Starting phenix.real_space_refine on Thu Mar 21 12:31:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c98_16505/03_2024/8c98_16505.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c98_16505/03_2024/8c98_16505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c98_16505/03_2024/8c98_16505.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c98_16505/03_2024/8c98_16505.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c98_16505/03_2024/8c98_16505.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c98_16505/03_2024/8c98_16505.pdb" } resolution = 3.66 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= 0.023 sd= 0.113 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: 5 Type Number sf(0) Gaussians P 1017 5.49 5 S 20 5.16 5 C 15050 2.51 5 N 5646 2.21 5 O 8551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30284 Number of models: 1 Model: "" Number of chains: 12 Chain: "2" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 286 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "E" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1454 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain breaks: 1 Chain: "J" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1055 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain breaks: 1 Chain: "L" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 671 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain breaks: 1 Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 734 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain breaks: 1 Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "A" Number of atoms: 21846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 21846 Classifications: {'DNA': 1, 'RNA': 1017} Modifications used: {'rna2p_pur': 95, 'rna2p_pyr': 52, 'rna3p_pur': 499, 'rna3p_pyr': 371} Incomplete info: {'p_only': 1} Link IDs: {'rna2p': 147, 'rna3p': 870} Unresolved chain links: 2 Chain breaks: 6 Unresolved chain link angles: 11 Unresolved chain link dihedrals: 8 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {' G:plan2': 1, ' G:plan': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 16.30, per 1000 atoms: 0.54 Number of scatterers: 30284 At special positions: 0 Unit cell: (131.25, 190, 167.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 1017 15.00 O 8551 8.00 N 5646 7.00 C 15050 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: 16.79 Conformation dependent library (CDL) restraints added in 1.6 seconds 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2006 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 12 sheets defined 39.5% alpha, 13.6% beta 335 base pairs and 521 stacking pairs defined. Time for finding SS restraints: 12.73 Creating SS restraints... Processing helix chain '2' and resid 10 through 17 Processing helix chain '2' and resid 17 through 24 removed outlier: 3.894A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 38 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 39 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 141 Processing helix chain 'E' and resid 154 through 164 removed outlier: 4.359A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 190 through 201 Processing helix chain 'J' and resid 25 through 37 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 89 through 96 Processing helix chain 'J' and resid 97 through 108 removed outlier: 4.084A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 121 removed outlier: 3.655A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 136 removed outlier: 3.682A pdb=" N ALA J 134 " --> pdb=" O ASN J 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 136 removed outlier: 3.957A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 19 removed outlier: 3.916A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 29 removed outlier: 4.435A pdb=" N ARG Q 27 " --> pdb=" O TYR Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 70 removed outlier: 4.321A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN Q 70 " --> pdb=" O ALA Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 101 through 117 removed outlier: 4.000A pdb=" N PHE Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA Q 117 " --> pdb=" O LYS Q 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 23 removed outlier: 3.865A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 3.860A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 62 removed outlier: 4.098A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 11 removed outlier: 3.840A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 removed outlier: 3.857A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 52 Processing helix chain 'Y' and resid 9 through 34 removed outlier: 3.809A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 56 removed outlier: 4.017A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 Processing sheet with id=AA1, first strand: chain 'E' and resid 118 through 121 removed outlier: 3.843A pdb=" N VAL E 121 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 123 through 125 removed outlier: 6.306A pdb=" N ILE J 54 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N TYR J 125 " --> pdb=" O ILE J 54 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL J 56 " --> pdb=" O TYR J 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 23 through 24 removed outlier: 5.779A pdb=" N LYS J 23 " --> pdb=" O ALA J 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'J' and resid 73 through 74 Processing sheet with id=AA5, first strand: chain 'R' and resid 11 through 14 removed outlier: 6.870A pdb=" N GLN R 6 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL R 38 " --> pdb=" O GLN R 6 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 19 through 22 removed outlier: 7.023A pdb=" N PHE R 93 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N HIS R 66 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL R 64 " --> pdb=" O ASP R 95 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR R 99 " --> pdb=" O LYS R 60 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 72 through 75 Processing sheet with id=AA8, first strand: chain 'S' and resid 2 through 10 removed outlier: 5.611A pdb=" N SER S 101 " --> pdb=" O HIS S 9 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N HIS S 102 " --> pdb=" O VAL S 76 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL S 76 " --> pdb=" O HIS S 102 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR S 104 " --> pdb=" O ILE S 74 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE S 74 " --> pdb=" O THR S 104 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL S 106 " --> pdb=" O THR S 72 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 13 through 14 removed outlier: 4.033A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TRP T 80 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL T 62 " --> pdb=" O TRP T 80 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LYS T 82 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR T 60 " --> pdb=" O LYS T 82 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TYR T 84 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL T 58 " --> pdb=" O TYR T 84 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR T 86 " --> pdb=" O GLU T 56 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.676A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'U' and resid 82 through 86 Processing sheet with id=AB3, first strand: chain 'Z' and resid 34 through 38 340 hydrogen bonds defined for protein. 981 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 853 hydrogen bonds 1378 hydrogen bond angles 0 basepair planarities 335 basepair parallelities 521 stacking parallelities Total time for adding SS restraints: 18.41 Time building geometry restraints manager: 17.69 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: 4501 1.33 - 1.45: 13501 1.45 - 1.57: 12918 1.57 - 1.69: 2027 1.69 - 1.81: 40 Bond restraints: 32987 Sorted by residual: bond pdb=" C1' U A 546 " pdb=" N1 U A 546 " ideal model delta sigma weight residual 1.480 1.573 -0.093 1.50e-02 4.44e+03 3.88e+01 bond pdb=" C1' U A 827 " pdb=" N1 U A 827 " ideal model delta sigma weight residual 1.480 1.573 -0.093 1.50e-02 4.44e+03 3.84e+01 bond pdb=" N MET Y 1 " pdb=" CA MET Y 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N MET J 1 " pdb=" CA MET J 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N MET T 1 " pdb=" CA MET T 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 ... (remaining 32982 not shown) Histogram of bond angle deviations from ideal: 99.77 - 106.61: 6120 106.61 - 113.44: 19596 113.44 - 120.28: 11979 120.28 - 127.11: 9484 127.11 - 133.94: 2379 Bond angle restraints: 49558 Sorted by residual: angle pdb=" N ALA S 64 " pdb=" CA ALA S 64 " pdb=" C ALA S 64 " ideal model delta sigma weight residual 107.73 112.44 -4.71 1.34e+00 5.57e-01 1.24e+01 angle pdb=" C4' U A1019 " pdb=" C3' U A1019 " pdb=" O3' U A1019 " ideal model delta sigma weight residual 109.40 113.45 -4.05 1.50e+00 4.44e-01 7.29e+00 angle pdb=" C3' U A1019 " pdb=" O3' U A1019 " pdb=" P A A1020 " ideal model delta sigma weight residual 120.20 123.94 -3.74 1.50e+00 4.44e-01 6.23e+00 angle pdb=" C4' A A 404 " pdb=" C3' A A 404 " pdb=" O3' A A 404 " ideal model delta sigma weight residual 109.40 112.81 -3.41 1.50e+00 4.44e-01 5.17e+00 angle pdb=" N LYS E 6 " pdb=" CA LYS E 6 " pdb=" CB LYS E 6 " ideal model delta sigma weight residual 113.65 110.36 3.29 1.47e+00 4.63e-01 5.00e+00 ... (remaining 49553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 18569 35.81 - 71.61: 2226 71.61 - 107.42: 276 107.42 - 143.23: 7 143.23 - 179.04: 3 Dihedral angle restraints: 21081 sinusoidal: 17992 harmonic: 3089 Sorted by residual: dihedral pdb=" O4' C A 323 " pdb=" C1' C A 323 " pdb=" N1 C A 323 " pdb=" C2 C A 323 " ideal model delta sinusoidal sigma weight residual -128.00 29.07 -157.07 1 1.70e+01 3.46e-03 6.38e+01 dihedral pdb=" O4' U A1313 " pdb=" C1' U A1313 " pdb=" N1 U A1313 " pdb=" C2 U A1313 " ideal model delta sinusoidal sigma weight residual 200.00 98.74 101.26 1 1.50e+01 4.44e-03 5.10e+01 dihedral pdb=" C4' U A 276 " pdb=" C3' U A 276 " pdb=" O3' U A 276 " pdb=" P G A 277 " ideal model delta sinusoidal sigma weight residual 220.00 40.96 179.04 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 21078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 5571 0.036 - 0.072: 663 0.072 - 0.108: 125 0.108 - 0.143: 47 0.143 - 0.179: 2 Chirality restraints: 6408 Sorted by residual: chirality pdb=" C3' U A1019 " pdb=" C4' U A1019 " pdb=" O3' U A1019 " pdb=" C2' U A1019 " both_signs ideal model delta sigma weight residual False -2.74 -2.57 -0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" C1' U A 827 " pdb=" O4' U A 827 " pdb=" C2' U A 827 " pdb=" N1 U A 827 " both_signs ideal model delta sigma weight residual False 2.47 2.62 -0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CA ILE S 103 " pdb=" N ILE S 103 " pdb=" C ILE S 103 " pdb=" CB ILE S 103 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 6405 not shown) Planarity restraints: 2468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 259 " 0.009 2.00e-02 2.50e+03 1.47e-02 6.47e+00 pdb=" N9 G A 259 " -0.002 2.00e-02 2.50e+03 pdb=" C8 G A 259 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G A 259 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G A 259 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A 259 " -0.011 2.00e-02 2.50e+03 pdb=" O6 G A 259 " 0.013 2.00e-02 2.50e+03 pdb=" N1 G A 259 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 259 " -0.039 2.00e-02 2.50e+03 pdb=" N2 G A 259 " 0.025 2.00e-02 2.50e+03 pdb=" N3 G A 259 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G A 259 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 269 " -0.014 2.00e-02 2.50e+03 1.51e-02 5.13e+00 pdb=" N1 C A 269 " 0.017 2.00e-02 2.50e+03 pdb=" C2 C A 269 " 0.033 2.00e-02 2.50e+03 pdb=" O2 C A 269 " -0.019 2.00e-02 2.50e+03 pdb=" N3 C A 269 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C A 269 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C A 269 " -0.006 2.00e-02 2.50e+03 pdb=" C5 C A 269 " -0.007 2.00e-02 2.50e+03 pdb=" C6 C A 269 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 239 " -0.009 2.00e-02 2.50e+03 1.44e-02 4.69e+00 pdb=" N1 C A 239 " 0.007 2.00e-02 2.50e+03 pdb=" C2 C A 239 " 0.035 2.00e-02 2.50e+03 pdb=" O2 C A 239 " -0.019 2.00e-02 2.50e+03 pdb=" N3 C A 239 " -0.004 2.00e-02 2.50e+03 pdb=" C4 C A 239 " 0.007 2.00e-02 2.50e+03 pdb=" N4 C A 239 " -0.009 2.00e-02 2.50e+03 pdb=" C5 C A 239 " -0.005 2.00e-02 2.50e+03 pdb=" C6 C A 239 " -0.002 2.00e-02 2.50e+03 ... (remaining 2465 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 241 2.52 - 3.11: 21985 3.11 - 3.71: 57922 3.71 - 4.30: 79359 4.30 - 4.90: 110115 Nonbonded interactions: 269622 Sorted by model distance: nonbonded pdb=" O2' A A 126 " pdb=" O4' A A 127 " model vdw 1.923 2.440 nonbonded pdb=" OD2 ASP Q 48 " pdb=" O2' U A 534 " model vdw 1.941 2.440 nonbonded pdb=" OP2 G A 117 " pdb=" O2' A A 119 " model vdw 1.983 2.440 nonbonded pdb=" O2' A A1383 " pdb=" O4' A A1384 " model vdw 1.996 2.440 nonbonded pdb=" O2' A A 299 " pdb=" O4' A A 300 " model vdw 2.004 2.440 ... (remaining 269617 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 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: 0.020 Extract box with map and model: 6.960 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 93.430 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 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 : 0.002 0.093 32987 Z= 0.105 Angle : 0.375 6.083 49558 Z= 0.199 Chirality : 0.027 0.179 6408 Planarity : 0.002 0.021 2468 Dihedral : 22.599 179.037 19075 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % 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: 1.35 (0.28), residues: 1050 helix: 2.69 (0.27), residues: 369 sheet: 0.18 (0.43), residues: 155 loop : -0.16 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 92 HIS 0.005 0.001 HIS Y 41 PHE 0.005 0.001 PHE S 75 TYR 0.006 0.001 TYR T 84 ARG 0.002 0.000 ARG Q 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 95 LEU cc_start: 0.4567 (pt) cc_final: 0.3917 (tt) REVERT: T 1 MET cc_start: 0.4070 (pmm) cc_final: 0.3846 (pmm) REVERT: Y 1 MET cc_start: 0.6249 (tpp) cc_final: 0.5874 (tpp) REVERT: Z 36 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6380 (mm-30) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.4268 time to fit residues: 46.3885 Evaluate side-chains 41 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 20.0000 chunk 154 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 185 optimal weight: 20.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 71 ASN R 6 GLN R 18 GLN Y 41 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 32987 Z= 0.334 Angle : 0.618 10.365 49558 Z= 0.311 Chirality : 0.033 0.199 6408 Planarity : 0.004 0.034 2468 Dihedral : 23.444 176.318 16959 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.57 % Allowed : 5.68 % Favored : 93.75 % 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: 1050 helix: 1.47 (0.26), residues: 375 sheet: 0.03 (0.44), residues: 142 loop : -0.61 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 60 HIS 0.007 0.002 HIS Z 33 PHE 0.021 0.002 PHE 2 18 TYR 0.015 0.002 TYR J 44 ARG 0.006 0.001 ARG 2 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 1.719 Fit side-chains REVERT: L 95 LEU cc_start: 0.4422 (pt) cc_final: 0.4064 (tt) REVERT: R 16 GLU cc_start: 0.7100 (mp0) cc_final: 0.6711 (mp0) REVERT: T 1 MET cc_start: 0.4208 (pmm) cc_final: 0.3881 (pmm) outliers start: 5 outliers final: 5 residues processed: 50 average time/residue: 0.4015 time to fit residues: 34.1018 Evaluate side-chains 46 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 34 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 chunk 126 optimal weight: 30.0000 chunk 51 optimal weight: 9.9990 chunk 185 optimal weight: 20.0000 chunk 200 optimal weight: 50.0000 chunk 165 optimal weight: 10.0000 chunk 184 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 97 ASN S 61 ASN T 48 GLN ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 32987 Z= 0.328 Angle : 0.601 8.952 49558 Z= 0.304 Chirality : 0.033 0.225 6408 Planarity : 0.004 0.035 2468 Dihedral : 23.505 174.432 16959 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.93 % Allowed : 8.86 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1050 helix: 0.92 (0.26), residues: 378 sheet: -0.04 (0.42), residues: 154 loop : -0.99 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 15 HIS 0.006 0.002 HIS E 165 PHE 0.021 0.002 PHE 2 18 TYR 0.012 0.002 TYR J 44 ARG 0.007 0.001 ARG Y 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 47 time to evaluate : 1.555 Fit side-chains REVERT: L 95 LEU cc_start: 0.4413 (pt) cc_final: 0.3985 (tt) REVERT: R 16 GLU cc_start: 0.7493 (mp0) cc_final: 0.7139 (mp0) REVERT: R 31 GLU cc_start: 0.7879 (pt0) cc_final: 0.7451 (pt0) REVERT: S 1 MET cc_start: 0.6887 (ttt) cc_final: 0.6609 (ttp) REVERT: Y 1 MET cc_start: 0.6658 (tpp) cc_final: 0.6364 (tpp) REVERT: Z 36 GLU cc_start: 0.6678 (pp20) cc_final: 0.6346 (pp20) outliers start: 17 outliers final: 11 residues processed: 59 average time/residue: 0.3357 time to fit residues: 36.2465 Evaluate side-chains 54 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 51 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 10.0000 chunk 139 optimal weight: 40.0000 chunk 96 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 124 optimal weight: 30.0000 chunk 186 optimal weight: 10.0000 chunk 197 optimal weight: 20.0000 chunk 97 optimal weight: 0.9980 chunk 176 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 32987 Z= 0.213 Angle : 0.510 9.270 49558 Z= 0.261 Chirality : 0.030 0.212 6408 Planarity : 0.004 0.031 2468 Dihedral : 23.430 174.977 16959 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.39 % Allowed : 11.25 % Favored : 86.36 % 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: -0.10 (0.25), residues: 1050 helix: 1.15 (0.26), residues: 375 sheet: -0.08 (0.41), residues: 155 loop : -0.95 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 15 HIS 0.003 0.001 HIS E 29 PHE 0.013 0.001 PHE 2 18 TYR 0.007 0.001 TYR J 44 ARG 0.003 0.000 ARG Q 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 47 time to evaluate : 1.646 Fit side-chains REVERT: L 95 LEU cc_start: 0.4568 (pt) cc_final: 0.4251 (tt) REVERT: S 1 MET cc_start: 0.6645 (ttt) cc_final: 0.6432 (ttp) REVERT: T 1 MET cc_start: 0.4575 (pmm) cc_final: 0.4072 (pmm) REVERT: Y 1 MET cc_start: 0.6269 (tpp) cc_final: 0.5973 (tpp) REVERT: Z 36 GLU cc_start: 0.6709 (pp20) cc_final: 0.6425 (pp20) outliers start: 21 outliers final: 16 residues processed: 64 average time/residue: 0.3484 time to fit residues: 39.7735 Evaluate side-chains 58 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 42 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 16 HIS Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 56 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 50.0000 chunk 111 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 30.0000 chunk 176 optimal weight: 20.0000 chunk 49 optimal weight: 0.6980 overall best weight: 7.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 7 HIS ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 32987 Z= 0.363 Angle : 0.634 8.511 49558 Z= 0.320 Chirality : 0.034 0.230 6408 Planarity : 0.004 0.032 2468 Dihedral : 23.579 178.718 16959 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 3.30 % Allowed : 11.70 % Favored : 85.00 % 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: -0.52 (0.25), residues: 1050 helix: 0.81 (0.26), residues: 382 sheet: -0.28 (0.40), residues: 154 loop : -1.24 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Q 60 HIS 0.005 0.002 HIS Y 41 PHE 0.024 0.002 PHE 2 18 TYR 0.012 0.002 TYR J 44 ARG 0.004 0.001 ARG T 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 47 time to evaluate : 1.633 Fit side-chains revert: symmetry clash REVERT: L 95 LEU cc_start: 0.4266 (pt) cc_final: 0.3830 (tt) REVERT: S 1 MET cc_start: 0.6749 (ttt) cc_final: 0.6545 (ttp) REVERT: T 79 ASP cc_start: 0.6934 (OUTLIER) cc_final: 0.6438 (p0) REVERT: Z 36 GLU cc_start: 0.6512 (pp20) cc_final: 0.6252 (pp20) outliers start: 29 outliers final: 25 residues processed: 69 average time/residue: 0.3421 time to fit residues: 42.4817 Evaluate side-chains 72 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 46 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 16 HIS Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 56 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 4.9990 chunk 177 optimal weight: 40.0000 chunk 38 optimal weight: 50.0000 chunk 115 optimal weight: 40.0000 chunk 48 optimal weight: 1.9990 chunk 197 optimal weight: 20.0000 chunk 163 optimal weight: 50.0000 chunk 91 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 59 ASN ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 32987 Z= 0.249 Angle : 0.546 8.678 49558 Z= 0.279 Chirality : 0.032 0.233 6408 Planarity : 0.004 0.032 2468 Dihedral : 23.525 178.079 16959 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 2.95 % Allowed : 13.30 % Favored : 83.75 % 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: -0.46 (0.25), residues: 1050 helix: 0.97 (0.26), residues: 376 sheet: -0.37 (0.39), residues: 158 loop : -1.25 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 15 HIS 0.004 0.001 HIS Y 41 PHE 0.014 0.002 PHE 2 18 TYR 0.008 0.001 TYR J 44 ARG 0.004 0.000 ARG Q 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 47 time to evaluate : 1.757 Fit side-chains revert: symmetry clash REVERT: L 95 LEU cc_start: 0.4300 (pt) cc_final: 0.3788 (tt) REVERT: R 16 GLU cc_start: 0.7468 (mp0) cc_final: 0.7199 (mp0) REVERT: Z 36 GLU cc_start: 0.6608 (pp20) cc_final: 0.6295 (pp20) outliers start: 26 outliers final: 23 residues processed: 68 average time/residue: 0.3511 time to fit residues: 43.1740 Evaluate side-chains 70 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 47 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 16 HIS Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 65 ASP Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 56 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 overall best weight: 9.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 32987 Z= 0.456 Angle : 0.704 8.524 49558 Z= 0.349 Chirality : 0.036 0.242 6408 Planarity : 0.005 0.035 2468 Dihedral : 23.574 179.788 16959 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 3.86 % Allowed : 14.55 % Favored : 81.59 % 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: -0.87 (0.25), residues: 1050 helix: 0.66 (0.26), residues: 377 sheet: -0.59 (0.39), residues: 157 loop : -1.53 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 60 HIS 0.008 0.002 HIS Y 41 PHE 0.026 0.003 PHE 2 18 TYR 0.017 0.002 TYR J 44 ARG 0.006 0.001 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 45 time to evaluate : 1.576 Fit side-chains REVERT: L 95 LEU cc_start: 0.4454 (pt) cc_final: 0.4074 (tt) REVERT: R 16 GLU cc_start: 0.7492 (mp0) cc_final: 0.7251 (mp0) REVERT: T 79 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6422 (p0) REVERT: Z 36 GLU cc_start: 0.6600 (pp20) cc_final: 0.6294 (pp20) outliers start: 34 outliers final: 22 residues processed: 74 average time/residue: 0.3895 time to fit residues: 50.9936 Evaluate side-chains 67 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 44 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 16 HIS Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 65 ASP Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 56 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 30.0000 chunk 78 optimal weight: 20.0000 chunk 117 optimal weight: 40.0000 chunk 59 optimal weight: 30.0000 chunk 38 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 178 optimal weight: 40.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 32987 Z= 0.371 Angle : 0.649 8.766 49558 Z= 0.327 Chirality : 0.036 0.276 6408 Planarity : 0.005 0.034 2468 Dihedral : 23.692 178.813 16959 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 3.52 % Allowed : 16.36 % Favored : 80.11 % 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: -0.99 (0.24), residues: 1050 helix: 0.60 (0.26), residues: 375 sheet: -0.68 (0.38), residues: 155 loop : -1.60 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Q 60 HIS 0.005 0.002 HIS Y 41 PHE 0.019 0.002 PHE 2 18 TYR 0.013 0.002 TYR J 44 ARG 0.005 0.001 ARG Y 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 45 time to evaluate : 1.617 Fit side-chains REVERT: L 95 LEU cc_start: 0.4221 (pt) cc_final: 0.3916 (tt) REVERT: R 37 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7397 (tp30) REVERT: T 79 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6412 (p0) REVERT: Z 36 GLU cc_start: 0.6494 (pp20) cc_final: 0.6166 (pp20) outliers start: 31 outliers final: 24 residues processed: 71 average time/residue: 0.3524 time to fit residues: 44.0729 Evaluate side-chains 69 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 43 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 16 HIS Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 65 ASP Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 56 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 30.0000 chunk 171 optimal weight: 30.0000 chunk 183 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 79 optimal weight: 30.0000 chunk 143 optimal weight: 30.0000 chunk 56 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 173 optimal weight: 30.0000 chunk 182 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 overall best weight: 9.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 32987 Z= 0.460 Angle : 0.728 11.725 49558 Z= 0.363 Chirality : 0.039 0.287 6408 Planarity : 0.005 0.033 2468 Dihedral : 23.830 179.949 16959 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 3.41 % Allowed : 17.05 % Favored : 79.55 % 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: -1.29 (0.24), residues: 1050 helix: 0.34 (0.26), residues: 380 sheet: -0.86 (0.37), residues: 155 loop : -1.80 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 60 HIS 0.006 0.002 HIS U 44 PHE 0.026 0.003 PHE 2 18 TYR 0.015 0.002 TYR J 74 ARG 0.005 0.001 ARG Y 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 44 time to evaluate : 1.773 Fit side-chains REVERT: J 92 MET cc_start: 0.7401 (tmm) cc_final: 0.6768 (tpt) REVERT: R 37 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7750 (tp30) REVERT: T 79 ASP cc_start: 0.6953 (OUTLIER) cc_final: 0.6641 (p0) REVERT: Z 36 GLU cc_start: 0.6558 (pp20) cc_final: 0.6320 (pp20) outliers start: 30 outliers final: 25 residues processed: 69 average time/residue: 0.3401 time to fit residues: 42.2479 Evaluate side-chains 68 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 41 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 16 HIS Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 53 MET Chi-restraints excluded: chain Z residue 56 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 10.0000 chunk 118 optimal weight: 50.0000 chunk 91 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 203 optimal weight: 40.0000 chunk 187 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 32987 Z= 0.364 Angle : 0.660 12.285 49558 Z= 0.333 Chirality : 0.036 0.302 6408 Planarity : 0.004 0.032 2468 Dihedral : 23.790 178.195 16959 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 2.95 % Allowed : 17.84 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.24), residues: 1050 helix: 0.55 (0.26), residues: 373 sheet: -0.81 (0.38), residues: 155 loop : -1.75 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Q 60 HIS 0.004 0.002 HIS Y 41 PHE 0.021 0.002 PHE 2 18 TYR 0.011 0.002 TYR J 44 ARG 0.004 0.001 ARG J 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 42 time to evaluate : 1.652 Fit side-chains REVERT: J 92 MET cc_start: 0.7471 (tmm) cc_final: 0.6775 (tpt) REVERT: R 37 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8278 (tp30) REVERT: R 45 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8308 (tm-30) REVERT: T 79 ASP cc_start: 0.6946 (OUTLIER) cc_final: 0.6643 (p0) REVERT: Z 36 GLU cc_start: 0.6564 (pp20) cc_final: 0.6351 (pp20) outliers start: 26 outliers final: 22 residues processed: 65 average time/residue: 0.3300 time to fit residues: 38.6991 Evaluate side-chains 65 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 41 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 16 HIS Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 53 MET Chi-restraints excluded: chain Z residue 56 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 162 optimal weight: 30.0000 chunk 67 optimal weight: 0.5980 chunk 166 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 142 optimal weight: 40.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.050408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.036741 restraints weight = 288572.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.037077 restraints weight = 133190.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.037461 restraints weight = 90896.825| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32987 Z= 0.215 Angle : 0.555 11.996 49558 Z= 0.283 Chirality : 0.032 0.296 6408 Planarity : 0.004 0.032 2468 Dihedral : 23.655 179.694 16959 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.61 % Allowed : 17.95 % Favored : 79.43 % 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: -0.81 (0.25), residues: 1050 helix: 0.86 (0.26), residues: 376 sheet: -0.72 (0.38), residues: 157 loop : -1.56 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 92 HIS 0.003 0.001 HIS S 9 PHE 0.011 0.001 PHE 2 18 TYR 0.007 0.001 TYR T 84 ARG 0.003 0.000 ARG 2 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3066.12 seconds wall clock time: 59 minutes 18.34 seconds (3558.34 seconds total)