Starting phenix.real_space_refine on Fri Feb 16 11:01:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wua_21908/02_2024/6wua_21908.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wua_21908/02_2024/6wua_21908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wua_21908/02_2024/6wua_21908.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wua_21908/02_2024/6wua_21908.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wua_21908/02_2024/6wua_21908.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wua_21908/02_2024/6wua_21908.pdb" } resolution = 3.2 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= -0.001 sd= 0.003 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 402 5.49 5 S 20 5.16 5 C 7975 2.51 5 N 2807 2.21 5 O 3990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c GLU 25": "OE1" <-> "OE2" Residue "g TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 46": "OE1" <-> "OE2" Residue "s GLU 20": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15195 Number of models: 1 Model: "" Number of chains: 9 Chain: "a" Number of atoms: 8569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 8569 Classifications: {'RNA': 402} Modifications used: {'rna2p_pur': 33, 'rna2p_pyr': 39, 'rna3p_pur': 177, 'rna3p_pyr': 153} Link IDs: {'rna2p': 71, 'rna3p': 330} Chain breaks: 1 Chain: "c" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain: "g" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1229 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 7, 'TRANS': 146} Chain: "i" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 990 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 120} Chain: "j" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 92} Chain: "m" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 870 Classifications: {'peptide': 110} Link IDs: {'CIS': 3, 'PTRANS': 2, 'TRANS': 104} Chain: "n" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "s" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 634 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "n" 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 14249 SG CYS n 24 57.908 83.292 49.350 1.00 17.98 S ATOM 14275 SG CYS n 27 61.128 84.467 48.757 1.00 19.90 S ATOM 14387 SG CYS n 40 60.686 82.934 52.027 1.00 18.14 S ATOM 14412 SG CYS n 43 59.723 86.442 51.550 1.00 17.83 S Time building chain proxies: 9.04, per 1000 atoms: 0.59 Number of scatterers: 15195 At special positions: 0 Unit cell: (109.7, 132.737, 127.252, 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 20 16.00 P 402 15.00 O 3990 8.00 N 2807 7.00 C 7975 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: 9.24 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 27 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 43 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 24 " Number of angles added : 6 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1538 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 10 sheets defined 42.4% alpha, 20.4% beta 123 base pairs and 199 stacking pairs defined. Time for finding SS restraints: 7.15 Creating SS restraints... Processing helix chain 'c' and resid 28 through 42 Processing helix chain 'c' and resid 45 through 50 Processing helix chain 'c' and resid 72 through 77 Processing helix chain 'c' and resid 82 through 95 removed outlier: 4.201A pdb=" N LYS c 92 " --> pdb=" O LYS c 88 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU c 93 " --> pdb=" O GLU c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 110 Processing helix chain 'c' and resid 111 through 119 Processing helix chain 'c' and resid 122 through 126 removed outlier: 3.565A pdb=" N ARG c 126 " --> pdb=" O LEU c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 142 removed outlier: 3.662A pdb=" N ALA c 132 " --> pdb=" O ALA c 128 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS c 134 " --> pdb=" O ARG c 130 " (cutoff:3.500A) Processing helix chain 'c' and resid 155 through 159 removed outlier: 3.635A pdb=" N GLY c 158 " --> pdb=" O ARG c 155 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 Processing helix chain 'g' and resid 35 through 53 removed outlier: 3.704A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.515A pdb=" N VAL g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 109 Processing helix chain 'g' and resid 115 through 128 removed outlier: 4.082A pdb=" N LYS g 122 " --> pdb=" O GLU g 118 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 145 Processing helix chain 'g' and resid 149 through 153 removed outlier: 3.674A pdb=" N HIS g 153 " --> pdb=" O ALA g 150 " (cutoff:3.500A) Processing helix chain 'i' and resid 35 through 39 removed outlier: 3.556A pdb=" N ILE i 39 " --> pdb=" O VAL i 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 35 through 39' Processing helix chain 'i' and resid 44 through 49 Processing helix chain 'i' and resid 49 through 55 Processing helix chain 'i' and resid 73 through 91 removed outlier: 3.741A pdb=" N GLY i 77 " --> pdb=" O ALA i 73 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE i 79 " --> pdb=" O GLN i 75 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP i 91 " --> pdb=" O LEU i 87 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 95 Processing helix chain 'i' and resid 96 through 101 removed outlier: 3.601A pdb=" N ALA i 101 " --> pdb=" O ALA i 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 31 Processing helix chain 'j' and resid 82 through 89 removed outlier: 3.711A pdb=" N LYS j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 19 Processing helix chain 'm' and resid 20 through 22 No H-bonds generated for 'chain 'm' and resid 20 through 22' Processing helix chain 'm' and resid 27 through 38 removed outlier: 3.703A pdb=" N VAL m 37 " --> pdb=" O VAL m 33 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 59 removed outlier: 3.557A pdb=" N ASP m 54 " --> pdb=" O ASN m 50 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU m 59 " --> pdb=" O ALA m 55 " (cutoff:3.500A) Processing helix chain 'm' and resid 60 through 63 Processing helix chain 'm' and resid 68 through 81 removed outlier: 3.840A pdb=" N GLU m 72 " --> pdb=" O ASP m 68 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 92 Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 4 through 12 removed outlier: 3.751A pdb=" N ALA n 8 " --> pdb=" O LYS n 4 " (cutoff:3.500A) Processing helix chain 'n' and resid 16 through 20 removed outlier: 3.796A pdb=" N ALA n 20 " --> pdb=" O SER n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 49 removed outlier: 3.985A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU n 46 " --> pdb=" O ILE n 42 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TYR n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 23 Processing helix chain 's' and resid 70 through 75 removed outlier: 3.801A pdb=" N PHE s 74 " --> pdb=" O LEU s 71 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA s 75 " --> pdb=" O GLY s 72 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'c' and resid 51 through 58 removed outlier: 3.958A pdb=" N THR c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'c' and resid 51 through 58 removed outlier: 3.958A pdb=" N THR c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL c 103 " --> pdb=" O ILE c 65 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE c 67 " --> pdb=" O VAL c 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 163 through 165 Processing sheet with id=AA4, first strand: chain 'c' and resid 163 through 165 removed outlier: 3.552A pdb=" N GLY c 147 " --> pdb=" O TYR c 202 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL c 197 " --> pdb=" O GLU c 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'g' and resid 74 through 79 removed outlier: 3.580A pdb=" N GLU g 74 " --> pdb=" O VAL g 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'i' and resid 6 through 12 removed outlier: 6.540A pdb=" N LYS i 27 " --> pdb=" O VAL i 63 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL i 65 " --> pdb=" O LYS i 27 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR i 29 " --> pdb=" O VAL i 65 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL i 67 " --> pdb=" O THR i 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'j' and resid 40 through 52 removed outlier: 6.457A pdb=" N LEU j 73 " --> pdb=" O PRO j 41 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER j 47 " --> pdb=" O MET j 67 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET j 67 " --> pdb=" O SER j 47 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE j 74 " --> pdb=" O ILE j 8 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'j' and resid 40 through 52 removed outlier: 6.457A pdb=" N LEU j 73 " --> pdb=" O PRO j 41 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER j 47 " --> pdb=" O MET j 67 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET j 67 " --> pdb=" O SER j 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'n' and resid 33 through 34 Processing sheet with id=AB1, first strand: chain 's' and resid 32 through 33 removed outlier: 3.684A pdb=" N TYR s 52 " --> pdb=" O THR s 33 " (cutoff:3.500A) 273 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 310 hydrogen bonds 494 hydrogen bond angles 0 basepair planarities 123 basepair parallelities 199 stacking parallelities Total time for adding SS restraints: 6.92 Time building geometry restraints manager: 9.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1771 1.32 - 1.44: 6560 1.44 - 1.56: 7140 1.56 - 1.68: 802 1.68 - 1.80: 36 Bond restraints: 16309 Sorted by residual: bond pdb=" CA PRO i 40 " pdb=" C PRO i 40 " ideal model delta sigma weight residual 1.527 1.502 0.025 1.35e-02 5.49e+03 3.36e+00 bond pdb=" N ALA m 106 " pdb=" CA ALA m 106 " ideal model delta sigma weight residual 1.457 1.441 0.017 1.10e-02 8.26e+03 2.27e+00 bond pdb=" C5 G a1237 " pdb=" C6 G a1237 " ideal model delta sigma weight residual 1.419 1.391 0.028 2.00e-02 2.50e+03 1.95e+00 bond pdb=" O3' G a1237 " pdb=" P C a1238 " ideal model delta sigma weight residual 1.607 1.588 0.019 1.50e-02 4.44e+03 1.65e+00 bond pdb=" P G a1237 " pdb=" O5' G a1237 " ideal model delta sigma weight residual 1.593 1.574 0.019 1.50e-02 4.44e+03 1.60e+00 ... (remaining 16304 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.29: 2449 106.29 - 113.37: 9470 113.37 - 120.44: 6380 120.44 - 127.52: 4867 127.52 - 134.59: 797 Bond angle restraints: 23963 Sorted by residual: angle pdb=" N PRO j 43 " pdb=" CA PRO j 43 " pdb=" C PRO j 43 " ideal model delta sigma weight residual 112.47 120.95 -8.48 2.06e+00 2.36e-01 1.70e+01 angle pdb=" C PRO i 40 " pdb=" N HIS i 41 " pdb=" CA HIS i 41 " ideal model delta sigma weight residual 121.54 113.84 7.70 1.91e+00 2.74e-01 1.63e+01 angle pdb=" N VAL c 75 " pdb=" CA VAL c 75 " pdb=" C VAL c 75 " ideal model delta sigma weight residual 113.71 110.15 3.56 9.50e-01 1.11e+00 1.40e+01 angle pdb=" C3' U a1226 " pdb=" O3' U a1226 " pdb=" P U a1227 " ideal model delta sigma weight residual 120.20 124.97 -4.77 1.50e+00 4.44e-01 1.01e+01 angle pdb=" C2' G a1019 " pdb=" C1' G a1019 " pdb=" N9 G a1019 " ideal model delta sigma weight residual 112.00 107.25 4.75 1.50e+00 4.44e-01 1.00e+01 ... (remaining 23958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.72: 9264 33.72 - 67.44: 1010 67.44 - 101.17: 132 101.17 - 134.89: 3 134.89 - 168.61: 3 Dihedral angle restraints: 10412 sinusoidal: 8021 harmonic: 2391 Sorted by residual: dihedral pdb=" O4' U a1040 " pdb=" C1' U a1040 " pdb=" N1 U a1040 " pdb=" C2 U a1040 " ideal model delta sinusoidal sigma weight residual 200.00 53.67 146.33 1 1.50e+01 4.44e-03 7.82e+01 dihedral pdb=" O4' C a1173 " pdb=" C1' C a1173 " pdb=" N1 C a1173 " pdb=" C2 C a1173 " ideal model delta sinusoidal sigma weight residual 200.00 65.56 134.44 1 1.50e+01 4.44e-03 7.25e+01 dihedral pdb=" O4' U a1152 " pdb=" C1' U a1152 " pdb=" N1 U a1152 " pdb=" C2 U a1152 " ideal model delta sinusoidal sigma weight residual 200.00 67.00 133.00 1 1.50e+01 4.44e-03 7.18e+01 ... (remaining 10409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2274 0.051 - 0.102: 608 0.102 - 0.153: 102 0.153 - 0.203: 17 0.203 - 0.254: 4 Chirality restraints: 3005 Sorted by residual: chirality pdb=" CA PRO j 43 " pdb=" N PRO j 43 " pdb=" C PRO j 43 " pdb=" CB PRO j 43 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C3' A a 974 " pdb=" C4' A a 974 " pdb=" O3' A a 974 " pdb=" C2' A a 974 " both_signs ideal model delta sigma weight residual False -2.48 -2.25 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C1' U a1226 " pdb=" O4' U a1226 " pdb=" C2' U a1226 " pdb=" N1 U a1226 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 3002 not shown) Planarity restraints: 1570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU j 42 " 0.046 5.00e-02 4.00e+02 7.01e-02 7.87e+00 pdb=" N PRO j 43 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO j 43 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO j 43 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G a1019 " -0.038 2.00e-02 2.50e+03 1.59e-02 7.56e+00 pdb=" N9 G a1019 " 0.036 2.00e-02 2.50e+03 pdb=" C8 G a1019 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G a1019 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G a1019 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G a1019 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G a1019 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G a1019 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G a1019 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G a1019 " 0.005 2.00e-02 2.50e+03 pdb=" N3 G a1019 " 0.009 2.00e-02 2.50e+03 pdb=" C4 G a1019 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU j 92 " 0.041 5.00e-02 4.00e+02 6.20e-02 6.16e+00 pdb=" N PRO j 93 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO j 93 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO j 93 " 0.029 5.00e-02 4.00e+02 ... (remaining 1567 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 114 2.57 - 3.16: 11330 3.16 - 3.74: 25652 3.74 - 4.32: 37749 4.32 - 4.90: 53156 Nonbonded interactions: 128001 Sorted by model distance: nonbonded pdb=" O2 U a 976 " pdb=" O2' G a1237 " model vdw 1.992 2.440 nonbonded pdb=" N2 G a1019 " pdb=" N6 A a1052 " model vdw 2.033 2.560 nonbonded pdb=" O4 U a 966 " pdb=" NZ LYS m 103 " model vdw 2.141 2.520 nonbonded pdb=" N1 G a1181 " pdb=" OP2 A a1184 " model vdw 2.166 2.520 nonbonded pdb=" O2' C a1038 " pdb=" O5' U a1039 " model vdw 2.182 2.440 ... (remaining 127996 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 individual isotropic 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: 3.780 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: 18.420 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 53.690 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 : 0.007 0.048 16309 Z= 0.414 Angle : 0.813 8.484 23963 Z= 0.424 Chirality : 0.047 0.254 3005 Planarity : 0.006 0.070 1570 Dihedral : 22.536 168.610 8874 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 15.38 % Favored : 84.49 % Rotamer: Outliers : 14.80 % Allowed : 15.80 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.41 (0.24), residues: 819 helix: -2.49 (0.24), residues: 306 sheet: -2.26 (0.38), residues: 139 loop : -3.57 (0.27), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP c 200 HIS 0.007 0.002 HIS i 41 PHE 0.019 0.002 PHE i 127 TYR 0.019 0.002 TYR i 72 ARG 0.005 0.001 ARG s 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 153 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 200 TRP cc_start: 0.8263 (OUTLIER) cc_final: 0.7747 (m100) REVERT: g 10 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.4988 (tpm170) REVERT: g 13 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7716 (tt) REVERT: i 88 LEU cc_start: 0.8452 (tt) cc_final: 0.8201 (tp) REVERT: j 4 GLN cc_start: 0.5306 (OUTLIER) cc_final: 0.4613 (tm-30) REVERT: m 66 GLU cc_start: 0.4542 (OUTLIER) cc_final: 0.4101 (tm-30) REVERT: m 75 LEU cc_start: 0.8030 (pp) cc_final: 0.7696 (mt) REVERT: m 100 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7656 (mp10) REVERT: m 109 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7715 (tpt-90) REVERT: n 6 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8458 (mtp) REVERT: s 6 LYS cc_start: 0.2590 (OUTLIER) cc_final: 0.2247 (pmtt) REVERT: s 7 LYS cc_start: 0.5564 (OUTLIER) cc_final: 0.3836 (pttt) REVERT: s 27 LYS cc_start: 0.5394 (OUTLIER) cc_final: 0.4796 (mptt) REVERT: s 36 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7015 (mtm110) outliers start: 103 outliers final: 57 residues processed: 233 average time/residue: 0.3470 time to fit residues: 110.0414 Evaluate side-chains 176 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 107 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 39 ARG Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 45 LYS Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 81 SER Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 10 ARG Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 64 GLN Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 155 ARG Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 83 ILE Chi-restraints excluded: chain i residue 130 ARG Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 48 LEU Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 41 GLU Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 103 LYS Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 6 MET Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 17 LYS Chi-restraints excluded: chain s residue 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 45 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 85 ASN g 28 ASN g 64 GLN g 86 GLN i 66 ASN i 81 HIS m 50 ASN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 63 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16309 Z= 0.239 Angle : 0.662 6.960 23963 Z= 0.344 Chirality : 0.041 0.209 3005 Planarity : 0.006 0.060 1570 Dihedral : 22.675 169.822 7332 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.97 % Favored : 88.03 % Rotamer: Outliers : 11.78 % Allowed : 20.11 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.27), residues: 819 helix: -1.14 (0.28), residues: 307 sheet: -1.34 (0.40), residues: 147 loop : -3.23 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 200 HIS 0.004 0.001 HIS c 68 PHE 0.012 0.002 PHE s 74 TYR 0.013 0.001 TYR s 52 ARG 0.004 0.000 ARG j 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 102 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 55 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7038 (tp30) REVERT: c 192 TYR cc_start: 0.7675 (m-80) cc_final: 0.7398 (m-80) REVERT: c 200 TRP cc_start: 0.8288 (OUTLIER) cc_final: 0.7639 (m100) REVERT: g 10 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.4921 (tpm170) REVERT: g 13 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7546 (tt) REVERT: i 88 LEU cc_start: 0.8338 (tt) cc_final: 0.8030 (tp) REVERT: m 74 ASN cc_start: 0.8101 (m-40) cc_final: 0.7624 (m110) REVERT: m 100 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7568 (mp10) REVERT: m 109 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7496 (tpt-90) REVERT: s 7 LYS cc_start: 0.5108 (OUTLIER) cc_final: 0.3679 (pttt) REVERT: s 27 LYS cc_start: 0.5522 (OUTLIER) cc_final: 0.5027 (mptt) outliers start: 82 outliers final: 56 residues processed: 176 average time/residue: 0.3054 time to fit residues: 77.1084 Evaluate side-chains 156 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 92 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 39 ARG Chi-restraints excluded: chain c residue 40 LYS Chi-restraints excluded: chain c residue 45 LYS Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 10 ARG Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain g residue 155 ARG Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 83 ILE Chi-restraints excluded: chain i residue 130 ARG Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 41 GLU Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 17 LYS Chi-restraints excluded: chain s residue 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 67 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 61 ASN g 86 GLN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 16309 Z= 0.381 Angle : 0.784 8.022 23963 Z= 0.400 Chirality : 0.047 0.245 3005 Planarity : 0.007 0.063 1570 Dihedral : 22.741 164.471 7302 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.68 % Favored : 86.32 % Rotamer: Outliers : 12.79 % Allowed : 21.98 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.28), residues: 819 helix: -0.80 (0.29), residues: 301 sheet: -0.98 (0.42), residues: 145 loop : -3.13 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 200 HIS 0.006 0.001 HIS i 41 PHE 0.017 0.002 PHE s 74 TYR 0.017 0.002 TYR i 72 ARG 0.005 0.001 ARG j 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 95 time to evaluate : 1.975 Fit side-chains revert: symmetry clash REVERT: c 192 TYR cc_start: 0.7634 (m-80) cc_final: 0.7328 (m-80) REVERT: c 200 TRP cc_start: 0.8303 (OUTLIER) cc_final: 0.7586 (m100) REVERT: g 13 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7582 (tt) REVERT: g 18 TYR cc_start: 0.6694 (m-80) cc_final: 0.6363 (m-80) REVERT: g 155 ARG cc_start: 0.4535 (OUTLIER) cc_final: 0.3727 (mmm160) REVERT: i 88 LEU cc_start: 0.8384 (tt) cc_final: 0.8046 (tp) REVERT: j 91 ASP cc_start: 0.4377 (OUTLIER) cc_final: 0.4118 (p0) REVERT: m 66 GLU cc_start: 0.5256 (OUTLIER) cc_final: 0.4886 (tm-30) REVERT: m 74 ASN cc_start: 0.8200 (m-40) cc_final: 0.7702 (m110) REVERT: m 100 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7687 (mp10) REVERT: n 6 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8274 (mtp) REVERT: s 6 LYS cc_start: 0.2702 (OUTLIER) cc_final: 0.2317 (pmtt) REVERT: s 7 LYS cc_start: 0.5476 (OUTLIER) cc_final: 0.3809 (pttt) REVERT: s 27 LYS cc_start: 0.5562 (OUTLIER) cc_final: 0.5273 (mptt) outliers start: 89 outliers final: 62 residues processed: 172 average time/residue: 0.2869 time to fit residues: 72.9334 Evaluate side-chains 167 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 95 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 39 ARG Chi-restraints excluded: chain c residue 40 LYS Chi-restraints excluded: chain c residue 48 ASP Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 61 ASN Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 164 SER Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain g residue 155 ARG Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 83 ILE Chi-restraints excluded: chain i residue 93 ASP Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain i residue 130 ARG Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 91 ASP Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 6 MET Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 17 LYS Chi-restraints excluded: chain s residue 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 51 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 52 optimal weight: 0.4980 chunk 73 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 57 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 61 ASN m 50 ASN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16309 Z= 0.197 Angle : 0.605 7.028 23963 Z= 0.316 Chirality : 0.038 0.193 3005 Planarity : 0.005 0.055 1570 Dihedral : 22.463 169.448 7281 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 11.21 % Allowed : 24.57 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.26 (0.28), residues: 819 helix: -0.32 (0.30), residues: 308 sheet: -0.54 (0.42), residues: 147 loop : -3.03 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 200 HIS 0.003 0.001 HIS g 153 PHE 0.009 0.001 PHE s 74 TYR 0.010 0.001 TYR i 72 ARG 0.004 0.000 ARG j 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 94 time to evaluate : 1.415 Fit side-chains revert: symmetry clash REVERT: c 200 TRP cc_start: 0.8276 (OUTLIER) cc_final: 0.7617 (m100) REVERT: g 13 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7490 (tt) REVERT: g 18 TYR cc_start: 0.6582 (m-80) cc_final: 0.6300 (m-80) REVERT: g 155 ARG cc_start: 0.4458 (OUTLIER) cc_final: 0.3814 (mmm160) REVERT: i 16 VAL cc_start: 0.9024 (OUTLIER) cc_final: 0.8774 (t) REVERT: i 88 LEU cc_start: 0.8269 (tt) cc_final: 0.7947 (tp) REVERT: j 91 ASP cc_start: 0.4255 (OUTLIER) cc_final: 0.3987 (p0) REVERT: m 66 GLU cc_start: 0.5218 (OUTLIER) cc_final: 0.4633 (tm-30) REVERT: m 74 ASN cc_start: 0.8211 (m-40) cc_final: 0.7692 (m-40) REVERT: m 100 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7304 (mp10) REVERT: m 105 ASN cc_start: 0.6139 (t0) cc_final: 0.5707 (t0) REVERT: m 109 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7486 (tpt-90) REVERT: s 7 LYS cc_start: 0.5147 (OUTLIER) cc_final: 0.3622 (pttt) REVERT: s 27 LYS cc_start: 0.5412 (OUTLIER) cc_final: 0.4552 (mptt) REVERT: s 37 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7122 (ptp-170) outliers start: 78 outliers final: 52 residues processed: 162 average time/residue: 0.2856 time to fit residues: 67.6447 Evaluate side-chains 155 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 92 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 39 ARG Chi-restraints excluded: chain c residue 40 LYS Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain c residue 164 SER Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain g residue 155 ARG Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 55 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain i residue 130 ARG Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 91 ASP Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 42 ASP Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 17 LYS Chi-restraints excluded: chain s residue 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 86 optimal weight: 0.0270 chunk 47 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 80 optimal weight: 0.1980 chunk 0 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 61 ASN m 105 ASN n 10 ASN n 38 HIS ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16309 Z= 0.124 Angle : 0.507 6.894 23963 Z= 0.265 Chirality : 0.034 0.184 3005 Planarity : 0.004 0.058 1570 Dihedral : 22.307 174.366 7271 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 7.04 % Allowed : 28.30 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % 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: -1.68 (0.29), residues: 819 helix: 0.17 (0.31), residues: 310 sheet: -0.23 (0.42), residues: 147 loop : -2.73 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 200 HIS 0.002 0.001 HIS c 6 PHE 0.005 0.001 PHE n 44 TYR 0.007 0.001 TYR c 183 ARG 0.005 0.000 ARG j 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 98 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: c 66 SER cc_start: 0.8733 (p) cc_final: 0.8526 (p) REVERT: c 200 TRP cc_start: 0.8274 (OUTLIER) cc_final: 0.7817 (m100) REVERT: g 13 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7282 (tt) REVERT: g 18 TYR cc_start: 0.6456 (m-80) cc_final: 0.6243 (m-80) REVERT: g 155 ARG cc_start: 0.4454 (OUTLIER) cc_final: 0.3918 (mmm160) REVERT: i 16 VAL cc_start: 0.9004 (OUTLIER) cc_final: 0.8780 (t) REVERT: i 88 LEU cc_start: 0.8271 (tt) cc_final: 0.7970 (tp) REVERT: j 48 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8475 (tp) REVERT: m 48 LEU cc_start: 0.7796 (mt) cc_final: 0.7292 (mp) REVERT: m 74 ASN cc_start: 0.8265 (m-40) cc_final: 0.7767 (m-40) REVERT: m 105 ASN cc_start: 0.5903 (t0) cc_final: 0.5523 (t0) REVERT: m 109 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7285 (tpt-90) REVERT: s 27 LYS cc_start: 0.5384 (OUTLIER) cc_final: 0.4365 (mptt) REVERT: s 37 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.6869 (ptp-170) outliers start: 49 outliers final: 27 residues processed: 139 average time/residue: 0.2928 time to fit residues: 59.6750 Evaluate side-chains 125 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 90 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 40 LYS Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain g residue 155 ARG Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 48 LEU Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 45 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 8.9990 chunk 104 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 61 ASN ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16309 Z= 0.232 Angle : 0.609 7.423 23963 Z= 0.316 Chirality : 0.039 0.204 3005 Planarity : 0.005 0.068 1570 Dihedral : 22.235 169.535 7231 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 8.91 % Allowed : 27.16 % Favored : 63.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % 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: -1.75 (0.29), residues: 819 helix: 0.04 (0.31), residues: 313 sheet: -0.14 (0.43), residues: 147 loop : -2.78 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 200 HIS 0.004 0.001 HIS i 41 PHE 0.013 0.002 PHE s 74 TYR 0.016 0.002 TYR g 154 ARG 0.005 0.000 ARG j 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 96 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: c 66 SER cc_start: 0.8805 (p) cc_final: 0.8543 (p) REVERT: c 200 TRP cc_start: 0.8360 (OUTLIER) cc_final: 0.7788 (m100) REVERT: g 18 TYR cc_start: 0.6593 (m-80) cc_final: 0.6373 (m-80) REVERT: i 16 VAL cc_start: 0.9030 (OUTLIER) cc_final: 0.8805 (t) REVERT: i 88 LEU cc_start: 0.8316 (tt) cc_final: 0.8067 (tp) REVERT: i 113 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.6941 (ptt90) REVERT: j 91 ASP cc_start: 0.4278 (OUTLIER) cc_final: 0.4046 (p0) REVERT: m 100 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7276 (mp10) REVERT: m 109 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7468 (tpt-90) REVERT: n 6 MET cc_start: 0.8688 (mmm) cc_final: 0.8034 (mmp) REVERT: s 27 LYS cc_start: 0.5345 (OUTLIER) cc_final: 0.4413 (mptt) REVERT: s 37 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.6963 (ptp-170) outliers start: 62 outliers final: 43 residues processed: 151 average time/residue: 0.2636 time to fit residues: 59.5427 Evaluate side-chains 144 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 93 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 61 ASN Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 164 SER Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain g residue 155 ARG Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 55 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 83 ILE Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 48 LEU Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 91 ASP Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 65 optimal weight: 0.0980 chunk 97 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 61 ASN g 86 GLN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16309 Z= 0.218 Angle : 0.605 9.856 23963 Z= 0.313 Chirality : 0.039 0.202 3005 Planarity : 0.005 0.061 1570 Dihedral : 22.230 169.232 7229 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 8.62 % Allowed : 26.87 % Favored : 64.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.68 (0.29), residues: 819 helix: 0.03 (0.30), residues: 314 sheet: -0.12 (0.42), residues: 147 loop : -2.66 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 200 HIS 0.007 0.001 HIS g 153 PHE 0.012 0.001 PHE s 74 TYR 0.017 0.002 TYR g 154 ARG 0.006 0.000 ARG j 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 93 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 200 TRP cc_start: 0.8354 (OUTLIER) cc_final: 0.7759 (m100) REVERT: g 18 TYR cc_start: 0.6646 (m-80) cc_final: 0.6405 (m-80) REVERT: g 155 ARG cc_start: 0.4189 (OUTLIER) cc_final: 0.3981 (mmm160) REVERT: i 16 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8796 (t) REVERT: i 88 LEU cc_start: 0.8323 (tt) cc_final: 0.8071 (tp) REVERT: i 113 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.6920 (ptt90) REVERT: j 91 ASP cc_start: 0.4244 (OUTLIER) cc_final: 0.4011 (p0) REVERT: m 74 ASN cc_start: 0.8267 (m-40) cc_final: 0.7680 (m-40) REVERT: m 100 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7259 (mp10) REVERT: m 105 ASN cc_start: 0.6070 (t0) cc_final: 0.5653 (t0) REVERT: m 109 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7465 (tpt-90) REVERT: s 27 LYS cc_start: 0.5303 (OUTLIER) cc_final: 0.4427 (mptt) REVERT: s 37 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7071 (ptp-170) outliers start: 60 outliers final: 45 residues processed: 146 average time/residue: 0.2604 time to fit residues: 57.4475 Evaluate side-chains 146 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 92 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 61 ASN Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 164 SER Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain g residue 155 ARG Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 55 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 48 LEU Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 91 ASP Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 61 ASN g 86 GLN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16309 Z= 0.276 Angle : 0.664 9.529 23963 Z= 0.342 Chirality : 0.042 0.221 3005 Planarity : 0.005 0.072 1570 Dihedral : 22.291 166.953 7229 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.21 % Favored : 87.79 % Rotamer: Outliers : 9.34 % Allowed : 26.87 % Favored : 63.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.74 (0.29), residues: 819 helix: -0.02 (0.31), residues: 307 sheet: -0.20 (0.42), residues: 147 loop : -2.63 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 200 HIS 0.007 0.001 HIS g 153 PHE 0.015 0.002 PHE s 74 TYR 0.019 0.002 TYR g 154 ARG 0.006 0.001 ARG j 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 93 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: c 200 TRP cc_start: 0.8357 (OUTLIER) cc_final: 0.7724 (m100) REVERT: g 18 TYR cc_start: 0.6696 (m-80) cc_final: 0.6446 (m-80) REVERT: g 155 ARG cc_start: 0.4108 (OUTLIER) cc_final: 0.3873 (mmm160) REVERT: i 16 VAL cc_start: 0.9045 (OUTLIER) cc_final: 0.8800 (t) REVERT: i 88 LEU cc_start: 0.8342 (tt) cc_final: 0.8103 (tp) REVERT: i 113 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.6997 (ptt90) REVERT: j 91 ASP cc_start: 0.4254 (OUTLIER) cc_final: 0.4001 (p0) REVERT: m 66 GLU cc_start: 0.5142 (OUTLIER) cc_final: 0.4575 (tm-30) REVERT: m 74 ASN cc_start: 0.8302 (m-40) cc_final: 0.7723 (m-40) REVERT: m 100 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7345 (mp10) REVERT: m 105 ASN cc_start: 0.6228 (t0) cc_final: 0.5870 (t0) REVERT: m 109 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7540 (tpt-90) REVERT: s 27 LYS cc_start: 0.5380 (OUTLIER) cc_final: 0.4526 (mptt) REVERT: s 37 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7095 (ptp-170) outliers start: 65 outliers final: 48 residues processed: 153 average time/residue: 0.2851 time to fit residues: 66.7724 Evaluate side-chains 150 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 92 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 61 ASN Chi-restraints excluded: chain c residue 66 SER Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 164 SER Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain g residue 155 ARG Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 55 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 83 ILE Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 48 LEU Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 91 ASP Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 61 ASN c 151 GLN g 86 GLN j 4 GLN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16309 Z= 0.148 Angle : 0.544 8.467 23963 Z= 0.284 Chirality : 0.036 0.180 3005 Planarity : 0.004 0.065 1570 Dihedral : 22.198 172.057 7229 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 6.47 % Allowed : 29.89 % Favored : 63.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.47 (0.30), residues: 819 helix: 0.17 (0.31), residues: 314 sheet: 0.01 (0.43), residues: 147 loop : -2.52 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 200 HIS 0.008 0.001 HIS g 153 PHE 0.010 0.001 PHE s 74 TYR 0.009 0.001 TYR c 183 ARG 0.008 0.000 ARG j 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 88 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 200 TRP cc_start: 0.8320 (OUTLIER) cc_final: 0.7741 (m100) REVERT: i 16 VAL cc_start: 0.9013 (OUTLIER) cc_final: 0.8784 (t) REVERT: i 88 LEU cc_start: 0.8285 (tt) cc_final: 0.8044 (tp) REVERT: i 113 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.6973 (ptt90) REVERT: j 48 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8501 (tp) REVERT: j 91 ASP cc_start: 0.4236 (OUTLIER) cc_final: 0.4006 (p0) REVERT: m 74 ASN cc_start: 0.8215 (m-40) cc_final: 0.7591 (m-40) REVERT: m 105 ASN cc_start: 0.5946 (t0) cc_final: 0.5549 (t0) REVERT: m 109 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7307 (tpt-90) REVERT: n 6 MET cc_start: 0.8565 (mmm) cc_final: 0.8169 (mmp) REVERT: s 27 LYS cc_start: 0.5271 (OUTLIER) cc_final: 0.4432 (mptt) REVERT: s 37 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7039 (ptp-170) outliers start: 45 outliers final: 31 residues processed: 130 average time/residue: 0.2690 time to fit residues: 53.0754 Evaluate side-chains 126 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 87 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 61 ASN Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain j residue 48 LEU Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 91 ASP Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 61 ASN c 151 GLN g 86 GLN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16309 Z= 0.189 Angle : 0.574 8.932 23963 Z= 0.298 Chirality : 0.037 0.191 3005 Planarity : 0.005 0.070 1570 Dihedral : 22.175 170.454 7223 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.23 % Favored : 88.77 % Rotamer: Outliers : 6.18 % Allowed : 29.60 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.45 (0.30), residues: 819 helix: 0.21 (0.31), residues: 314 sheet: 0.02 (0.43), residues: 147 loop : -2.53 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 200 HIS 0.008 0.001 HIS g 153 PHE 0.013 0.001 PHE s 74 TYR 0.020 0.002 TYR g 154 ARG 0.008 0.000 ARG g 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 91 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 200 TRP cc_start: 0.8323 (OUTLIER) cc_final: 0.7727 (m100) REVERT: i 16 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.8801 (t) REVERT: i 88 LEU cc_start: 0.8314 (tt) cc_final: 0.8085 (tp) REVERT: i 113 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.6928 (ptt90) REVERT: j 80 THR cc_start: 0.5261 (t) cc_final: 0.5044 (p) REVERT: j 91 ASP cc_start: 0.4235 (OUTLIER) cc_final: 0.3996 (p0) REVERT: m 74 ASN cc_start: 0.8248 (m-40) cc_final: 0.7623 (m-40) REVERT: m 100 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7167 (mp10) REVERT: m 105 ASN cc_start: 0.6064 (t0) cc_final: 0.5707 (t0) REVERT: n 6 MET cc_start: 0.8632 (mmm) cc_final: 0.8103 (mmp) REVERT: s 27 LYS cc_start: 0.5356 (OUTLIER) cc_final: 0.4492 (mptt) REVERT: s 37 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7049 (ptp-170) outliers start: 43 outliers final: 36 residues processed: 128 average time/residue: 0.2544 time to fit residues: 49.4333 Evaluate side-chains 134 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 91 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 61 ASN Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 55 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain j residue 48 LEU Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 91 ASP Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 95 optimal weight: 0.0770 chunk 39 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 61 ASN g 86 GLN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.074798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.062335 restraints weight = 50434.679| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.39 r_work: 0.3033 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16309 Z= 0.293 Angle : 0.679 9.798 23963 Z= 0.349 Chirality : 0.042 0.230 3005 Planarity : 0.005 0.069 1570 Dihedral : 22.266 166.902 7222 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.58 % Favored : 87.42 % Rotamer: Outliers : 8.19 % Allowed : 27.73 % Favored : 64.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.58 (0.29), residues: 819 helix: 0.08 (0.31), residues: 309 sheet: -0.08 (0.43), residues: 147 loop : -2.54 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 200 HIS 0.008 0.001 HIS g 153 PHE 0.017 0.002 PHE s 74 TYR 0.016 0.002 TYR i 72 ARG 0.009 0.001 ARG g 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2874.61 seconds wall clock time: 53 minutes 19.49 seconds (3199.49 seconds total)