Starting phenix.real_space_refine on Sun Jul 21 01:45:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pp6_17796/07_2024/8pp6_17796_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pp6_17796/07_2024/8pp6_17796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pp6_17796/07_2024/8pp6_17796.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pp6_17796/07_2024/8pp6_17796.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pp6_17796/07_2024/8pp6_17796_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pp6_17796/07_2024/8pp6_17796_neut.cif" } resolution = 3.18 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= 0.004 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 Zn 1 6.06 5 P 311 5.49 5 S 19 5.16 5 C 7396 2.51 5 N 2487 2.21 5 O 3104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 77": "OD1" <-> "OD2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "F ASP 68": "OD1" <-> "OD2" Residue "G GLU 91": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13318 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 808 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 742 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 753 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3180 Classifications: {'DNA': 156} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 155} Chain: "J" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3214 Classifications: {'DNA': 156} Link IDs: {'rna3p': 155} Chain: "K" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 283 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "M" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12495 SG CYS K 27 64.981 84.416 37.321 1.00133.28 S ATOM 12514 SG CYS K 30 63.315 85.615 34.414 1.00141.72 S ATOM 12602 SG CYS K 41 62.188 86.617 38.206 1.00135.85 S ATOM 12622 SG CYS K 44 61.221 83.403 36.536 1.00137.92 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LYS A 36 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 36 " occ=0.00 residue: pdb=" N ARG A 129 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG A 129 " occ=0.00 residue: pdb=" N LYS E 36 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS E 36 " occ=0.00 residue: pdb=" N LYS H 122 " occ=0.00 ... (8 atoms not shown) pdb=" OXT LYS H 122 " occ=0.00 Time building chain proxies: 7.59, per 1000 atoms: 0.57 Number of scatterers: 13318 At special positions: 0 Unit cell: (117.058, 124.716, 123.622, 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) Zn 1 29.99 S 19 16.00 P 311 15.00 O 3104 8.00 N 2487 7.00 C 7396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.93 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 27 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 44 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 30 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 41 " Number of angles added : 6 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1634 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 10 sheets defined 66.2% alpha, 4.6% beta 139 base pairs and 284 stacking pairs defined. Time for finding SS restraints: 6.36 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.096A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.562A 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 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.072A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.586A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 44 through 72 removed outlier: 4.547A pdb=" N VAL C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 89 removed outlier: 3.552A pdb=" N LEU C 82 " --> pdb=" O ILE C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.555A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.546A 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 42 removed outlier: 3.524A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.059A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 15 through 21 Processing helix chain 'G' and resid 25 through 35 Processing helix chain 'G' and resid 44 through 72 removed outlier: 4.346A pdb=" N VAL G 48 " --> pdb=" O ALA G 44 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL G 61 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 89 removed outlier: 3.743A pdb=" N LEU G 82 " --> pdb=" O ILE G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 96 Processing helix chain 'G' and resid 111 through 115 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.866A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 Processing helix chain 'M' and resid 22 through 34 removed outlier: 3.521A pdb=" N VAL M 26 " --> pdb=" O THR M 22 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE M 30 " --> pdb=" O VAL M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.867A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 41 through 42 removed outlier: 7.060A pdb=" N ARG C 41 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 99 through 101 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 41 through 42 removed outlier: 7.071A pdb=" N ARG G 41 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 76 through 77 Processing sheet with id=AA9, first strand: chain 'K' and resid 24 through 25 Processing sheet with id=AB1, first strand: chain 'M' and resid 12 through 16 removed outlier: 3.844A pdb=" N LEU M 69 " --> pdb=" O LYS M 6 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 360 hydrogen bonds 720 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 284 stacking parallelities Total time for adding SS restraints: 5.41 Time building geometry restraints manager: 6.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2782 1.33 - 1.46: 4521 1.46 - 1.58: 6230 1.58 - 1.70: 621 1.70 - 1.82: 32 Bond restraints: 14186 Sorted by residual: bond pdb=" CB THR F 71 " pdb=" CG2 THR F 71 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.37e+00 bond pdb=" C4' DC I 70 " pdb=" O4' DC I 70 " ideal model delta sigma weight residual 1.450 1.428 0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C3' DT J 14 " pdb=" C2' DT J 14 " ideal model delta sigma weight residual 1.525 1.545 -0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" O4' DC I 10 " pdb=" C1' DC I 10 " ideal model delta sigma weight residual 1.414 1.394 0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" O4' DT J 9 " pdb=" C1' DT J 9 " ideal model delta sigma weight residual 1.414 1.395 0.019 2.00e-02 2.50e+03 9.30e-01 ... (remaining 14181 not shown) Histogram of bond angle deviations from ideal: 98.07 - 105.23: 1328 105.23 - 112.39: 8009 112.39 - 119.55: 4457 119.55 - 126.71: 5774 126.71 - 133.87: 917 Bond angle restraints: 20485 Sorted by residual: angle pdb=" N THR K 31 " pdb=" CA THR K 31 " pdb=" CB THR K 31 " ideal model delta sigma weight residual 113.65 109.91 3.74 1.47e+00 4.63e-01 6.46e+00 angle pdb=" N THR K 31 " pdb=" CA THR K 31 " pdb=" C THR K 31 " ideal model delta sigma weight residual 113.72 110.04 3.68 1.52e+00 4.33e-01 5.85e+00 angle pdb=" C3' DC I 5 " pdb=" C2' DC I 5 " pdb=" C1' DC I 5 " ideal model delta sigma weight residual 101.60 98.07 3.53 1.50e+00 4.44e-01 5.55e+00 angle pdb=" CB LYS K 54 " pdb=" CG LYS K 54 " pdb=" CD LYS K 54 " ideal model delta sigma weight residual 111.30 116.27 -4.97 2.30e+00 1.89e-01 4.67e+00 angle pdb=" C VAL F 70 " pdb=" N THR F 71 " pdb=" CA THR F 71 " ideal model delta sigma weight residual 120.31 117.16 3.15 1.52e+00 4.33e-01 4.28e+00 ... (remaining 20480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.13: 5751 26.13 - 52.25: 1670 52.25 - 78.38: 336 78.38 - 104.50: 1 104.50 - 130.63: 1 Dihedral angle restraints: 7759 sinusoidal: 5232 harmonic: 2527 Sorted by residual: dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sinusoidal sigma weight residual 220.00 89.37 130.63 1 3.50e+01 8.16e-04 1.29e+01 dihedral pdb=" CG ARG C 70 " pdb=" CD ARG C 70 " pdb=" NE ARG C 70 " pdb=" CZ ARG C 70 " ideal model delta sinusoidal sigma weight residual 90.00 134.18 -44.18 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG F 78 " pdb=" CD ARG F 78 " pdb=" NE ARG F 78 " pdb=" CZ ARG F 78 " ideal model delta sinusoidal sigma weight residual -180.00 -136.22 -43.78 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 7756 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1295 0.025 - 0.049: 711 0.049 - 0.074: 224 0.074 - 0.099: 56 0.099 - 0.123: 41 Chirality restraints: 2327 Sorted by residual: chirality pdb=" CA ILE G 78 " pdb=" N ILE G 78 " pdb=" C ILE G 78 " pdb=" CB ILE G 78 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA PRO D 47 " pdb=" N PRO D 47 " pdb=" C PRO D 47 " pdb=" CB PRO D 47 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.61e-01 ... (remaining 2324 not shown) Planarity restraints: 1513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " 0.025 2.00e-02 2.50e+03 1.05e-02 3.29e+00 pdb=" N9 DG I 47 " -0.024 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -55 " -0.021 2.00e-02 2.50e+03 9.12e-03 2.50e+00 pdb=" N9 DG I -55 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DG I -55 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG I -55 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG I -55 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG I -55 " -0.000 2.00e-02 2.50e+03 pdb=" O6 DG I -55 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG I -55 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I -55 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I -55 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I -55 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DG I -55 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 36 " 0.021 2.00e-02 2.50e+03 1.03e-02 2.41e+00 pdb=" N1 DC I 36 " -0.019 2.00e-02 2.50e+03 pdb=" C2 DC I 36 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DC I 36 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DC I 36 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 36 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 36 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 36 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC I 36 " -0.005 2.00e-02 2.50e+03 ... (remaining 1510 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2422 2.79 - 3.32: 10621 3.32 - 3.85: 24345 3.85 - 4.37: 29835 4.37 - 4.90: 41911 Nonbonded interactions: 109134 Sorted by model distance: nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.263 2.440 nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU E 59 " model vdw 2.360 2.440 nonbonded pdb=" OE1 GLU H 73 " pdb=" NH2 ARG H 76 " model vdw 2.398 2.520 nonbonded pdb=" O LEU E 61 " pdb=" NH1 ARG F 36 " model vdw 2.419 2.520 nonbonded pdb=" OG1 THR D 85 " pdb=" OP1 DA J -34 " model vdw 2.429 2.440 ... (remaining 109129 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 36 through 133) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 29 through 122) } 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=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 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: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 44.550 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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 : 0.005 0.039 14186 Z= 0.253 Angle : 0.563 5.488 20485 Z= 0.337 Chirality : 0.035 0.123 2327 Planarity : 0.004 0.046 1513 Dihedral : 26.622 130.630 6125 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.14 % Allowed : 11.19 % Favored : 88.68 % 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: 1.64 (0.28), residues: 852 helix: 2.20 (0.22), residues: 542 sheet: 0.73 (1.53), residues: 18 loop : -1.10 (0.32), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 25 HIS 0.003 0.001 HIS E 39 PHE 0.015 0.002 PHE K 39 TYR 0.012 0.002 TYR B 72 ARG 0.008 0.001 ARG G 70 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 318 time to evaluate : 0.925 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: E 79 LYS cc_start: 0.7642 (tttp) cc_final: 0.7429 (tttm) REVERT: K 25 TRP cc_start: 0.8057 (p-90) cc_final: 0.7686 (p-90) outliers start: 1 outliers final: 1 residues processed: 318 average time/residue: 0.3377 time to fit residues: 141.4835 Evaluate side-chains 256 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 255 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 109 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN F 93 GLN ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS G 83 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 14186 Z= 0.397 Angle : 0.646 12.719 20485 Z= 0.378 Chirality : 0.039 0.131 2327 Planarity : 0.005 0.038 1513 Dihedral : 29.571 133.856 4377 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.32 % Allowed : 16.37 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.29), residues: 852 helix: 2.36 (0.22), residues: 549 sheet: -0.98 (1.02), residues: 28 loop : -0.99 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP K 25 HIS 0.004 0.001 HIS B 75 PHE 0.014 0.002 PHE E 67 TYR 0.033 0.003 TYR H 80 ARG 0.007 0.001 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 256 time to evaluate : 1.004 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: M 1 MET cc_start: 0.6807 (mmm) cc_final: 0.6436 (tpp) REVERT: M 45 PHE cc_start: 0.8033 (t80) cc_final: 0.7611 (t80) outliers start: 39 outliers final: 27 residues processed: 272 average time/residue: 0.3211 time to fit residues: 116.0659 Evaluate side-chains 258 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 231 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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: 0.8040 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14186 Z= 0.205 Angle : 0.552 10.175 20485 Z= 0.328 Chirality : 0.033 0.126 2327 Planarity : 0.004 0.035 1513 Dihedral : 29.310 130.765 4375 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.86 % Allowed : 21.42 % Favored : 75.72 % 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: 2.17 (0.29), residues: 852 helix: 2.70 (0.22), residues: 548 sheet: -1.13 (1.00), residues: 28 loop : -1.00 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 25 HIS 0.004 0.001 HIS F 75 PHE 0.022 0.002 PHE K 39 TYR 0.015 0.002 TYR G 38 ARG 0.007 0.001 ARG G 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 256 time to evaluate : 1.120 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: B 88 TYR cc_start: 0.7184 (m-10) cc_final: 0.6849 (m-10) REVERT: E 73 GLU cc_start: 0.7672 (tp30) cc_final: 0.7471 (tp30) REVERT: M 1 MET cc_start: 0.6858 (mmm) cc_final: 0.6371 (tpp) REVERT: M 45 PHE cc_start: 0.8073 (t80) cc_final: 0.7606 (t80) outliers start: 21 outliers final: 15 residues processed: 262 average time/residue: 0.3290 time to fit residues: 115.4911 Evaluate side-chains 253 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 238 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 42 ARG Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 50 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 102 optimal weight: 0.5980 chunk 108 optimal weight: 0.0000 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14186 Z= 0.179 Angle : 0.532 9.961 20485 Z= 0.318 Chirality : 0.032 0.126 2327 Planarity : 0.004 0.037 1513 Dihedral : 29.179 131.130 4375 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.00 % Allowed : 21.42 % Favored : 75.58 % 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: 2.42 (0.30), residues: 852 helix: 2.90 (0.22), residues: 550 sheet: -0.70 (1.07), residues: 28 loop : -0.97 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 25 HIS 0.003 0.001 HIS F 75 PHE 0.015 0.001 PHE K 39 TYR 0.019 0.002 TYR D 80 ARG 0.010 0.001 ARG K 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 254 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 98 LEU cc_start: 0.8207 (mm) cc_final: 0.7995 (mm) REVERT: M 1 MET cc_start: 0.7013 (mmm) cc_final: 0.6624 (tpp) REVERT: M 45 PHE cc_start: 0.8058 (t80) cc_final: 0.7599 (t80) outliers start: 22 outliers final: 13 residues processed: 263 average time/residue: 0.3072 time to fit residues: 109.3369 Evaluate side-chains 258 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 245 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 44 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14186 Z= 0.222 Angle : 0.560 10.934 20485 Z= 0.328 Chirality : 0.033 0.123 2327 Planarity : 0.004 0.035 1513 Dihedral : 29.195 131.712 4375 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.68 % Allowed : 21.15 % Favored : 75.17 % 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: 2.32 (0.29), residues: 852 helix: 2.81 (0.22), residues: 555 sheet: -0.88 (1.02), residues: 28 loop : -1.06 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP K 25 HIS 0.003 0.001 HIS B 75 PHE 0.013 0.001 PHE K 39 TYR 0.028 0.002 TYR D 80 ARG 0.008 0.000 ARG K 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 244 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 1 MET cc_start: 0.7078 (mmm) cc_final: 0.6726 (tpp) REVERT: M 45 PHE cc_start: 0.8085 (t80) cc_final: 0.7456 (t80) outliers start: 27 outliers final: 21 residues processed: 255 average time/residue: 0.3170 time to fit residues: 109.4139 Evaluate side-chains 258 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 237 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 42 ARG Chi-restraints excluded: chain M residue 44 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 108 optimal weight: 0.0170 chunk 89 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14186 Z= 0.172 Angle : 0.551 10.474 20485 Z= 0.322 Chirality : 0.032 0.126 2327 Planarity : 0.004 0.032 1513 Dihedral : 29.077 131.842 4375 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.59 % Allowed : 24.42 % Favored : 72.99 % 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: 2.48 (0.29), residues: 852 helix: 2.97 (0.22), residues: 555 sheet: -1.14 (1.00), residues: 28 loop : -1.03 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP K 25 HIS 0.003 0.001 HIS E 113 PHE 0.012 0.001 PHE K 39 TYR 0.018 0.002 TYR C 56 ARG 0.006 0.000 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 255 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 1 MET cc_start: 0.7253 (mmm) cc_final: 0.6934 (tpp) REVERT: M 42 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6560 (mpp80) REVERT: M 45 PHE cc_start: 0.8037 (t80) cc_final: 0.7401 (t80) outliers start: 19 outliers final: 15 residues processed: 262 average time/residue: 0.3077 time to fit residues: 110.4017 Evaluate side-chains 260 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 244 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain M residue 42 ARG Chi-restraints excluded: chain M residue 44 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN M 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14186 Z= 0.190 Angle : 0.563 12.859 20485 Z= 0.327 Chirality : 0.033 0.282 2327 Planarity : 0.004 0.044 1513 Dihedral : 29.088 132.337 4375 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.14 % Allowed : 24.01 % Favored : 72.85 % 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: 2.48 (0.29), residues: 852 helix: 2.98 (0.22), residues: 553 sheet: -1.33 (0.98), residues: 28 loop : -1.00 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP K 25 HIS 0.004 0.001 HIS C 30 PHE 0.011 0.001 PHE K 39 TYR 0.023 0.002 TYR B 88 ARG 0.009 0.000 ARG K 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 253 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 45 PHE cc_start: 0.8105 (t80) cc_final: 0.7461 (t80) outliers start: 23 outliers final: 19 residues processed: 261 average time/residue: 0.2897 time to fit residues: 103.5498 Evaluate side-chains 261 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 242 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 42 ARG Chi-restraints excluded: chain M residue 68 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 103 optimal weight: 30.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14186 Z= 0.229 Angle : 0.580 14.094 20485 Z= 0.335 Chirality : 0.033 0.236 2327 Planarity : 0.004 0.043 1513 Dihedral : 29.131 132.649 4375 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.68 % Allowed : 24.01 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.29), residues: 852 helix: 2.87 (0.22), residues: 557 sheet: -1.45 (0.96), residues: 28 loop : -1.07 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP K 25 HIS 0.003 0.001 HIS E 113 PHE 0.011 0.001 PHE E 67 TYR 0.034 0.002 TYR B 88 ARG 0.007 0.000 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 243 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 45 PHE cc_start: 0.8111 (t80) cc_final: 0.7471 (t80) outliers start: 27 outliers final: 22 residues processed: 254 average time/residue: 0.2944 time to fit residues: 101.4191 Evaluate side-chains 259 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 237 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 42 ARG Chi-restraints excluded: chain M residue 68 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 103 optimal weight: 30.0000 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14186 Z= 0.291 Angle : 0.612 14.324 20485 Z= 0.351 Chirality : 0.035 0.249 2327 Planarity : 0.004 0.040 1513 Dihedral : 29.226 132.992 4375 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.37 % Allowed : 23.87 % Favored : 71.76 % 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: 2.10 (0.29), residues: 852 helix: 2.66 (0.22), residues: 557 sheet: -1.57 (0.91), residues: 28 loop : -1.12 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.005 TRP K 25 HIS 0.003 0.001 HIS B 75 PHE 0.011 0.002 PHE E 67 TYR 0.038 0.003 TYR B 88 ARG 0.006 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 243 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 33 ARG cc_start: 0.8479 (mmm-85) cc_final: 0.8113 (mmm-85) REVERT: M 45 PHE cc_start: 0.8120 (t80) cc_final: 0.7464 (t80) outliers start: 32 outliers final: 26 residues processed: 255 average time/residue: 0.2940 time to fit residues: 101.1959 Evaluate side-chains 261 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 235 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 42 ARG Chi-restraints excluded: chain M residue 68 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 111 optimal weight: 50.0000 chunk 102 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN F 25 ASN ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14186 Z= 0.180 Angle : 0.568 11.477 20485 Z= 0.332 Chirality : 0.033 0.243 2327 Planarity : 0.004 0.046 1513 Dihedral : 29.034 131.811 4375 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.73 % Allowed : 25.38 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.29), residues: 852 helix: 2.85 (0.22), residues: 555 sheet: -1.39 (0.93), residues: 28 loop : -0.98 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 25 HIS 0.003 0.001 HIS E 113 PHE 0.013 0.001 PHE E 67 TYR 0.021 0.002 TYR C 56 ARG 0.007 0.000 ARG C 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 250 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 45 PHE cc_start: 0.8092 (t80) cc_final: 0.7441 (t80) outliers start: 20 outliers final: 16 residues processed: 258 average time/residue: 0.2913 time to fit residues: 102.3203 Evaluate side-chains 262 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 246 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 42 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN F 25 ASN ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.082617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.055167 restraints weight = 37258.368| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.67 r_work: 0.2742 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14186 Z= 0.266 Angle : 0.598 12.170 20485 Z= 0.345 Chirality : 0.035 0.182 2327 Planarity : 0.004 0.044 1513 Dihedral : 29.178 132.261 4375 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.86 % Allowed : 25.78 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.29), residues: 852 helix: 2.69 (0.22), residues: 554 sheet: -1.52 (0.87), residues: 28 loop : -1.01 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP K 25 HIS 0.003 0.001 HIS B 75 PHE 0.011 0.001 PHE E 67 TYR 0.038 0.003 TYR B 88 ARG 0.006 0.001 ARG C 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2991.43 seconds wall clock time: 53 minutes 35.83 seconds (3215.83 seconds total)