Starting phenix.real_space_refine on Sat Nov 16 13:24:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce1_16597/11_2024/8ce1_16597.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce1_16597/11_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_16597/11_2024/8ce1_16597.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce1_16597/11_2024/8ce1_16597.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce1_16597/11_2024/8ce1_16597.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce1_16597/11_2024/8ce1_16597.cif" } 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. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 7.18, per 1000 atoms: 0.63 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 - 3.00 Amino acid : True - 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: 2.86 Conformation dependent library (CDL) restraints added in 1.5 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: 1.11 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: 3.15 Time building geometry restraints manager: 3.32 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: 0.00 - 2.91: 15550 2.91 - 5.83: 379 5.83 - 8.74: 64 8.74 - 11.66: 10 11.66 - 14.57: 3 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 3.040 nonbonded pdb=" OH TYR C 54 " pdb=" O SER C 193 " model vdw 2.227 3.040 nonbonded pdb=" O VAL B 159 " pdb=" OG SER B 162 " model vdw 2.294 3.040 nonbonded pdb=" OE2 GLU B 10 " pdb=" NH2 ARG B 68 " model vdw 2.319 3.120 nonbonded pdb=" O VAL b 159 " pdb=" OG SER b 162 " model vdw 2.349 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 27.610 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.320 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 5 poor density : 149 time to evaluate : 1.274 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: 0.2507 time to fit residues: 53.6886 Evaluate side-chains 130 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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: 1.9990 chunk 59 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 128 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 169 ASN 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: 0.7867 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11730 Z= 0.223 Angle : 0.653 9.102 16006 Z= 0.322 Chirality : 0.042 0.156 1870 Planarity : 0.007 0.085 1978 Dihedral : 5.380 59.016 1580 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.20 % Allowed : 10.15 % Favored : 87.65 % 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: 0.64 (0.22), residues: 1446 helix: 1.03 (0.16), residues: 974 sheet: -0.08 (0.92), residues: 44 loop : -0.80 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP b 55 HIS 0.006 0.001 HIS D 38 PHE 0.013 0.001 PHE b 7 TYR 0.009 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 157 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.156 Fit side-chains REVERT: a 48 LEU cc_start: 0.8338 (mp) cc_final: 0.8085 (mt) REVERT: a 59 GLU cc_start: 0.7187 (pm20) cc_final: 0.6895 (pm20) REVERT: C 59 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8275 (mp) outliers start: 26 outliers final: 17 residues processed: 142 average time/residue: 0.2304 time to fit residues: 47.7098 Evaluate side-chains 141 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 1.337 ------------------------------------------------------------------------------- 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 2 MET 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 30 VAL Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 104 THR 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 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: 2.9990 chunk 107 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7953 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11730 Z= 0.247 Angle : 0.640 9.119 16006 Z= 0.312 Chirality : 0.042 0.157 1870 Planarity : 0.006 0.077 1978 Dihedral : 4.827 48.332 1574 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.62 % Allowed : 12.27 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.22), residues: 1446 helix: 1.32 (0.17), residues: 980 sheet: -1.40 (0.67), residues: 68 loop : -0.38 (0.32), residues: 398 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 0.010 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 161 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 1.339 Fit side-chains REVERT: a 48 LEU cc_start: 0.8400 (mp) cc_final: 0.8167 (mt) REVERT: a 59 GLU cc_start: 0.7204 (pm20) cc_final: 0.6995 (mm-30) REVERT: c 54 TYR cc_start: 0.7465 (OUTLIER) cc_final: 0.7124 (t80) REVERT: c 80 ILE cc_start: 0.8932 (mm) cc_final: 0.8680 (mt) REVERT: c 96 MET cc_start: 0.7860 (mtt) cc_final: 0.7635 (mtt) REVERT: A 61 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7349 (mt) REVERT: A 154 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6326 (pt0) outliers start: 31 outliers final: 17 residues processed: 148 average time/residue: 0.2412 time to fit residues: 51.8209 Evaluate side-chains 147 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 b residue 104 THR Chi-restraints excluded: chain b residue 185 MET Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 54 TYR Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 114 optimal weight: 0.2980 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 81 GLN d 38 HIS ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 11730 Z= 0.376 Angle : 0.701 8.800 16006 Z= 0.342 Chirality : 0.045 0.177 1870 Planarity : 0.006 0.074 1978 Dihedral : 4.661 21.638 1572 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.55 % Allowed : 13.45 % Favored : 82.99 % 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: 0.97 (0.22), residues: 1446 helix: 1.26 (0.17), residues: 972 sheet: -0.40 (1.06), residues: 36 loop : -0.57 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 55 HIS 0.006 0.001 HIS C 174 PHE 0.013 0.002 PHE D 5 TYR 0.014 0.002 TYR A 100 ARG 0.005 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 178 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 1.304 Fit side-chains REVERT: a 1 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6838 (ptp) REVERT: a 160 ASP cc_start: 0.8280 (p0) cc_final: 0.8033 (p0) REVERT: b 156 ARG cc_start: 0.7959 (ttm-80) cc_final: 0.7497 (mtm-85) REVERT: c 80 ILE cc_start: 0.8984 (mm) cc_final: 0.8743 (mt) REVERT: c 96 MET cc_start: 0.7952 (mtt) cc_final: 0.7722 (mtt) REVERT: c 204 TRP cc_start: 0.8084 (m100) cc_final: 0.7770 (m100) REVERT: c 230 LYS cc_start: 0.8016 (pttp) cc_final: 0.7686 (ttpt) REVERT: A 1 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6577 (ptp) REVERT: A 61 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7600 (mt) REVERT: A 154 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6401 (pt0) REVERT: C 80 ILE cc_start: 0.8994 (mm) cc_final: 0.8757 (mt) REVERT: C 204 TRP cc_start: 0.7965 (m100) cc_final: 0.7597 (m100) outliers start: 42 outliers final: 30 residues processed: 159 average time/residue: 0.2387 time to fit residues: 54.8943 Evaluate side-chains 161 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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 30 VAL Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain d residue 50 VAL 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 61 LEU Chi-restraints excluded: chain A residue 191 VAL 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 228 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 123 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11730 Z= 0.236 Angle : 0.610 9.335 16006 Z= 0.296 Chirality : 0.041 0.161 1870 Planarity : 0.006 0.072 1978 Dihedral : 4.416 21.667 1572 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.28 % Allowed : 15.40 % Favored : 82.32 % 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: 1.27 (0.23), residues: 1446 helix: 1.54 (0.17), residues: 986 sheet: -0.63 (1.01), residues: 36 loop : -0.61 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 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 0.004 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 163 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.219 Fit side-chains REVERT: b 156 ARG cc_start: 0.7930 (ttm-80) cc_final: 0.7553 (mtm-85) REVERT: c 80 ILE cc_start: 0.8891 (mm) cc_final: 0.8666 (mt) REVERT: c 204 TRP cc_start: 0.8084 (m100) cc_final: 0.7737 (m100) REVERT: c 230 LYS cc_start: 0.8103 (pttp) cc_final: 0.7765 (ttpt) REVERT: A 61 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7473 (mt) REVERT: A 154 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6382 (pt0) REVERT: C 80 ILE cc_start: 0.8945 (mm) cc_final: 0.8736 (mt) outliers start: 27 outliers final: 16 residues processed: 150 average time/residue: 0.2457 time to fit residues: 52.5686 Evaluate side-chains 150 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 A residue 3 MET Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 61 LEU 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 C residue 21 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11730 Z= 0.282 Angle : 0.628 9.433 16006 Z= 0.304 Chirality : 0.042 0.164 1870 Planarity : 0.005 0.072 1978 Dihedral : 4.371 21.109 1572 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.37 % Allowed : 16.33 % Favored : 81.30 % 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: 1.32 (0.23), residues: 1446 helix: 1.59 (0.17), residues: 986 sheet: -0.72 (1.00), residues: 36 loop : -0.60 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP c 20 HIS 0.004 0.001 HIS c 174 PHE 0.009 0.001 PHE D 5 TYR 0.011 0.001 TYR A 100 ARG 0.004 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 161 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 1.223 Fit side-chains REVERT: a 1 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6887 (ptp) REVERT: b 156 ARG cc_start: 0.7942 (ttm-80) cc_final: 0.7558 (mtm-85) REVERT: c 80 ILE cc_start: 0.8919 (mm) cc_final: 0.8702 (mt) REVERT: c 204 TRP cc_start: 0.8121 (m100) cc_final: 0.7786 (m-10) REVERT: c 230 LYS cc_start: 0.8194 (pttp) cc_final: 0.7868 (ttpt) REVERT: A 30 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6584 (mt-10) REVERT: A 61 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7513 (mt) REVERT: A 154 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6411 (pt0) REVERT: C 80 ILE cc_start: 0.8951 (mm) cc_final: 0.8747 (mt) REVERT: C 204 TRP cc_start: 0.8005 (m100) cc_final: 0.7614 (m100) outliers start: 28 outliers final: 21 residues processed: 149 average time/residue: 0.2474 time to fit residues: 52.5546 Evaluate side-chains 155 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 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 182 THR Chi-restraints excluded: chain c residue 228 MET Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 61 LEU 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 172 LEU 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 228 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.0570 chunk 78 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11730 Z= 0.181 Angle : 0.589 12.172 16006 Z= 0.281 Chirality : 0.040 0.152 1870 Planarity : 0.005 0.070 1978 Dihedral : 4.196 20.585 1572 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.20 % Allowed : 16.84 % Favored : 80.96 % 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: 1.70 (0.23), residues: 1446 helix: 1.92 (0.17), residues: 980 sheet: -0.52 (1.02), residues: 36 loop : -0.56 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 55 HIS 0.002 0.000 HIS a 186 PHE 0.009 0.001 PHE b 7 TYR 0.007 0.001 TYR A 100 ARG 0.005 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 155 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 1.249 Fit side-chains REVERT: a 1 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6738 (ptp) REVERT: b 156 ARG cc_start: 0.7895 (ttm-80) cc_final: 0.7597 (mtm-85) REVERT: c 80 ILE cc_start: 0.8879 (mm) cc_final: 0.8652 (mt) REVERT: c 204 TRP cc_start: 0.8096 (m100) cc_final: 0.7758 (m-10) REVERT: c 230 LYS cc_start: 0.8185 (pttp) cc_final: 0.7839 (ttpt) REVERT: d 54 ARG cc_start: 0.8098 (tpp-160) cc_final: 0.7861 (mpt180) REVERT: A 30 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6600 (mt-10) REVERT: A 154 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6406 (pt0) outliers start: 26 outliers final: 19 residues processed: 144 average time/residue: 0.2470 time to fit residues: 51.0679 Evaluate side-chains 148 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 1.179 ------------------------------------------------------------------------------- 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 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 219 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 228 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 106 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 121 THR 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: 1.9990 chunk 81 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11730 Z= 0.254 Angle : 0.621 10.948 16006 Z= 0.297 Chirality : 0.042 0.159 1870 Planarity : 0.005 0.070 1978 Dihedral : 4.212 20.329 1572 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.28 % Allowed : 17.26 % Favored : 80.46 % 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: 1.60 (0.23), residues: 1446 helix: 1.85 (0.17), residues: 980 sheet: -0.71 (1.01), residues: 36 loop : -0.57 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP c 20 HIS 0.003 0.001 HIS C 174 PHE 0.009 0.001 PHE D 5 TYR 0.011 0.001 TYR A 100 ARG 0.003 0.000 ARG b 216 *********************** 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 161 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 1.316 Fit side-chains REVERT: a 1 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6626 (ptp) REVERT: b 156 ARG cc_start: 0.7921 (ttm-80) cc_final: 0.7623 (mtm-85) REVERT: c 80 ILE cc_start: 0.8925 (mm) cc_final: 0.8690 (mt) REVERT: c 88 MET cc_start: 0.8828 (mmm) cc_final: 0.8544 (mmp) REVERT: c 204 TRP cc_start: 0.8118 (m100) cc_final: 0.7798 (m-10) REVERT: c 230 LYS cc_start: 0.8220 (pttp) cc_final: 0.7905 (ttpt) REVERT: A 30 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6604 (mt-10) REVERT: A 154 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6505 (pt0) REVERT: C 80 ILE cc_start: 0.8963 (mm) cc_final: 0.8758 (mt) REVERT: C 204 TRP cc_start: 0.8060 (m100) cc_final: 0.7660 (m100) outliers start: 27 outliers final: 20 residues processed: 149 average time/residue: 0.2402 time to fit residues: 51.2860 Evaluate side-chains 157 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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 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 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 171 MET 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 C residue 21 PHE Chi-restraints excluded: chain C residue 121 THR 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: 4.9990 chunk 127 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2968 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= 0.193 Angle : 0.590 10.570 16006 Z= 0.282 Chirality : 0.040 0.150 1870 Planarity : 0.005 0.069 1978 Dihedral : 4.129 20.086 1572 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.20 % Allowed : 17.68 % Favored : 80.12 % 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: 1.83 (0.23), residues: 1446 helix: 1.99 (0.17), residues: 980 sheet: -1.23 (0.67), residues: 66 loop : -0.26 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 55 HIS 0.002 0.000 HIS a 186 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 158 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 1.351 Fit side-chains REVERT: a 1 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6682 (ptp) REVERT: b 156 ARG cc_start: 0.7908 (ttm-80) cc_final: 0.7620 (mtm-85) REVERT: c 80 ILE cc_start: 0.8894 (mm) cc_final: 0.8665 (mt) REVERT: c 91 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7231 (mp) REVERT: c 204 TRP cc_start: 0.8118 (m100) cc_final: 0.7792 (m-10) REVERT: c 230 LYS cc_start: 0.8194 (pttp) cc_final: 0.7888 (ttpt) REVERT: A 30 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6595 (mt-10) REVERT: A 154 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6460 (pt0) outliers start: 26 outliers final: 19 residues processed: 148 average time/residue: 0.2513 time to fit residues: 52.7968 Evaluate side-chains 148 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 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 A residue 3 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 170 ILE Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 227 LEU 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: 6.9990 chunk 141 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11730 Z= 0.334 Angle : 0.661 10.440 16006 Z= 0.318 Chirality : 0.043 0.164 1870 Planarity : 0.005 0.070 1978 Dihedral : 4.297 20.365 1572 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.95 % Allowed : 18.02 % Favored : 80.03 % 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: 1.36 (0.23), residues: 1446 helix: 1.62 (0.17), residues: 994 sheet: -0.73 (1.00), residues: 36 loop : -0.65 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 20 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 0.008 0.000 ARG b 48 ********************** 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 to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: a 1 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6987 (ptp) REVERT: b 156 ARG cc_start: 0.7923 (ttm-80) cc_final: 0.7609 (mtm-85) REVERT: c 80 ILE cc_start: 0.8939 (mm) cc_final: 0.8703 (mt) REVERT: c 91 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7344 (mp) REVERT: c 204 TRP cc_start: 0.8171 (m100) cc_final: 0.7848 (m-10) REVERT: c 230 LYS cc_start: 0.8215 (pttp) cc_final: 0.7907 (ttpt) REVERT: A 30 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6631 (mt-10) REVERT: A 154 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6513 (pt0) REVERT: C 80 ILE cc_start: 0.9013 (mm) cc_final: 0.8786 (mt) REVERT: C 204 TRP cc_start: 0.8062 (m100) cc_final: 0.7695 (m100) outliers start: 23 outliers final: 20 residues processed: 148 average time/residue: 0.2300 time to fit residues: 49.0047 Evaluate side-chains 158 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.351 ------------------------------------------------------------------------------- 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 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 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 171 MET 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 C residue 21 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 227 LEU 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: 0.0770 chunk 103 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 31 optimal weight: 0.2980 chunk 112 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.161727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.136295 restraints weight = 13686.173| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.56 r_work: 0.3408 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11730 Z= 0.170 Angle : 0.591 10.205 16006 Z= 0.286 Chirality : 0.040 0.196 1870 Planarity : 0.005 0.070 1978 Dihedral : 4.128 19.617 1572 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.95 % Allowed : 18.10 % Favored : 79.95 % 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: 1.96 (0.17), residues: 988 sheet: -1.65 (0.71), residues: 56 loop : -0.36 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 55 HIS 0.002 0.000 HIS a 186 PHE 0.008 0.001 PHE b 7 TYR 0.006 0.001 TYR A 100 ARG 0.004 0.000 ARG B 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2215.71 seconds wall clock time: 40 minutes 57.41 seconds (2457.41 seconds total)