Starting phenix.real_space_refine on Thu Feb 15 06:26:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce1_16597/02_2024/8ce1_16597.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce1_16597/02_2024/8ce1_16597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce1_16597/02_2024/8ce1_16597.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce1_16597/02_2024/8ce1_16597.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce1_16597/02_2024/8ce1_16597.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce1_16597/02_2024/8ce1_16597.pdb" } resolution = 3.47 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= 0.009 sd= 0.110 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 7496 2.51 5 N 1974 2.21 5 O 1910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 10": "OE1" <-> "OE2" Residue "A GLU 30": "OE1" <-> "OE2" Residue "C GLU 229": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11438 Number of models: 1 Model: "" Number of chains: 8 Chain: "a" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1595 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 6, 'TRANS': 196} Chain: "b" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1656 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 202} Chain: "c" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1930 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 11, 'TRANS': 229} Chain: "d" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 538 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "A" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1595 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 6, 'TRANS': 196} Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1656 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 202} Chain: "C" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1930 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 11, 'TRANS': 229} Chain: "D" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 538 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 65} Time building chain proxies: 6.61, per 1000 atoms: 0.58 Number of scatterers: 11438 At special positions: 0 Unit cell: (83.52, 120.93, 107.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1910 8.00 N 1974 7.00 C 7496 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: 4.53 Conformation dependent library (CDL) restraints added in 3.0 seconds 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2704 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 5 sheets defined 73.5% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'a' and resid 42 through 50 Processing helix chain 'a' and resid 70 through 75 Processing helix chain 'a' and resid 92 through 100 removed outlier: 3.931A pdb=" N TYR a 100 " --> pdb=" O ASN a 96 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 116 removed outlier: 3.720A pdb=" N ALA a 116 " --> pdb=" O ALA a 112 " (cutoff:3.500A) Processing helix chain 'a' and resid 125 through 129 Processing helix chain 'a' and resid 130 through 141 removed outlier: 3.830A pdb=" N VAL a 137 " --> pdb=" O GLN a 133 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA a 138 " --> pdb=" O GLN a 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 142 through 144 No H-bonds generated for 'chain 'a' and resid 142 through 144' Processing helix chain 'a' and resid 160 through 177 removed outlier: 3.874A pdb=" N GLN a 177 " --> pdb=" O GLN a 173 " (cutoff:3.500A) Processing helix chain 'b' and resid 3 through 17 removed outlier: 3.662A pdb=" N PHE b 7 " --> pdb=" O PHE b 3 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N HIS b 17 " --> pdb=" O VAL b 13 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 20 No H-bonds generated for 'chain 'b' and resid 18 through 20' Processing helix chain 'b' and resid 21 through 40 removed outlier: 4.396A pdb=" N LEU b 25 " --> pdb=" O ILE b 21 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE b 35 " --> pdb=" O VAL b 31 " (cutoff:3.500A) Proline residue: b 36 - end of helix Processing helix chain 'b' and resid 42 through 66 Proline residue: b 51 - end of helix Processing helix chain 'b' and resid 66 through 77 removed outlier: 4.330A pdb=" N PHE b 70 " --> pdb=" O LEU b 66 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASP b 72 " --> pdb=" O ARG b 68 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASP b 73 " --> pdb=" O LEU b 69 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU b 74 " --> pdb=" O PHE b 70 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN b 75 " --> pdb=" O ARG b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 84 removed outlier: 3.920A pdb=" N GLN b 81 " --> pdb=" O GLY b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 88 through 119 removed outlier: 3.587A pdb=" N VAL b 92 " --> pdb=" O PRO b 88 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU b 106 " --> pdb=" O MET b 102 " (cutoff:3.500A) Proline residue: b 107 - end of helix Proline residue: b 113 - end of helix removed outlier: 3.503A pdb=" N LEU b 119 " --> pdb=" O VAL b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 151 Proline residue: b 138 - end of helix Proline residue: b 146 - end of helix Processing helix chain 'b' and resid 159 through 169 Proline residue: b 167 - end of helix Processing helix chain 'b' and resid 169 through 185 removed outlier: 3.594A pdb=" N MET b 185 " --> pdb=" O ASP b 181 " (cutoff:3.500A) Processing helix chain 'b' and resid 189 through 220 Proline residue: b 208 - end of helix removed outlier: 4.405A pdb=" N ALA b 213 " --> pdb=" O PHE b 209 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA b 214 " --> pdb=" O ALA b 210 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 9 Processing helix chain 'c' and resid 10 through 41 Proline residue: c 23 - end of helix Processing helix chain 'c' and resid 50 through 54 removed outlier: 3.592A pdb=" N SER c 53 " --> pdb=" O GLN c 50 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR c 54 " --> pdb=" O GLY c 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 50 through 54' Processing helix chain 'c' and resid 55 through 83 removed outlier: 3.986A pdb=" N LEU c 59 " --> pdb=" O ARG c 55 " (cutoff:3.500A) Proline residue: c 62 - end of helix removed outlier: 3.853A pdb=" N SER c 67 " --> pdb=" O ALA c 63 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR c 71 " --> pdb=" O SER c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 86 through 120 removed outlier: 3.698A pdb=" N ASN c 90 " --> pdb=" O MET c 86 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA c 94 " --> pdb=" O ASN c 90 " (cutoff:3.500A) Proline residue: c 98 - end of helix Proline residue: c 117 - end of helix Processing helix chain 'c' and resid 126 through 149 removed outlier: 3.568A pdb=" N PHE c 149 " --> pdb=" O LEU c 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 151 through 184 Proline residue: c 171 - end of helix Processing helix chain 'c' and resid 198 through 229 removed outlier: 3.882A pdb=" N LEU c 202 " --> pdb=" O MET c 198 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG c 222 " --> pdb=" O LEU c 218 " (cutoff:3.500A) Processing helix chain 'c' and resid 232 through 242 removed outlier: 3.846A pdb=" N SER c 236 " --> pdb=" O ARG c 232 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 12 removed outlier: 3.911A pdb=" N PHE d 12 " --> pdb=" O TRP d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 17 through 69 removed outlier: 4.292A pdb=" N VAL d 21 " --> pdb=" O TYR d 17 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TRP d 22 " --> pdb=" O ALA d 18 " (cutoff:3.500A) Proline residue: d 31 - end of helix Processing helix chain 'A' and resid 41 through 50 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.926A pdb=" N TYR A 100 " --> pdb=" O ASN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.616A pdb=" N ALA A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 130 through 141 removed outlier: 3.817A pdb=" N VAL A 137 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 145 removed outlier: 3.504A pdb=" N THR A 145 " --> pdb=" O LEU A 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 145' Processing helix chain 'A' and resid 160 through 177 removed outlier: 3.790A pdb=" N GLN A 177 " --> pdb=" O GLN A 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 17 removed outlier: 3.598A pdb=" N PHE B 7 " --> pdb=" O PHE B 3 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N HIS B 17 " --> pdb=" O VAL B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 21 Processing helix chain 'B' and resid 22 through 40 removed outlier: 3.880A pdb=" N PHE B 35 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Proline residue: B 36 - end of helix Processing helix chain 'B' and resid 42 through 66 Proline residue: B 51 - end of helix Processing helix chain 'B' and resid 66 through 77 removed outlier: 4.263A pdb=" N PHE B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASP B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASP B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 74 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 removed outlier: 3.656A pdb=" N GLN B 81 " --> pdb=" O GLY B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 120 removed outlier: 3.544A pdb=" N VAL B 92 " --> pdb=" O PRO B 88 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU B 106 " --> pdb=" O MET B 102 " (cutoff:3.500A) Proline residue: B 107 - end of helix Proline residue: B 113 - end of helix removed outlier: 3.563A pdb=" N GLY B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 151 Proline residue: B 138 - end of helix Proline residue: B 146 - end of helix Processing helix chain 'B' and resid 158 through 185 removed outlier: 4.101A pdb=" N SER B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Proline residue: B 167 - end of helix Proline residue: B 171 - end of helix removed outlier: 3.616A pdb=" N MET B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 220 Proline residue: B 208 - end of helix removed outlier: 4.120A pdb=" N ALA B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 8 Processing helix chain 'C' and resid 10 through 41 Proline residue: C 23 - end of helix Processing helix chain 'C' and resid 50 through 54 removed outlier: 3.645A pdb=" N SER C 53 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR C 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 50 through 54' Processing helix chain 'C' and resid 55 through 83 removed outlier: 4.094A pdb=" N LEU C 59 " --> pdb=" O ARG C 55 " (cutoff:3.500A) Proline residue: C 62 - end of helix removed outlier: 3.788A pdb=" N SER C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 120 removed outlier: 3.740A pdb=" N ASN C 90 " --> pdb=" O MET C 86 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) Proline residue: C 98 - end of helix Proline residue: C 117 - end of helix Processing helix chain 'C' and resid 126 through 149 removed outlier: 3.645A pdb=" N PHE C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 181 Proline residue: C 171 - end of helix Processing helix chain 'C' and resid 199 through 229 removed outlier: 3.806A pdb=" N ARG C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 242 removed outlier: 3.734A pdb=" N SER C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 12 removed outlier: 3.885A pdb=" N PHE D 12 " --> pdb=" O TRP D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 69 Proline residue: D 31 - end of helix removed outlier: 3.742A pdb=" N HIS D 43 " --> pdb=" O SER D 39 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 17 through 26 removed outlier: 6.864A pdb=" N LEU a 18 " --> pdb=" O GLU a 12 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N GLU a 12 " --> pdb=" O LEU a 18 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER a 20 " --> pdb=" O LEU a 10 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU a 10 " --> pdb=" O SER a 20 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU a 22 " --> pdb=" O GLU a 8 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU a 4 " --> pdb=" O LEU a 26 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU a 9 " --> pdb=" O ALA a 57 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ALA a 57 " --> pdb=" O LEU a 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 32 through 34 Processing sheet with id=AA3, first strand: chain 'a' and resid 78 through 81 removed outlier: 6.211A pdb=" N LEU a 79 " --> pdb=" O ILE a 151 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ASP a 153 " --> pdb=" O LEU a 79 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE a 81 " --> pdb=" O ASP a 153 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N TRP a 150 " --> pdb=" O ILE a 182 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N THR a 184 " --> pdb=" O TRP a 150 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU a 152 " --> pdb=" O THR a 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 16 through 25 removed outlier: 6.787A pdb=" N LEU A 18 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLU A 12 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N SER A 20 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU A 10 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU A 22 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A 9 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA A 57 " --> pdb=" O LEU A 9 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 78 through 81 removed outlier: 6.214A pdb=" N LEU A 79 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ASP A 153 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE A 81 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL A 32 " --> pdb=" O VAL A 181 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 2136 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.47 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2570 1.33 - 1.45: 2490 1.45 - 1.57: 6560 1.57 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 11730 Sorted by residual: bond pdb=" CA MET C 198 " pdb=" C MET C 198 " ideal model delta sigma weight residual 1.523 1.474 0.049 1.61e-02 3.86e+03 9.24e+00 bond pdb=" CA ALA C 197 " pdb=" C ALA C 197 " ideal model delta sigma weight residual 1.522 1.487 0.035 1.33e-02 5.65e+03 6.92e+00 bond pdb=" CB TRP C 39 " pdb=" CG TRP C 39 " ideal model delta sigma weight residual 1.498 1.570 -0.072 3.10e-02 1.04e+03 5.33e+00 bond pdb=" C ILE c 22 " pdb=" N PRO c 23 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.97e+00 bond pdb=" N MET C 198 " pdb=" CA MET C 198 " ideal model delta sigma weight residual 1.460 1.428 0.032 1.45e-02 4.76e+03 4.89e+00 ... (remaining 11725 not shown) Histogram of bond angle deviations from ideal: 96.70 - 104.21: 209 104.21 - 111.72: 5483 111.72 - 119.24: 4353 119.24 - 126.75: 5685 126.75 - 134.27: 276 Bond angle restraints: 16006 Sorted by residual: angle pdb=" N MET C 198 " pdb=" CA MET C 198 " pdb=" C MET C 198 " ideal model delta sigma weight residual 110.44 96.70 13.74 1.20e+00 6.94e-01 1.31e+02 angle pdb=" N GLN c 16 " pdb=" CA GLN c 16 " pdb=" CB GLN c 16 " ideal model delta sigma weight residual 110.30 118.21 -7.91 1.54e+00 4.22e-01 2.64e+01 angle pdb=" CA TRP C 39 " pdb=" CB TRP C 39 " pdb=" CG TRP C 39 " ideal model delta sigma weight residual 113.60 122.59 -8.99 1.90e+00 2.77e-01 2.24e+01 angle pdb=" N GLN C 16 " pdb=" CA GLN C 16 " pdb=" CB GLN C 16 " ideal model delta sigma weight residual 110.30 117.56 -7.26 1.54e+00 4.22e-01 2.22e+01 angle pdb=" N ALA C 197 " pdb=" CA ALA C 197 " pdb=" C ALA C 197 " ideal model delta sigma weight residual 113.56 107.21 6.35 1.39e+00 5.18e-01 2.09e+01 ... (remaining 16001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 5888 16.10 - 32.21: 729 32.21 - 48.31: 193 48.31 - 64.41: 25 64.41 - 80.51: 7 Dihedral angle restraints: 6842 sinusoidal: 2660 harmonic: 4182 Sorted by residual: dihedral pdb=" CA ASN C 181 " pdb=" C ASN C 181 " pdb=" N THR C 182 " pdb=" CA THR C 182 " ideal model delta harmonic sigma weight residual 180.00 155.68 24.32 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA THR C 182 " pdb=" C THR C 182 " pdb=" N LEU C 183 " pdb=" CA LEU C 183 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA LEU A 110 " pdb=" C LEU A 110 " pdb=" N GLU A 111 " pdb=" CA GLU A 111 " ideal model delta harmonic sigma weight residual 180.00 156.50 23.50 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 6839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1357 0.057 - 0.114: 401 0.114 - 0.171: 96 0.171 - 0.228: 12 0.228 - 0.285: 4 Chirality restraints: 1870 Sorted by residual: chirality pdb=" CB VAL a 70 " pdb=" CA VAL a 70 " pdb=" CG1 VAL a 70 " pdb=" CG2 VAL a 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB VAL A 70 " pdb=" CA VAL A 70 " pdb=" CG1 VAL A 70 " pdb=" CG2 VAL A 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA TRP b 55 " pdb=" N TRP b 55 " pdb=" C TRP b 55 " pdb=" CB TRP b 55 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1867 not shown) Planarity restraints: 1978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE b 35 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO b 36 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO b 36 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO b 36 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 89 " 0.063 5.00e-02 4.00e+02 9.45e-02 1.43e+01 pdb=" N PRO B 90 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO B 90 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 90 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU b 89 " -0.061 5.00e-02 4.00e+02 9.06e-02 1.31e+01 pdb=" N PRO b 90 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO b 90 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO b 90 " -0.050 5.00e-02 4.00e+02 ... (remaining 1975 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 515 2.73 - 3.27: 11691 3.27 - 3.82: 19175 3.82 - 4.36: 22688 4.36 - 4.90: 38499 Nonbonded interactions: 92568 Sorted by model distance: nonbonded pdb=" OH TYR c 54 " pdb=" O SER c 193 " model vdw 2.189 2.440 nonbonded pdb=" OH TYR C 54 " pdb=" O SER C 193 " model vdw 2.227 2.440 nonbonded pdb=" O VAL B 159 " pdb=" OG SER B 162 " model vdw 2.294 2.440 nonbonded pdb=" OE2 GLU B 10 " pdb=" NH2 ARG B 68 " model vdw 2.319 2.520 nonbonded pdb=" O VAL b 159 " pdb=" OG SER b 162 " model vdw 2.349 2.440 ... (remaining 92563 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.680 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 33.740 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 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: 42.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 : 0.006 0.072 11730 Z= 0.382 Angle : 1.081 14.571 16006 Z= 0.548 Chirality : 0.058 0.285 1870 Planarity : 0.010 0.110 1978 Dihedral : 15.030 80.514 4138 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.70 % Favored : 97.23 % Rotamer: Outliers : 0.42 % Allowed : 7.36 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.21), residues: 1446 helix: -0.03 (0.16), residues: 962 sheet: -0.84 (0.83), residues: 48 loop : -1.09 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP c 20 HIS 0.012 0.002 HIS A 174 PHE 0.022 0.002 PHE B 142 TYR 0.021 0.003 TYR C 54 ARG 0.015 0.001 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 194 ILE cc_start: 0.7607 (mt) cc_final: 0.7387 (mm) outliers start: 5 outliers final: 4 residues processed: 151 average time/residue: 0.2520 time to fit residues: 53.6544 Evaluate side-chains 130 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 198 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 5.9990 chunk 107 optimal weight: 0.0270 chunk 59 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 128 optimal weight: 0.5980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 169 ASN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 HIS B 17 HIS B 100 HIS ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11730 Z= 0.201 Angle : 0.644 9.524 16006 Z= 0.316 Chirality : 0.041 0.157 1870 Planarity : 0.007 0.086 1978 Dihedral : 5.385 59.397 1580 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.12 % Allowed : 9.90 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.22), residues: 1446 helix: 0.98 (0.16), residues: 980 sheet: -0.07 (0.91), residues: 44 loop : -0.89 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP b 55 HIS 0.006 0.001 HIS D 38 PHE 0.014 0.001 PHE b 7 TYR 0.010 0.001 TYR A 100 ARG 0.005 0.000 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 1.227 Fit side-chains REVERT: a 48 LEU cc_start: 0.8278 (mp) cc_final: 0.8016 (mt) REVERT: a 59 GLU cc_start: 0.7093 (pm20) cc_final: 0.6823 (pm20) REVERT: c 230 LYS cc_start: 0.7981 (pttp) cc_final: 0.7630 (ttpt) REVERT: C 59 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8233 (mp) REVERT: C 198 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8430 (tmm) outliers start: 25 outliers final: 15 residues processed: 145 average time/residue: 0.2429 time to fit residues: 50.9185 Evaluate side-chains 145 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 3 MET Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 219 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 198 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 129 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11730 Z= 0.219 Angle : 0.621 9.179 16006 Z= 0.300 Chirality : 0.041 0.153 1870 Planarity : 0.006 0.075 1978 Dihedral : 4.987 56.891 1577 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.45 % Allowed : 12.52 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.22), residues: 1446 helix: 1.41 (0.17), residues: 980 sheet: -0.34 (0.88), residues: 48 loop : -0.65 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP c 20 HIS 0.003 0.001 HIS a 174 PHE 0.012 0.001 PHE b 7 TYR 0.009 0.001 TYR A 100 ARG 0.003 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 1.158 Fit side-chains REVERT: a 3 MET cc_start: 0.7054 (OUTLIER) cc_final: 0.6822 (mtm) REVERT: a 48 LEU cc_start: 0.8340 (mp) cc_final: 0.8073 (mt) REVERT: a 59 GLU cc_start: 0.7173 (pm20) cc_final: 0.6961 (pm20) REVERT: c 54 TYR cc_start: 0.7454 (OUTLIER) cc_final: 0.7100 (t80) REVERT: A 154 GLU cc_start: 0.6760 (mt-10) cc_final: 0.6278 (pt0) REVERT: C 59 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8397 (mp) REVERT: C 198 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8156 (tmm) outliers start: 29 outliers final: 13 residues processed: 143 average time/residue: 0.2188 time to fit residues: 46.0285 Evaluate side-chains 141 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 3 MET Chi-restraints excluded: chain a residue 20 SER Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain c residue 54 TYR Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 198 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 36 optimal weight: 0.0970 chunk 114 optimal weight: 0.9980 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 38 HIS ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 11730 Z= 0.374 Angle : 0.694 8.811 16006 Z= 0.338 Chirality : 0.045 0.176 1870 Planarity : 0.006 0.074 1978 Dihedral : 4.840 55.233 1575 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.55 % Allowed : 12.77 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.22), residues: 1446 helix: 1.33 (0.17), residues: 968 sheet: -1.66 (0.71), residues: 56 loop : -0.39 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP c 20 HIS 0.006 0.001 HIS C 174 PHE 0.013 0.002 PHE D 5 TYR 0.013 0.002 TYR A 100 ARG 0.006 0.001 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 132 time to evaluate : 1.367 Fit side-chains REVERT: a 1 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6883 (ptp) REVERT: c 80 ILE cc_start: 0.8984 (mm) cc_final: 0.8729 (mt) REVERT: c 204 TRP cc_start: 0.8095 (m100) cc_final: 0.7776 (m100) REVERT: c 230 LYS cc_start: 0.8182 (pttp) cc_final: 0.7730 (ttpt) REVERT: d 54 ARG cc_start: 0.8363 (tpp-160) cc_final: 0.7783 (mpt-90) REVERT: A 154 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6406 (pt0) REVERT: C 80 ILE cc_start: 0.9003 (mm) cc_final: 0.8763 (mt) REVERT: C 204 TRP cc_start: 0.7969 (m100) cc_final: 0.7602 (m100) outliers start: 42 outliers final: 33 residues processed: 155 average time/residue: 0.2224 time to fit residues: 50.1959 Evaluate side-chains 161 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 3 MET Chi-restraints excluded: chain a residue 20 SER Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 104 THR Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 185 MET Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain b residue 205 THR Chi-restraints excluded: chain b residue 219 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 123 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11730 Z= 0.226 Angle : 0.601 9.345 16006 Z= 0.290 Chirality : 0.041 0.160 1870 Planarity : 0.005 0.072 1978 Dihedral : 4.376 19.569 1572 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.54 % Allowed : 14.72 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.23), residues: 1446 helix: 1.55 (0.17), residues: 986 sheet: -0.46 (1.03), residues: 36 loop : -0.59 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 55 HIS 0.003 0.001 HIS c 174 PHE 0.009 0.001 PHE b 7 TYR 0.009 0.001 TYR A 100 ARG 0.003 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 134 time to evaluate : 1.308 Fit side-chains revert: symmetry clash REVERT: c 80 ILE cc_start: 0.8895 (mm) cc_final: 0.8663 (mt) REVERT: c 204 TRP cc_start: 0.8075 (m100) cc_final: 0.7746 (m100) REVERT: c 230 LYS cc_start: 0.8181 (pttp) cc_final: 0.7767 (ttpt) REVERT: A 1 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6438 (ptp) REVERT: A 154 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6394 (pt0) REVERT: C 80 ILE cc_start: 0.8933 (mm) cc_final: 0.8720 (mt) REVERT: C 198 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.7952 (ttt) outliers start: 30 outliers final: 21 residues processed: 147 average time/residue: 0.2580 time to fit residues: 54.1194 Evaluate side-chains 152 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 3 MET Chi-restraints excluded: chain a residue 20 SER Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 185 MET Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain b residue 219 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 137 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11730 Z= 0.249 Angle : 0.604 9.463 16006 Z= 0.291 Chirality : 0.041 0.158 1870 Planarity : 0.005 0.071 1978 Dihedral : 4.290 19.000 1572 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.88 % Allowed : 15.40 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.23), residues: 1446 helix: 1.64 (0.17), residues: 986 sheet: -0.51 (1.03), residues: 36 loop : -0.58 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 55 HIS 0.003 0.001 HIS C 174 PHE 0.009 0.001 PHE b 7 TYR 0.010 0.001 TYR A 100 ARG 0.003 0.000 ARG b 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 1.374 Fit side-chains revert: symmetry clash REVERT: a 1 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6859 (ptp) REVERT: c 80 ILE cc_start: 0.8906 (mm) cc_final: 0.8684 (mt) REVERT: c 204 TRP cc_start: 0.8096 (m100) cc_final: 0.7755 (m-10) REVERT: c 229 GLU cc_start: 0.7482 (mp0) cc_final: 0.7265 (mp0) REVERT: c 230 LYS cc_start: 0.8202 (pttp) cc_final: 0.7681 (ttpt) REVERT: d 54 ARG cc_start: 0.8385 (tpp-160) cc_final: 0.8088 (mpt180) REVERT: A 1 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6424 (ptp) REVERT: A 154 GLU cc_start: 0.6887 (mt-10) cc_final: 0.6420 (pt0) REVERT: C 80 ILE cc_start: 0.8936 (mm) cc_final: 0.8731 (mt) REVERT: C 198 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.7923 (ttt) outliers start: 34 outliers final: 26 residues processed: 152 average time/residue: 0.2480 time to fit residues: 54.3030 Evaluate side-chains 160 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 131 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 3 MET Chi-restraints excluded: chain a residue 20 SER Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 185 MET Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain b residue 219 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.0870 chunk 78 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11730 Z= 0.181 Angle : 0.579 12.517 16006 Z= 0.275 Chirality : 0.039 0.148 1870 Planarity : 0.005 0.070 1978 Dihedral : 4.125 18.178 1572 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.37 % Allowed : 16.16 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.23), residues: 1446 helix: 1.92 (0.17), residues: 982 sheet: -1.14 (0.68), residues: 66 loop : -0.26 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 55 HIS 0.003 0.000 HIS C 184 PHE 0.009 0.001 PHE b 7 TYR 0.007 0.001 TYR A 100 ARG 0.004 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: a 1 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6731 (ptp) REVERT: c 80 ILE cc_start: 0.8869 (mm) cc_final: 0.8643 (mt) REVERT: c 91 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7338 (mp) REVERT: c 204 TRP cc_start: 0.8075 (m100) cc_final: 0.7719 (m-10) REVERT: c 229 GLU cc_start: 0.7332 (mp0) cc_final: 0.6803 (mp0) REVERT: c 230 LYS cc_start: 0.8181 (pttp) cc_final: 0.7740 (ttpt) REVERT: A 1 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6348 (ptp) REVERT: A 30 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6608 (mt-10) REVERT: A 154 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6385 (pt0) REVERT: C 198 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.7276 (tmt) outliers start: 28 outliers final: 20 residues processed: 145 average time/residue: 0.2471 time to fit residues: 51.4362 Evaluate side-chains 156 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 3 MET Chi-restraints excluded: chain a residue 20 SER Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 185 MET Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain b residue 219 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 131 optimal weight: 0.0030 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11730 Z= 0.317 Angle : 0.647 11.025 16006 Z= 0.309 Chirality : 0.043 0.164 1870 Planarity : 0.005 0.070 1978 Dihedral : 4.225 19.021 1572 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.88 % Allowed : 15.99 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.23), residues: 1446 helix: 1.70 (0.17), residues: 982 sheet: -0.49 (1.04), residues: 36 loop : -0.60 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 55 HIS 0.005 0.001 HIS C 174 PHE 0.010 0.001 PHE D 5 TYR 0.013 0.001 TYR A 100 ARG 0.003 0.000 ARG c 220 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 132 time to evaluate : 1.368 Fit side-chains revert: symmetry clash REVERT: a 1 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6809 (ptp) REVERT: c 80 ILE cc_start: 0.8946 (mm) cc_final: 0.8704 (mt) REVERT: c 91 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7397 (mp) REVERT: c 204 TRP cc_start: 0.8132 (m100) cc_final: 0.7794 (m-10) REVERT: c 229 GLU cc_start: 0.7462 (mp0) cc_final: 0.7258 (mp0) REVERT: c 230 LYS cc_start: 0.8244 (pttp) cc_final: 0.7741 (ttpt) REVERT: A 1 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6486 (ptp) REVERT: A 30 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6634 (mt-10) REVERT: A 154 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6509 (pt0) REVERT: C 198 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.7137 (tmt) REVERT: C 204 TRP cc_start: 0.8056 (m100) cc_final: 0.7665 (m100) outliers start: 34 outliers final: 24 residues processed: 152 average time/residue: 0.2296 time to fit residues: 50.7109 Evaluate side-chains 160 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 131 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 3 MET Chi-restraints excluded: chain a residue 20 SER Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 185 MET Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain b residue 219 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 76 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11730 Z= 0.184 Angle : 0.583 10.737 16006 Z= 0.280 Chirality : 0.040 0.211 1870 Planarity : 0.005 0.070 1978 Dihedral : 4.086 18.339 1572 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.28 % Allowed : 16.16 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.23), residues: 1446 helix: 1.96 (0.17), residues: 982 sheet: -1.18 (0.68), residues: 66 loop : -0.26 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 55 HIS 0.002 0.000 HIS a 174 PHE 0.008 0.001 PHE b 7 TYR 0.007 0.001 TYR A 100 ARG 0.004 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 138 time to evaluate : 1.308 Fit side-chains revert: symmetry clash REVERT: a 1 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6644 (ptp) REVERT: c 80 ILE cc_start: 0.8885 (mm) cc_final: 0.8658 (mt) REVERT: c 91 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7357 (mp) REVERT: c 204 TRP cc_start: 0.8064 (m100) cc_final: 0.7756 (m-10) REVERT: c 229 GLU cc_start: 0.7244 (mp0) cc_final: 0.6742 (mp0) REVERT: c 230 LYS cc_start: 0.8209 (pttp) cc_final: 0.7771 (ttpt) REVERT: A 1 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6355 (ptp) REVERT: A 30 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6632 (mt-10) REVERT: A 154 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6454 (pt0) REVERT: C 198 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7253 (tmt) outliers start: 27 outliers final: 19 residues processed: 150 average time/residue: 0.2525 time to fit residues: 53.8971 Evaluate side-chains 157 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 3 MET Chi-restraints excluded: chain a residue 20 SER Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 185 MET Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain b residue 219 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 chunk 130 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 11730 Z= 0.496 Angle : 0.747 10.762 16006 Z= 0.362 Chirality : 0.047 0.175 1870 Planarity : 0.006 0.070 1978 Dihedral : 4.478 19.858 1572 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.45 % Allowed : 16.41 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.23), residues: 1446 helix: 1.35 (0.17), residues: 982 sheet: -0.55 (1.04), residues: 36 loop : -0.64 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP c 20 HIS 0.007 0.001 HIS C 174 PHE 0.014 0.002 PHE D 5 TYR 0.017 0.002 TYR A 100 ARG 0.004 0.000 ARG c 220 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 131 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 1 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6925 (ptp) REVERT: c 16 GLN cc_start: 0.8060 (mt0) cc_final: 0.7299 (mp10) REVERT: c 49 GLN cc_start: 0.7286 (tt0) cc_final: 0.7012 (tm-30) REVERT: c 80 ILE cc_start: 0.8994 (mm) cc_final: 0.8742 (mt) REVERT: c 91 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7564 (mp) REVERT: c 204 TRP cc_start: 0.8186 (m100) cc_final: 0.7859 (m100) REVERT: c 230 LYS cc_start: 0.8321 (pttp) cc_final: 0.7658 (ttpt) REVERT: d 54 ARG cc_start: 0.8374 (tpp-160) cc_final: 0.8066 (mpt180) REVERT: A 1 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.6705 (ptp) REVERT: A 30 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6661 (mt-10) REVERT: A 154 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6499 (pt0) REVERT: C 88 MET cc_start: 0.8846 (mmm) cc_final: 0.8625 (mmt) REVERT: C 128 ARG cc_start: 0.6583 (tpp-160) cc_final: 0.6206 (mmt180) REVERT: C 153 ARG cc_start: 0.7372 (ttm110) cc_final: 0.7014 (mtt90) REVERT: C 198 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.7048 (tmt) outliers start: 29 outliers final: 23 residues processed: 148 average time/residue: 0.2489 time to fit residues: 52.1981 Evaluate side-chains 157 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 129 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 3 MET Chi-restraints excluded: chain a residue 20 SER Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 185 MET Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain b residue 219 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.158575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.133581 restraints weight = 13753.324| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.69 r_work: 0.3373 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11730 Z= 0.195 Angle : 0.604 10.110 16006 Z= 0.290 Chirality : 0.041 0.163 1870 Planarity : 0.005 0.070 1978 Dihedral : 4.216 17.915 1572 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.28 % Allowed : 16.67 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.23), residues: 1446 helix: 1.79 (0.17), residues: 982 sheet: -0.34 (1.04), residues: 36 loop : -0.64 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP c 20 HIS 0.002 0.001 HIS C 6 PHE 0.008 0.001 PHE D 5 TYR 0.010 0.001 TYR c 58 ARG 0.005 0.000 ARG B 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2233.49 seconds wall clock time: 41 minutes 16.70 seconds (2476.70 seconds total)