DT J -39 " 0.053 2.00e-02 2.50e+03 pdb=" C7 DT J -39 " 0.162 2.00e-02 2.50e+03 pdb=" C6 DT J -39 " 0.068 2.00e-02 2.50e+03 pdb=" H3 DT J -39 " -0.025 2.00e-02 2.50e+03 pdb=" H6 DT J -39 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT J -72 " 0.422 2.00e-02 2.50e+03 1.66e-01 8.27e+02 pdb=" N1 DT J -72 " -0.041 2.00e-02 2.50e+03 pdb=" C2 DT J -72 " -0.114 2.00e-02 2.50e+03 pdb=" O2 DT J -72 " -0.214 2.00e-02 2.50e+03 pdb=" N3 DT J -72 " -0.046 2.00e-02 2.50e+03 pdb=" C4 DT J -72 " 0.063 2.00e-02 2.50e+03 pdb=" O4 DT J -72 " 0.238 2.00e-02 2.50e+03 pdb=" C5 DT J -72 " -0.049 2.00e-02 2.50e+03 pdb=" C7 DT J -72 " -0.068 2.00e-02 2.50e+03 pdb=" C6 DT J -72 " -0.096 2.00e-02 2.50e+03 pdb=" H3 DT J -72 " 0.015 2.00e-02 2.50e+03 pdb=" H6 DT J -72 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT J -47 " -0.306 2.00e-02 2.50e+03 1.59e-01 7.61e+02 pdb=" N1 DT J -47 " -0.067 2.00e-02 2.50e+03 pdb=" C2 DT J -47 " 0.081 2.00e-02 2.50e+03 pdb=" O2 DT J -47 " 0.347 2.00e-02 2.50e+03 pdb=" N3 DT J -47 " -0.064 2.00e-02 2.50e+03 pdb=" C4 DT J -47 " -0.086 2.00e-02 2.50e+03 pdb=" O4 DT J -47 " -0.167 2.00e-02 2.50e+03 pdb=" C5 DT J -47 " 0.021 2.00e-02 2.50e+03 pdb=" C7 DT J -47 " 0.181 2.00e-02 2.50e+03 pdb=" C6 DT J -47 " 0.024 2.00e-02 2.50e+03 pdb=" H3 DT J -47 " -0.035 2.00e-02 2.50e+03 pdb=" H6 DT J -47 " 0.070 2.00e-02 2.50e+03 ... (remaining 2498 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.16: 1099 2.16 - 2.77: 36051 2.77 - 3.38: 65221 3.38 - 3.99: 91349 3.99 - 4.60: 130381 Nonbonded interactions: 324101 Sorted by model distance: nonbonded pdb=" HG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 1.556 1.850 nonbonded pdb=" HG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 1.568 1.850 nonbonded pdb=" OP1 DA I 28 " pdb=" HG1 THR B 80 " model vdw 1.569 1.850 nonbonded pdb=" OP1 DG J 28 " pdb=" HG1 THR F 80 " model vdw 1.585 1.850 nonbonded pdb=" HG SER K 455 " pdb=" OD1 ASP K 457 " model vdw 1.592 1.850 ... (remaining 324096 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: 0.710 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: 0.320 Extract box with map and model: 4.770 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 83.010 Find NCS groups from input model: 0.680 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 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 0.054 13590 Z= 0.750 Angle : 1.934 14.578 19596 Z= 1.278 Chirality : 0.088 0.739 2232 Planarity : 0.038 0.207 1456 Dihedral : 27.616 175.980 5861 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 0.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.56 % Allowed : 2.09 % Favored : 97.35 % 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: -0.81 (0.25), residues: 832 helix: -0.37 (0.18), residues: 582 sheet: None (None), residues: 0 loop : -0.57 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.043 TRP K 481 HIS 0.018 0.004 HIS B 75 PHE 0.063 0.017 PHE D 65 TYR 0.171 0.024 TYR A 41 ARG 0.012 0.001 ARG E 134 *********************** 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 397 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 393 time to evaluate : 1.377 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: 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: 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: 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: 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: 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: 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 51 ILE cc_start: 0.7354 (mt) cc_final: 0.6662 (mt) REVERT: A 60 LEU cc_start: 0.8464 (mt) cc_final: 0.6794 (mp) REVERT: A 117 VAL cc_start: 0.7217 (m) cc_final: 0.6961 (p) REVERT: D 99 ARG cc_start: 0.7331 (mtt180) cc_final: 0.7105 (tpp80) REVERT: E 60 LEU cc_start: 0.8481 (mt) cc_final: 0.8231 (mp) REVERT: F 98 TYR cc_start: 0.4468 (m-10) cc_final: 0.4247 (m-10) outliers start: 4 outliers final: 4 residues processed: 397 average time/residue: 0.6603 time to fit residues: 350.7817 Evaluate side-chains 317 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 313 time to evaluate : 1.436 ------------------------------------------------------------------------------- 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: 4.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 13590 Z= 0.293 Angle : 0.743 5.256 19596 Z= 0.460 Chirality : 0.045 0.355 2232 Planarity : 0.005 0.032 1456 Dihedral : 31.436 171.891 4153 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.14 % Allowed : 1.82 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.26), residues: 832 helix: 0.75 (0.19), residues: 585 sheet: -2.99 (1.49), residues: 10 loop : -0.78 (0.35), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP K 481 HIS 0.004 0.001 HIS K 476 PHE 0.027 0.002 PHE C 25 TYR 0.021 0.002 TYR G 57 ARG 0.006 0.001 ARG E 128 *********************** 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 360 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 359 time to evaluate : 1.446 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: 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: 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: 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: 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: 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 46 VAL cc_start: 0.8187 (t) cc_final: 0.7934 (t) REVERT: B 72 TYR cc_start: 0.7073 (m-80) cc_final: 0.6758 (m-80) REVERT: H 98 VAL cc_start: 0.8018 (t) cc_final: 0.7772 (t) outliers start: 1 outliers final: 1 residues processed: 359 average time/residue: 0.6303 time to fit residues: 309.0407 Evaluate side-chains 313 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 312 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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: 6.9990 chunk 30 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 67 ASN H 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13590 Z= 0.290 Angle : 0.695 5.123 19596 Z= 0.436 Chirality : 0.044 0.355 2232 Planarity : 0.005 0.040 1456 Dihedral : 31.070 170.895 4153 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 832 helix: 0.85 (0.20), residues: 582 sheet: -3.13 (1.36), residues: 10 loop : -0.87 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP K 481 HIS 0.006 0.001 HIS K 476 PHE 0.019 0.002 PHE D 65 TYR 0.016 0.002 TYR D 37 ARG 0.004 0.001 ARG B 45 *********************** 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 337 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 1.484 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: 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: 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: 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: 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: 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: F 71 THR cc_start: 0.7124 (m) cc_final: 0.6913 (m) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.6062 time to fit residues: 280.2393 Evaluate side-chains 298 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 1.586 ------------------------------------------------------------------------------- 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: 10.0000 chunk 73 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 67 ASN D 109 HIS ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 13590 Z= 0.342 Angle : 0.700 5.455 19596 Z= 0.439 Chirality : 0.046 0.348 2232 Planarity : 0.005 0.038 1456 Dihedral : 30.850 173.361 4153 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.26), residues: 832 helix: 0.40 (0.20), residues: 578 sheet: -3.84 (1.16), residues: 10 loop : -0.99 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP K 481 HIS 0.007 0.001 HIS K 476 PHE 0.018 0.002 PHE H 65 TYR 0.024 0.002 TYR F 72 ARG 0.006 0.001 ARG B 45 *********************** 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 327 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 1.446 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: 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: 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: 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: 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: 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: 327 average time/residue: 0.5879 time to fit residues: 264.1164 Evaluate side-chains 285 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.386 ------------------------------------------------------------------------------- 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: 6.9990 chunk 59 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.6118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 13590 Z= 0.395 Angle : 0.725 5.402 19596 Z= 0.456 Chirality : 0.049 0.350 2232 Planarity : 0.005 0.045 1456 Dihedral : 30.842 173.587 4153 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 22.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % 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: -0.84 (0.26), residues: 832 helix: -0.10 (0.20), residues: 581 sheet: -4.03 (1.05), residues: 10 loop : -1.25 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP K 481 HIS 0.006 0.002 HIS B 75 PHE 0.014 0.003 PHE B 61 TYR 0.018 0.002 TYR F 72 ARG 0.006 0.001 ARG F 45 *********************** 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 311 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 1.322 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8598 (p0) cc_final: 0.8327 (p0) REVERT: B 97 LEU cc_start: 0.7311 (tp) cc_final: 0.7059 (tt) REVERT: H 65 PHE cc_start: 0.6317 (t80) cc_final: 0.6059 (t80) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.5873 time to fit residues: 250.0960 Evaluate side-chains 271 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.567 ------------------------------------------------------------------------------- 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: 5.9990 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.6278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13590 Z= 0.284 Angle : 0.659 5.265 19596 Z= 0.415 Chirality : 0.044 0.350 2232 Planarity : 0.004 0.041 1456 Dihedral : 30.855 173.007 4153 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.27), residues: 832 helix: 0.27 (0.20), residues: 585 sheet: -3.88 (1.14), residues: 10 loop : -1.24 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 481 HIS 0.012 0.002 HIS G 82 PHE 0.015 0.002 PHE D 65 TYR 0.019 0.002 TYR F 72 ARG 0.004 0.001 ARG F 45 *********************** 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 311 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 1.486 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: 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: 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: 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: 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 77 ASP cc_start: 0.8574 (p0) cc_final: 0.8353 (p0) REVERT: B 97 LEU cc_start: 0.7170 (tp) cc_final: 0.6955 (tt) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.5840 time to fit residues: 250.7812 Evaluate side-chains 276 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.439 ------------------------------------------------------------------------------- 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: 10.0000 chunk 11 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 112 GLN H 67 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.6769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 13590 Z= 0.423 Angle : 0.734 5.424 19596 Z= 0.462 Chirality : 0.050 0.349 2232 Planarity : 0.006 0.048 1456 Dihedral : 30.901 174.808 4153 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 27.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.26), residues: 832 helix: -0.41 (0.20), residues: 584 sheet: -4.05 (1.13), residues: 10 loop : -1.58 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP K 481 HIS 0.007 0.002 HIS E 39 PHE 0.021 0.003 PHE C 25 TYR 0.018 0.003 TYR D 40 ARG 0.007 0.001 ARG E 63 *********************** 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 293 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 1.505 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.6202 time to fit residues: 251.2614 Evaluate side-chains 260 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 1.647 ------------------------------------------------------------------------------- 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: 5.9990 chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 70 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 81 optimal weight: 0.0470 chunk 94 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 overall best weight: 1.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.6681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13590 Z= 0.202 Angle : 0.640 5.565 19596 Z= 0.398 Chirality : 0.040 0.356 2232 Planarity : 0.004 0.036 1456 Dihedral : 30.909 170.970 4153 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.28), residues: 832 helix: 0.84 (0.21), residues: 585 sheet: -3.59 (1.25), residues: 10 loop : -1.37 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 481 HIS 0.006 0.001 HIS G 82 PHE 0.029 0.002 PHE C 25 TYR 0.025 0.002 TYR F 72 ARG 0.003 0.000 ARG A 53 *********************** 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 311 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 1.559 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: 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: 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: 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: 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: D 43 LYS cc_start: 0.7988 (mtmm) cc_final: 0.7782 (mtpt) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.5863 time to fit residues: 250.1086 Evaluate side-chains 271 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.543 ------------------------------------------------------------------------------- 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: 6.9990 chunk 97 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.6940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 13590 Z= 0.278 Angle : 0.648 7.173 19596 Z= 0.406 Chirality : 0.044 0.350 2232 Planarity : 0.004 0.038 1456 Dihedral : 30.820 172.907 4153 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.27), residues: 832 helix: 0.62 (0.20), residues: 585 sheet: -2.85 (1.59), residues: 10 loop : -1.47 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 481 HIS 0.005 0.001 HIS G 82 PHE 0.023 0.002 PHE C 25 TYR 0.016 0.002 TYR F 72 ARG 0.004 0.000 ARG E 63 *********************** 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 300 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.435 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: 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: 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: 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: 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 77 ASP cc_start: 0.8461 (p0) cc_final: 0.8156 (p0) REVERT: D 43 LYS cc_start: 0.8047 (mtmm) cc_final: 0.7814 (mtpp) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.5826 time to fit residues: 241.9076 Evaluate side-chains 259 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 1.413 ------------------------------------------------------------------------------- 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: 9.9990 chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.7007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13590 Z= 0.228 Angle : 0.628 6.668 19596 Z= 0.393 Chirality : 0.041 0.351 2232 Planarity : 0.004 0.037 1456 Dihedral : 30.786 172.162 4153 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.20 (0.28), residues: 832 helix: 0.83 (0.21), residues: 587 sheet: -2.63 (1.69), residues: 10 loop : -1.40 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 481 HIS 0.005 0.001 HIS G 82 PHE 0.017 0.002 PHE D 65 TYR 0.017 0.002 TYR F 72 ARG 0.003 0.000 ARG F 36 ********************** 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 296 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 1.648 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: 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: 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: 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: 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 77 ASP cc_start: 0.8489 (p0) cc_final: 0.8188 (p0) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.5789 time to fit residues: 235.6116 Evaluate side-chains 263 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.608 ------------------------------------------------------------------------------- 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: 0.7980 chunk 26 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.028070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2288 r_free = 0.2288 target = 0.021416 restraints weight = 265720.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2350 r_free = 0.2350 target = 0.023065 restraints weight = 82497.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.024078 restraints weight = 38758.992| |-----------------------------------------------------------------------------| r_work (final): 0.2386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.7330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 13590 Z= 0.382 Angle : 0.699 6.514 19596 Z= 0.440 Chirality : 0.049 0.347 2232 Planarity : 0.005 0.045 1456 Dihedral : 30.799 175.875 4153 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 24.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.27), residues: 832 helix: -0.10 (0.20), residues: 586 sheet: -2.89 (1.61), residues: 10 loop : -1.68 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP K 481 HIS 0.007 0.002 HIS G 82 PHE 0.020 0.003 PHE E 84 TYR 0.018 0.002 TYR F 51 ARG 0.007 0.001 ARG E 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7073.92 seconds wall clock time: 125 minutes 21.97 seconds (7521.97 seconds total)