Starting phenix.real_space_refine on Sun Sep 29 04:16:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xaq_33097/09_2024/7xaq_33097.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xaq_33097/09_2024/7xaq_33097.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xaq_33097/09_2024/7xaq_33097.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xaq_33097/09_2024/7xaq_33097.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xaq_33097/09_2024/7xaq_33097.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xaq_33097/09_2024/7xaq_33097.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9808 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 172 5.49 5 S 42 5.16 5 C 8005 2.51 5 N 2379 2.21 5 O 2798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13396 Number of models: 1 Model: "" Number of chains: 10 Chain: "F" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 880 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "J" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 883 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "E" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 880 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "I" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 883 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "B" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1658 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 194} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1626 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 192} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1667 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 194} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1626 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 192} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1667 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 194} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1626 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 192} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 9.95, per 1000 atoms: 0.74 Number of scatterers: 13396 At special positions: 0 Unit cell: (249.05, 156.4, 96.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 172 15.00 O 2798 8.00 N 2379 7.00 C 8005 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: 3.54 Conformation dependent library (CDL) restraints added in 1.3 seconds 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2286 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 0 sheets defined 79.5% alpha, 0.0% beta 72 base pairs and 115 stacking pairs defined. Time for finding SS restraints: 5.27 Creating SS restraints... Processing helix chain 'B' and resid 6 through 27 removed outlier: 3.579A pdb=" N LEU B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 42 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 57 through 77 removed outlier: 4.627A pdb=" N ARG B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N HIS B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 97 Processing helix chain 'B' and resid 100 through 113 Processing helix chain 'B' and resid 119 through 148 removed outlier: 4.899A pdb=" N GLU B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 173 removed outlier: 4.180A pdb=" N HIS B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.749A pdb=" N ASP B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 198 removed outlier: 4.014A pdb=" N HIS B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 29 Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 59 through 76 removed outlier: 5.675A pdb=" N MET A 65 " --> pdb=" O TYR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 98 Processing helix chain 'A' and resid 99 through 114 removed outlier: 4.041A pdb=" N TYR A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 147 Processing helix chain 'A' and resid 155 through 175 removed outlier: 3.658A pdb=" N ALA A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 171 " --> pdb=" O HIS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 198 Processing helix chain 'G' and resid 5 through 29 removed outlier: 4.121A pdb=" N LYS G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 44 removed outlier: 3.795A pdb=" N GLY G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 52 removed outlier: 3.814A pdb=" N ILE G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 77 removed outlier: 3.520A pdb=" N ILE G 60 " --> pdb=" O SER G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 83 Processing helix chain 'G' and resid 84 through 98 removed outlier: 3.810A pdb=" N LEU G 88 " --> pdb=" O ASP G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 114 removed outlier: 3.593A pdb=" N GLU G 111 " --> pdb=" O ASP G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 148 Processing helix chain 'G' and resid 154 through 173 removed outlier: 4.309A pdb=" N HIS G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 183 Processing helix chain 'G' and resid 185 through 198 Processing helix chain 'C' and resid 8 through 29 Processing helix chain 'C' and resid 35 through 44 removed outlier: 3.931A pdb=" N ILE C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 52 Processing helix chain 'C' and resid 56 through 76 Processing helix chain 'C' and resid 85 through 98 Processing helix chain 'C' and resid 99 through 114 removed outlier: 3.864A pdb=" N GLU C 111 " --> pdb=" O ASP C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 148 removed outlier: 3.725A pdb=" N VAL C 123 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASP C 147 " --> pdb=" O GLU C 143 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY C 148 " --> pdb=" O ARG C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 173 removed outlier: 3.987A pdb=" N HIS C 158 " --> pdb=" O PRO C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 removed outlier: 3.741A pdb=" N VAL C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 198 Processing helix chain 'H' and resid 5 through 29 Processing helix chain 'H' and resid 35 through 44 removed outlier: 3.568A pdb=" N ILE H 39 " --> pdb=" O THR H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 51 Processing helix chain 'H' and resid 56 through 76 removed outlier: 3.833A pdb=" N ILE H 60 " --> pdb=" O SER H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 83 Processing helix chain 'H' and resid 84 through 97 removed outlier: 4.270A pdb=" N LEU H 88 " --> pdb=" O ASP H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 116 removed outlier: 3.646A pdb=" N THR H 116 " --> pdb=" O LYS H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 146 Processing helix chain 'H' and resid 154 through 175 removed outlier: 3.995A pdb=" N HIS H 158 " --> pdb=" O PRO H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 183 Processing helix chain 'H' and resid 185 through 198 removed outlier: 3.624A pdb=" N PHE H 189 " --> pdb=" O GLN H 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 30 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 57 through 76 removed outlier: 3.822A pdb=" N TYR D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 98 Processing helix chain 'D' and resid 99 through 114 Processing helix chain 'D' and resid 119 through 147 removed outlier: 3.636A pdb=" N VAL D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 173 removed outlier: 4.100A pdb=" N HIS D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 185 through 198 676 hydrogen bonds defined for protein. 2013 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 182 hydrogen bonds 364 hydrogen bond angles 0 basepair planarities 72 basepair parallelities 115 stacking parallelities Total time for adding SS restraints: 4.03 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1929 1.32 - 1.44: 4660 1.44 - 1.57: 7033 1.57 - 1.69: 341 1.69 - 1.82: 78 Bond restraints: 14041 Sorted by residual: bond pdb=" N ASP B 99 " pdb=" CA ASP B 99 " ideal model delta sigma weight residual 1.460 1.417 0.044 7.10e-03 1.98e+04 3.79e+01 bond pdb=" CA ASP B 99 " pdb=" C ASP B 99 " ideal model delta sigma weight residual 1.534 1.477 0.057 9.50e-03 1.11e+04 3.59e+01 bond pdb=" O3' DA F 42 " pdb=" P DA F 43 " ideal model delta sigma weight residual 1.607 1.667 -0.060 1.50e-02 4.44e+03 1.62e+01 bond pdb=" O3' DC I 3 " pdb=" P DG I 4 " ideal model delta sigma weight residual 1.607 1.665 -0.058 1.50e-02 4.44e+03 1.47e+01 bond pdb=" C ARG A 179 " pdb=" O ARG A 179 " ideal model delta sigma weight residual 1.237 1.193 0.043 1.19e-02 7.06e+03 1.31e+01 ... (remaining 14036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 19297 3.15 - 6.30: 324 6.30 - 9.45: 30 9.45 - 12.60: 6 12.60 - 15.75: 2 Bond angle restraints: 19659 Sorted by residual: angle pdb=" N THR A 49 " pdb=" CA THR A 49 " pdb=" C THR A 49 " ideal model delta sigma weight residual 111.82 100.25 11.57 1.16e+00 7.43e-01 9.95e+01 angle pdb=" N ASP B 71 " pdb=" CA ASP B 71 " pdb=" C ASP B 71 " ideal model delta sigma weight residual 112.38 102.44 9.94 1.22e+00 6.72e-01 6.63e+01 angle pdb=" N GLU A 183 " pdb=" CA GLU A 183 " pdb=" C GLU A 183 " ideal model delta sigma weight residual 113.41 103.49 9.92 1.22e+00 6.72e-01 6.61e+01 angle pdb=" N GLN B 101 " pdb=" CA GLN B 101 " pdb=" C GLN B 101 " ideal model delta sigma weight residual 110.80 95.05 15.75 2.13e+00 2.20e-01 5.47e+01 angle pdb=" N VAL A 34 " pdb=" CA VAL A 34 " pdb=" C VAL A 34 " ideal model delta sigma weight residual 110.21 101.91 8.30 1.13e+00 7.83e-01 5.39e+01 ... (remaining 19654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.29: 6964 31.29 - 62.57: 974 62.57 - 93.86: 45 93.86 - 125.14: 0 125.14 - 156.43: 2 Dihedral angle restraints: 7985 sinusoidal: 4460 harmonic: 3525 Sorted by residual: dihedral pdb=" CA TYR A 61 " pdb=" C TYR A 61 " pdb=" N LEU A 62 " pdb=" CA LEU A 62 " ideal model delta harmonic sigma weight residual 180.00 150.28 29.72 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA TYR A 51 " pdb=" C TYR A 51 " pdb=" N LYS A 52 " pdb=" CA LYS A 52 " ideal model delta harmonic sigma weight residual 180.00 150.32 29.68 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA GLY D 48 " pdb=" C GLY D 48 " pdb=" N THR D 49 " pdb=" CA THR D 49 " ideal model delta harmonic sigma weight residual 180.00 150.99 29.01 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 7982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1986 0.091 - 0.182: 104 0.182 - 0.272: 15 0.272 - 0.363: 8 0.363 - 0.454: 2 Chirality restraints: 2115 Sorted by residual: chirality pdb=" CA PRO G 5 " pdb=" N PRO G 5 " pdb=" C PRO G 5 " pdb=" CB PRO G 5 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CA GLU A 183 " pdb=" N GLU A 183 " pdb=" C GLU A 183 " pdb=" CB GLU A 183 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" C3' DT J 2 " pdb=" C4' DT J 2 " pdb=" O3' DT J 2 " pdb=" C2' DT J 2 " both_signs ideal model delta sigma weight residual False -2.66 -2.31 -0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 2112 not shown) Planarity restraints: 1934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 98 " 0.021 2.00e-02 2.50e+03 4.41e-02 1.94e+01 pdb=" C ARG B 98 " -0.076 2.00e-02 2.50e+03 pdb=" O ARG B 98 " 0.030 2.00e-02 2.50e+03 pdb=" N ASP B 99 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS G 77 " -0.019 2.00e-02 2.50e+03 4.02e-02 1.61e+01 pdb=" C HIS G 77 " 0.069 2.00e-02 2.50e+03 pdb=" O HIS G 77 " -0.027 2.00e-02 2.50e+03 pdb=" N SER G 78 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 32 " 0.042 2.00e-02 2.50e+03 2.48e-02 1.54e+01 pdb=" N1 DT I 32 " -0.063 2.00e-02 2.50e+03 pdb=" C2 DT I 32 " -0.009 2.00e-02 2.50e+03 pdb=" O2 DT I 32 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DT I 32 " 0.017 2.00e-02 2.50e+03 pdb=" C4 DT I 32 " 0.009 2.00e-02 2.50e+03 pdb=" O4 DT I 32 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DT I 32 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT I 32 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DT I 32 " 0.005 2.00e-02 2.50e+03 ... (remaining 1931 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 58 2.42 - 3.04: 8276 3.04 - 3.66: 23566 3.66 - 4.28: 34081 4.28 - 4.90: 50703 Nonbonded interactions: 116684 Sorted by model distance: nonbonded pdb=" O HIS G 77 " pdb=" OE2 GLU G 79 " model vdw 1.800 3.040 nonbonded pdb=" C PRO B 100 " pdb=" N ARG B 102 " model vdw 1.932 3.350 nonbonded pdb=" O ILE D 45 " pdb=" OG1 THR D 49 " model vdw 1.980 3.040 nonbonded pdb=" O GLU B 17 " pdb=" OG1 THR B 21 " model vdw 2.004 3.040 nonbonded pdb=" O PHE D 134 " pdb=" OG1 THR D 138 " model vdw 2.045 3.040 ... (remaining 116679 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' and (resid 7 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 204)) selection = (chain 'B' and ((resid 7 and (name N or name CA or name C or name O or name CB ) \ ) or resid 8 through 77 or (resid 78 through 83 and (name N or name CA or name C \ or name O or name CB )) or resid 84 through 202 or (resid 203 through 204 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 7 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 204)) selection = (chain 'D' and (resid 7 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 204)) selection = (chain 'G' and ((resid 7 and (name N or name CA or name C or name O or name CB ) \ ) or resid 8 through 77 or (resid 78 through 83 and (name N or name CA or name C \ or name O or name CB )) or resid 84 through 202 or (resid 203 through 204 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'H' and ((resid 7 and (name N or name CA or name C or name O or name CB ) \ ) or resid 8 through 77 or (resid 78 through 83 and (name N or name CA or name C \ or name O or name CB )) or resid 84 through 202 or (resid 203 through 204 and ( \ name N or name CA or name C or name O or name CB )))) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 37.100 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5253 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 14041 Z= 0.388 Angle : 1.015 15.751 19659 Z= 0.606 Chirality : 0.053 0.454 2115 Planarity : 0.006 0.054 1934 Dihedral : 23.456 156.429 5699 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.81 % Favored : 87.93 % Rotamer: Outliers : 2.87 % Allowed : 4.35 % Favored : 92.78 % Cbeta Deviations : 0.09 % 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: -4.12 (0.21), residues: 1185 helix: -2.39 (0.14), residues: 866 sheet: None (None), residues: 0 loop : -3.15 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 163 HIS 0.006 0.001 HIS A 53 PHE 0.034 0.003 PHE A 26 TYR 0.025 0.003 TYR B 159 ARG 0.016 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 165 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 ASP cc_start: 0.6144 (m-30) cc_final: 0.5900 (t0) REVERT: B 66 LEU cc_start: 0.8897 (mt) cc_final: 0.8354 (mt) REVERT: B 85 LYS cc_start: -0.1364 (OUTLIER) cc_final: -0.1692 (mmtt) REVERT: B 101 GLN cc_start: 0.4956 (OUTLIER) cc_final: 0.4635 (tm-30) REVERT: B 126 LEU cc_start: 0.5024 (mp) cc_final: 0.4569 (tt) REVERT: B 191 PHE cc_start: 0.5872 (t80) cc_final: 0.5494 (t80) REVERT: B 198 ARG cc_start: 0.6576 (mtm110) cc_final: 0.6069 (mmm-85) REVERT: A 97 MET cc_start: 0.7757 (mtm) cc_final: 0.7287 (ttp) REVERT: A 167 HIS cc_start: 0.5832 (t-90) cc_final: 0.5614 (t-90) REVERT: A 177 PHE cc_start: 0.5628 (OUTLIER) cc_final: 0.4935 (t80) REVERT: G 38 MET cc_start: 0.8025 (ttm) cc_final: 0.7621 (mtp) REVERT: G 127 HIS cc_start: 0.9041 (m-70) cc_final: 0.8749 (m-70) REVERT: G 128 LYS cc_start: 0.9262 (ptmt) cc_final: 0.9061 (ptpp) REVERT: G 199 MET cc_start: 0.1008 (ppp) cc_final: 0.0010 (ppp) REVERT: C 199 MET cc_start: 0.2544 (mtm) cc_final: 0.0259 (mmm) REVERT: H 65 MET cc_start: 0.8568 (mmp) cc_final: 0.8202 (mmp) REVERT: H 79 GLU cc_start: 0.0825 (OUTLIER) cc_final: -0.0880 (mm-30) REVERT: D 92 TYR cc_start: 0.8051 (t80) cc_final: 0.7806 (t80) REVERT: D 130 ARG cc_start: 0.8887 (tmm160) cc_final: 0.8651 (ttp80) outliers start: 29 outliers final: 8 residues processed: 191 average time/residue: 0.3509 time to fit residues: 88.8296 Evaluate side-chains 114 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain H residue 79 GLU Chi-restraints excluded: chain H residue 81 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 0.0170 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 0.1980 chunk 104 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 GLN B 53 HIS B 158 HIS A 185 GLN G 118 GLN C 101 GLN ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5187 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14041 Z= 0.238 Angle : 0.763 10.048 19659 Z= 0.421 Chirality : 0.041 0.195 2115 Planarity : 0.006 0.048 1934 Dihedral : 25.297 151.659 3264 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.86 % Favored : 91.05 % Rotamer: Outliers : 3.07 % Allowed : 10.78 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.23), residues: 1185 helix: -1.05 (0.16), residues: 871 sheet: None (None), residues: 0 loop : -2.53 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 178 HIS 0.010 0.001 HIS H 174 PHE 0.024 0.002 PHE H 54 TYR 0.025 0.002 TYR A 51 ARG 0.011 0.001 ARG H 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 124 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 ASP cc_start: 0.6459 (m-30) cc_final: 0.5902 (t0) REVERT: B 24 LYS cc_start: 0.4541 (pttp) cc_final: 0.4300 (pttp) REVERT: B 191 PHE cc_start: 0.5797 (t80) cc_final: 0.5511 (t80) REVERT: B 198 ARG cc_start: 0.6576 (mtm110) cc_final: 0.6282 (mmm-85) REVERT: A 13 ARG cc_start: 0.7706 (mmp-170) cc_final: 0.7500 (mmp80) REVERT: A 97 MET cc_start: 0.7842 (mtm) cc_final: 0.7518 (ttp) REVERT: A 167 HIS cc_start: 0.5811 (t-90) cc_final: 0.5560 (t-170) REVERT: G 38 MET cc_start: 0.8001 (ttm) cc_final: 0.7675 (mtp) REVERT: G 127 HIS cc_start: 0.8959 (m-70) cc_final: 0.8660 (m-70) REVERT: G 128 LYS cc_start: 0.9247 (ptmt) cc_final: 0.9045 (ptpp) REVERT: G 199 MET cc_start: 0.1385 (ppp) cc_final: 0.0479 (ppp) REVERT: C 199 MET cc_start: 0.2367 (mtm) cc_final: -0.0288 (mmp) REVERT: H 64 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9172 (mt) REVERT: H 199 MET cc_start: 0.4076 (ptt) cc_final: 0.3634 (ptt) outliers start: 31 outliers final: 14 residues processed: 146 average time/residue: 0.3059 time to fit residues: 61.4829 Evaluate side-chains 113 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 137 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 82 optimal weight: 0.0470 chunk 33 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN A 118 GLN A 185 GLN H 152 ASN D 174 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5208 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14041 Z= 0.226 Angle : 0.729 12.279 19659 Z= 0.401 Chirality : 0.041 0.182 2115 Planarity : 0.005 0.047 1934 Dihedral : 25.147 151.582 3243 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.35 % Favored : 91.56 % Rotamer: Outliers : 2.47 % Allowed : 13.65 % Favored : 83.88 % 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: -1.68 (0.23), residues: 1185 helix: -0.56 (0.16), residues: 875 sheet: None (None), residues: 0 loop : -2.43 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 178 HIS 0.007 0.001 HIS B 190 PHE 0.034 0.002 PHE A 93 TYR 0.027 0.002 TYR A 51 ARG 0.007 0.001 ARG B 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 191 PHE cc_start: 0.5790 (t80) cc_final: 0.5432 (t80) REVERT: B 198 ARG cc_start: 0.6687 (mtm110) cc_final: 0.6121 (mmm-85) REVERT: A 97 MET cc_start: 0.7824 (mtm) cc_final: 0.7509 (ttp) REVERT: A 167 HIS cc_start: 0.5772 (t-90) cc_final: 0.5517 (t-170) REVERT: G 38 MET cc_start: 0.8103 (ttm) cc_final: 0.7734 (mtp) REVERT: G 127 HIS cc_start: 0.8970 (m-70) cc_final: 0.8662 (m-70) REVERT: G 128 LYS cc_start: 0.9216 (ptmt) cc_final: 0.8989 (pttm) REVERT: H 199 MET cc_start: 0.3586 (ptt) cc_final: 0.3117 (ptt) outliers start: 25 outliers final: 16 residues processed: 131 average time/residue: 0.2812 time to fit residues: 51.9677 Evaluate side-chains 106 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 137 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 6.9990 chunk 90 optimal weight: 30.0000 chunk 62 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 128 optimal weight: 40.0000 chunk 63 optimal weight: 9.9990 chunk 115 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 overall best weight: 2.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 HIS G 167 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5332 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 14041 Z= 0.327 Angle : 0.814 12.823 19659 Z= 0.448 Chirality : 0.044 0.220 2115 Planarity : 0.006 0.065 1934 Dihedral : 25.203 152.603 3243 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.62 % Favored : 90.30 % Rotamer: Outliers : 4.85 % Allowed : 15.53 % Favored : 79.62 % 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: -1.66 (0.24), residues: 1185 helix: -0.60 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -2.29 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 178 HIS 0.009 0.002 HIS A 53 PHE 0.032 0.003 PHE A 93 TYR 0.031 0.003 TYR A 51 ARG 0.008 0.001 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 112 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 ARG cc_start: 0.6709 (mtm110) cc_final: 0.6165 (mmm-85) REVERT: A 13 ARG cc_start: 0.7346 (mmp-170) cc_final: 0.7079 (mmp80) REVERT: G 127 HIS cc_start: 0.9006 (m-70) cc_final: 0.8733 (m-70) REVERT: G 128 LYS cc_start: 0.9234 (ptmt) cc_final: 0.8990 (ptpp) REVERT: C 199 MET cc_start: 0.2374 (mtt) cc_final: 0.1620 (mtt) REVERT: H 103 TYR cc_start: 0.9480 (t80) cc_final: 0.9256 (m-10) REVERT: H 199 MET cc_start: 0.3700 (ptt) cc_final: 0.2593 (ptt) outliers start: 49 outliers final: 30 residues processed: 152 average time/residue: 0.2534 time to fit residues: 55.6946 Evaluate side-chains 121 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 91 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 137 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 0.0870 chunk 115 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN H 185 GLN D 167 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5309 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14041 Z= 0.246 Angle : 0.741 10.869 19659 Z= 0.409 Chirality : 0.042 0.226 2115 Planarity : 0.005 0.050 1934 Dihedral : 25.188 151.892 3243 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.69 % Favored : 91.22 % Rotamer: Outliers : 3.76 % Allowed : 18.79 % Favored : 77.45 % 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 (0.24), residues: 1185 helix: -0.29 (0.17), residues: 884 sheet: None (None), residues: 0 loop : -2.36 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 178 HIS 0.008 0.001 HIS H 174 PHE 0.036 0.002 PHE A 93 TYR 0.028 0.002 TYR A 51 ARG 0.008 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 106 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 ARG cc_start: 0.6677 (mtm110) cc_final: 0.6096 (mmm-85) REVERT: G 127 HIS cc_start: 0.9001 (m-70) cc_final: 0.8746 (m-70) REVERT: G 128 LYS cc_start: 0.9206 (ptmt) cc_final: 0.9003 (pttm) REVERT: G 193 MET cc_start: 0.2291 (tpp) cc_final: 0.2069 (tpp) REVERT: C 199 MET cc_start: 0.2052 (mtt) cc_final: 0.1278 (mtt) REVERT: H 103 TYR cc_start: 0.9486 (t80) cc_final: 0.9207 (m-80) REVERT: H 199 MET cc_start: 0.2153 (ptt) cc_final: 0.1850 (ptt) outliers start: 38 outliers final: 28 residues processed: 135 average time/residue: 0.2774 time to fit residues: 53.2385 Evaluate side-chains 125 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 97 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 195 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 8.9990 chunk 115 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 75 optimal weight: 50.0000 chunk 31 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 59 optimal weight: 0.0870 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 overall best weight: 1.2560 ------------------------------------------------------------------------------- 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: 0.5296 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14041 Z= 0.233 Angle : 0.729 15.465 19659 Z= 0.403 Chirality : 0.041 0.224 2115 Planarity : 0.005 0.048 1934 Dihedral : 25.164 150.830 3243 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.44 % Favored : 91.48 % Rotamer: Outliers : 3.36 % Allowed : 20.08 % Favored : 76.56 % 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: -1.01 (0.24), residues: 1185 helix: -0.07 (0.17), residues: 890 sheet: None (None), residues: 0 loop : -2.28 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 178 HIS 0.008 0.001 HIS H 174 PHE 0.040 0.002 PHE A 93 TYR 0.027 0.002 TYR A 51 ARG 0.006 0.000 ARG G 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 109 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 ARG cc_start: 0.6783 (mtm110) cc_final: 0.6154 (mmm-85) REVERT: A 51 TYR cc_start: 0.5208 (m-80) cc_final: 0.4960 (m-80) REVERT: A 96 ARG cc_start: 0.4875 (mtp85) cc_final: 0.4354 (tpm170) REVERT: A 167 HIS cc_start: 0.6190 (t-90) cc_final: 0.5928 (t-170) REVERT: A 191 PHE cc_start: 0.4393 (OUTLIER) cc_final: 0.4143 (t80) REVERT: G 97 MET cc_start: 0.1226 (ptt) cc_final: 0.0915 (ptp) REVERT: G 174 HIS cc_start: 0.0683 (OUTLIER) cc_final: 0.0019 (t70) REVERT: C 199 MET cc_start: 0.1830 (mtt) cc_final: 0.0828 (mtt) REVERT: H 103 TYR cc_start: 0.9461 (t80) cc_final: 0.9193 (m-80) REVERT: H 124 GLU cc_start: 0.9594 (mm-30) cc_final: 0.9255 (pp20) REVERT: H 199 MET cc_start: 0.1781 (ptt) cc_final: 0.1237 (ptt) outliers start: 34 outliers final: 24 residues processed: 134 average time/residue: 0.2675 time to fit residues: 50.8349 Evaluate side-chains 124 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 98 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 195 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 93 optimal weight: 30.0000 chunk 72 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 128 optimal weight: 0.0020 chunk 80 optimal weight: 0.9980 chunk 78 optimal weight: 50.0000 chunk 59 optimal weight: 0.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5292 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14041 Z= 0.223 Angle : 0.726 12.999 19659 Z= 0.399 Chirality : 0.040 0.177 2115 Planarity : 0.005 0.052 1934 Dihedral : 25.148 149.900 3243 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.19 % Favored : 91.73 % Rotamer: Outliers : 3.86 % Allowed : 20.77 % Favored : 75.37 % 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: -0.79 (0.24), residues: 1185 helix: 0.08 (0.17), residues: 891 sheet: None (None), residues: 0 loop : -2.19 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.008 0.001 HIS H 174 PHE 0.040 0.002 PHE A 93 TYR 0.026 0.002 TYR A 51 ARG 0.014 0.001 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 104 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 ARG cc_start: 0.6805 (mtm110) cc_final: 0.6139 (mmm-85) REVERT: B 199 MET cc_start: 0.4437 (tmm) cc_final: 0.4222 (tmm) REVERT: A 38 MET cc_start: 0.6127 (ttt) cc_final: 0.5458 (mmp) REVERT: A 96 ARG cc_start: 0.4875 (mtp85) cc_final: 0.4321 (tpm170) REVERT: A 167 HIS cc_start: 0.6156 (t-90) cc_final: 0.5892 (t-170) REVERT: A 191 PHE cc_start: 0.4424 (OUTLIER) cc_final: 0.4095 (t80) REVERT: G 38 MET cc_start: 0.7870 (ttm) cc_final: 0.7579 (ptp) REVERT: G 174 HIS cc_start: 0.0674 (OUTLIER) cc_final: 0.0016 (t70) REVERT: C 199 MET cc_start: 0.1478 (mtt) cc_final: -0.0116 (mtt) REVERT: H 103 TYR cc_start: 0.9427 (t80) cc_final: 0.9168 (m-80) REVERT: H 199 MET cc_start: 0.1776 (ptt) cc_final: 0.1159 (ptt) outliers start: 39 outliers final: 30 residues processed: 134 average time/residue: 0.2691 time to fit residues: 51.7028 Evaluate side-chains 129 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 97 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 92 TYR Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 195 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 38 optimal weight: 0.0040 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5292 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14041 Z= 0.219 Angle : 0.714 12.290 19659 Z= 0.396 Chirality : 0.040 0.179 2115 Planarity : 0.005 0.046 1934 Dihedral : 25.144 149.063 3243 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.35 % Favored : 91.56 % Rotamer: Outliers : 3.46 % Allowed : 21.76 % Favored : 74.78 % 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: -0.67 (0.24), residues: 1185 helix: 0.17 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -2.13 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 178 HIS 0.009 0.001 HIS H 174 PHE 0.031 0.002 PHE G 76 TYR 0.025 0.002 TYR A 51 ARG 0.009 0.001 ARG A 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 101 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 ARG cc_start: 0.6817 (mtm110) cc_final: 0.6146 (mmm-85) REVERT: B 199 MET cc_start: 0.4249 (tmm) cc_final: 0.4039 (tmm) REVERT: A 38 MET cc_start: 0.6181 (ttt) cc_final: 0.5705 (mmp) REVERT: A 96 ARG cc_start: 0.5064 (mtp85) cc_final: 0.4501 (tpm170) REVERT: A 167 HIS cc_start: 0.6186 (t-90) cc_final: 0.5933 (t-170) REVERT: A 191 PHE cc_start: 0.4441 (OUTLIER) cc_final: 0.4121 (t80) REVERT: G 38 MET cc_start: 0.7935 (ttm) cc_final: 0.7652 (ptp) REVERT: G 174 HIS cc_start: 0.0853 (OUTLIER) cc_final: 0.0192 (t70) REVERT: C 199 MET cc_start: 0.1361 (mtt) cc_final: 0.0622 (mtt) REVERT: H 103 TYR cc_start: 0.9409 (t80) cc_final: 0.9161 (m-80) REVERT: H 199 MET cc_start: 0.1375 (ptt) cc_final: 0.0966 (ptt) outliers start: 35 outliers final: 30 residues processed: 125 average time/residue: 0.2809 time to fit residues: 49.9772 Evaluate side-chains 129 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 97 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 195 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 0.2980 chunk 122 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 78 optimal weight: 50.0000 chunk 126 optimal weight: 0.7980 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 174 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5380 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 14041 Z= 0.296 Angle : 0.780 12.001 19659 Z= 0.432 Chirality : 0.044 0.282 2115 Planarity : 0.005 0.065 1934 Dihedral : 25.246 148.959 3243 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 24.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.28 % Favored : 90.63 % Rotamer: Outliers : 3.96 % Allowed : 22.45 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.24), residues: 1185 helix: -0.03 (0.17), residues: 885 sheet: None (None), residues: 0 loop : -2.13 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 178 HIS 0.010 0.001 HIS H 174 PHE 0.030 0.003 PHE B 189 TYR 0.027 0.002 TYR A 51 ARG 0.010 0.001 ARG A 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 95 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 ARG cc_start: 0.6798 (mtm110) cc_final: 0.6165 (mmm-85) REVERT: A 38 MET cc_start: 0.6872 (ttt) cc_final: 0.6231 (mmp) REVERT: A 96 ARG cc_start: 0.5072 (mtp85) cc_final: 0.4395 (tpm170) REVERT: A 191 PHE cc_start: 0.4575 (OUTLIER) cc_final: 0.4348 (t80) REVERT: G 174 HIS cc_start: 0.0959 (OUTLIER) cc_final: 0.0287 (t70) REVERT: C 199 MET cc_start: 0.1204 (mtt) cc_final: -0.0026 (mtt) REVERT: H 103 TYR cc_start: 0.9386 (t80) cc_final: 0.9142 (m-80) REVERT: H 199 MET cc_start: 0.1394 (ptt) cc_final: 0.0801 (ptt) outliers start: 40 outliers final: 34 residues processed: 127 average time/residue: 0.2822 time to fit residues: 51.1172 Evaluate side-chains 125 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 89 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 92 TYR Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 195 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5460 moved from start: 0.5984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 14041 Z= 0.362 Angle : 0.869 13.065 19659 Z= 0.478 Chirality : 0.048 0.333 2115 Planarity : 0.007 0.115 1934 Dihedral : 25.435 148.480 3243 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 30.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.70 % Favored : 90.21 % Rotamer: Outliers : 3.66 % Allowed : 23.54 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1185 helix: -0.52 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -2.20 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 178 HIS 0.011 0.002 HIS A 53 PHE 0.036 0.003 PHE A 93 TYR 0.030 0.003 TYR B 159 ARG 0.013 0.001 ARG G 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 92 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 ARG cc_start: 0.6789 (mtm110) cc_final: 0.6049 (mmm-85) REVERT: A 27 LEU cc_start: 0.2151 (OUTLIER) cc_final: 0.1924 (mt) REVERT: A 98 ARG cc_start: 0.4331 (mmt-90) cc_final: 0.4109 (mmt180) REVERT: A 191 PHE cc_start: 0.4806 (OUTLIER) cc_final: 0.4559 (t80) REVERT: G 174 HIS cc_start: 0.1262 (OUTLIER) cc_final: 0.0615 (t70) REVERT: C 199 MET cc_start: 0.1425 (mtt) cc_final: -0.0329 (mtt) REVERT: H 103 TYR cc_start: 0.9362 (t80) cc_final: 0.9108 (m-80) REVERT: H 193 MET cc_start: 0.2027 (mmm) cc_final: 0.1814 (mmm) REVERT: H 199 MET cc_start: 0.1063 (ptt) cc_final: 0.0666 (ptt) outliers start: 37 outliers final: 30 residues processed: 123 average time/residue: 0.2890 time to fit residues: 50.4405 Evaluate side-chains 115 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 82 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 195 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 50.0000 chunk 15 optimal weight: 20.0000 chunk 29 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 108 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 0.0010 chunk 92 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5062 r_free = 0.5062 target = 0.159426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.144662 restraints weight = 103873.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.144975 restraints weight = 66758.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.145180 restraints weight = 47930.201| |-----------------------------------------------------------------------------| r_work (final): 0.4775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4869 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14041 Z= 0.246 Angle : 0.776 14.275 19659 Z= 0.426 Chirality : 0.043 0.303 2115 Planarity : 0.005 0.046 1934 Dihedral : 25.388 146.785 3243 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 22.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.11 % Favored : 90.80 % Rotamer: Outliers : 3.46 % Allowed : 24.04 % Favored : 72.50 % 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: -1.15 (0.24), residues: 1185 helix: -0.20 (0.17), residues: 881 sheet: None (None), residues: 0 loop : -2.17 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 178 HIS 0.009 0.001 HIS H 174 PHE 0.031 0.002 PHE B 189 TYR 0.021 0.002 TYR C 103 ARG 0.020 0.001 ARG C 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3106.35 seconds wall clock time: 56 minutes 6.14 seconds (3366.14 seconds total)