Starting phenix.real_space_refine on Tue Mar 19 03:21:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xaq_33097/03_2024/7xaq_33097.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xaq_33097/03_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_33097/03_2024/7xaq_33097.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xaq_33097/03_2024/7xaq_33097.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xaq_33097/03_2024/7xaq_33097.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xaq_33097/03_2024/7xaq_33097.pdb" } 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 Residue "B GLU 4": "OE1" <-> "OE2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 13": "NH1" <-> "NH2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G GLU 79": "OE1" <-> "OE2" Residue "G ASP 80": "OD1" <-> "OD2" Residue "G ARG 83": "NH1" <-> "NH2" Residue "G GLU 151": "OE1" <-> "OE2" Residue "G GLU 180": "OE1" <-> "OE2" Residue "G GLU 183": "OE1" <-> "OE2" Residue "G GLU 186": "OE1" <-> "OE2" Residue "C ARG 9": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "H GLU 4": "OE1" <-> "OE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H ARG 13": "NH1" <-> "NH2" Residue "H GLU 17": "OE1" <-> "OE2" Residue "H GLU 28": "OE1" <-> "OE2" Residue "H ARG 63": "NH1" <-> "NH2" Residue "H ARG 83": "NH1" <-> "NH2" Residue "H GLU 135": "OE1" <-> "OE2" Residue "H GLU 186": "OE1" <-> "OE2" Residue "D ARG 9": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D GLU 151": "OE1" <-> "OE2" Residue "D ARG 179": "NH1" <-> "NH2" Residue "D GLU 180": "OE1" <-> "OE2" Residue "D GLU 186": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 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: 7.40, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.93 Conformation dependent library (CDL) restraints added in 1.9 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: 5.08 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: 4.10 Time building geometry restraints manager: 7.35 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: 95.05 - 102.95: 262 102.95 - 110.84: 5424 110.84 - 118.74: 6167 118.74 - 126.64: 7200 126.64 - 134.54: 606 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 2.440 nonbonded pdb=" O GLU B 17 " pdb=" OG1 THR B 21 " model vdw 2.004 2.440 nonbonded pdb=" O PHE D 134 " pdb=" OG1 THR D 138 " model vdw 2.045 2.440 ... (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 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: 6.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 13.580 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 42.300 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.180 ------------------------------------------------------------------------------- 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 : 1.279 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: 0.3510 time to fit residues: 88.2080 Evaluate side-chains 114 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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: 9.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 34 optimal weight: 0.0170 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.9220 ------------------------------------------------------------------------------- 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 C 101 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5213 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14041 Z= 0.235 Angle : 0.750 10.082 19659 Z= 0.414 Chirality : 0.041 0.208 2115 Planarity : 0.005 0.056 1934 Dihedral : 25.316 151.526 3264 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.44 % Favored : 91.39 % Rotamer: Outliers : 3.07 % Allowed : 11.08 % Favored : 85.86 % 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: -2.28 (0.23), residues: 1185 helix: -1.05 (0.16), residues: 881 sheet: None (None), residues: 0 loop : -2.48 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 178 HIS 0.011 0.001 HIS H 174 PHE 0.021 0.002 PHE H 54 TYR 0.022 0.002 TYR G 92 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 154 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 123 time to evaluate : 1.328 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: symmetry clash REVERT: B 20 ASP cc_start: 0.6459 (m-30) cc_final: 0.5912 (t0) REVERT: B 191 PHE cc_start: 0.5806 (t80) cc_final: 0.5535 (t80) REVERT: B 193 MET cc_start: 0.5508 (mtm) cc_final: 0.5252 (mtm) REVERT: B 198 ARG cc_start: 0.6602 (mtm110) cc_final: 0.6198 (mmm-85) REVERT: A 97 MET cc_start: 0.7809 (mtm) cc_final: 0.7500 (ttp) REVERT: A 167 HIS cc_start: 0.5786 (t-90) cc_final: 0.5520 (t-170) REVERT: G 38 MET cc_start: 0.8018 (ttm) cc_final: 0.7688 (mtp) REVERT: G 127 HIS cc_start: 0.9000 (m-70) cc_final: 0.8705 (m-70) REVERT: G 128 LYS cc_start: 0.9250 (ptmt) cc_final: 0.9048 (ptpp) REVERT: G 199 MET cc_start: 0.1506 (ppp) cc_final: 0.0608 (ppp) REVERT: C 199 MET cc_start: 0.2253 (mtm) cc_final: -0.0405 (mmp) REVERT: H 64 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9148 (mt) REVERT: H 199 MET cc_start: 0.3907 (ptt) cc_final: 0.3463 (ptt) outliers start: 31 outliers final: 15 residues processed: 144 average time/residue: 0.3072 time to fit residues: 61.0790 Evaluate side-chains 115 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 138 THR 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 140 LEU Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 78 SER 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: 0.8980 chunk 37 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 33 optimal weight: 0.0970 chunk 120 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5213 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14041 Z= 0.212 Angle : 0.712 11.947 19659 Z= 0.392 Chirality : 0.040 0.178 2115 Planarity : 0.005 0.049 1934 Dihedral : 25.169 151.723 3245 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.03 % Favored : 90.89 % Rotamer: Outliers : 2.77 % Allowed : 13.65 % Favored : 83.58 % 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: -1.57 (0.24), residues: 1185 helix: -0.53 (0.16), residues: 889 sheet: None (None), residues: 0 loop : -2.28 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.005 0.001 HIS B 127 PHE 0.033 0.002 PHE A 93 TYR 0.020 0.002 TYR A 51 ARG 0.006 0.001 ARG A 96 *********************** 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 140 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 112 time to evaluate : 1.284 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 191 PHE cc_start: 0.5770 (t80) cc_final: 0.5444 (t80) REVERT: B 198 ARG cc_start: 0.6646 (mtm110) cc_final: 0.6058 (mmm-85) REVERT: A 97 MET cc_start: 0.7786 (mtm) cc_final: 0.7476 (ttp) REVERT: A 167 HIS cc_start: 0.5791 (t-90) cc_final: 0.5546 (t-170) REVERT: G 38 MET cc_start: 0.8114 (ttm) cc_final: 0.7749 (mtp) REVERT: G 127 HIS cc_start: 0.8950 (m-70) cc_final: 0.8639 (m-70) REVERT: G 128 LYS cc_start: 0.9215 (ptmt) cc_final: 0.8982 (pttm) REVERT: H 199 MET cc_start: 0.3154 (ptt) cc_final: 0.2688 (ptt) outliers start: 28 outliers final: 18 residues processed: 133 average time/residue: 0.2750 time to fit residues: 51.7460 Evaluate side-chains 109 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 138 THR 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 21 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 199 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 7.9990 chunk 90 optimal weight: 30.0000 chunk 62 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 121 optimal weight: 0.0070 chunk 128 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 115 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 overall best weight: 2.7002 ------------------------------------------------------------------------------- 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 H 152 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5341 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 14041 Z= 0.310 Angle : 0.800 13.715 19659 Z= 0.436 Chirality : 0.044 0.217 2115 Planarity : 0.006 0.055 1934 Dihedral : 25.230 152.695 3245 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 25.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.62 % Favored : 90.30 % Rotamer: Outliers : 4.85 % Allowed : 15.73 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.24), residues: 1185 helix: -0.45 (0.17), residues: 890 sheet: None (None), residues: 0 loop : -2.22 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 178 HIS 0.011 0.002 HIS A 53 PHE 0.031 0.003 PHE C 95 TYR 0.024 0.002 TYR A 92 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 160 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 111 time to evaluate : 1.232 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 191 PHE cc_start: 0.5380 (t80) cc_final: 0.4951 (t80) REVERT: B 198 ARG cc_start: 0.6637 (mtm110) cc_final: 0.6096 (mmm-85) REVERT: A 167 HIS cc_start: 0.5801 (t-90) cc_final: 0.5571 (t-170) REVERT: G 127 HIS cc_start: 0.9016 (m-70) cc_final: 0.8740 (m-70) REVERT: G 128 LYS cc_start: 0.9233 (ptmt) cc_final: 0.8987 (ptpp) REVERT: C 199 MET cc_start: 0.1326 (mtt) cc_final: 0.0638 (mtt) REVERT: H 199 MET cc_start: 0.3222 (ptt) cc_final: 0.2249 (ptt) outliers start: 49 outliers final: 30 residues processed: 152 average time/residue: 0.2653 time to fit residues: 57.5164 Evaluate side-chains 126 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 96 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASP 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 119 VAL Chi-restraints excluded: chain B residue 138 THR 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 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 65 MET 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 C residue 184 ASP 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 chunk 53 optimal weight: 0.0980 chunk 109 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5333 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14041 Z= 0.259 Angle : 0.743 10.027 19659 Z= 0.411 Chirality : 0.042 0.198 2115 Planarity : 0.005 0.047 1934 Dihedral : 25.233 152.286 3243 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 24.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.03 % Favored : 90.89 % Rotamer: Outliers : 4.15 % Allowed : 18.89 % Favored : 76.95 % 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: -1.25 (0.24), residues: 1185 helix: -0.26 (0.17), residues: 890 sheet: None (None), residues: 0 loop : -2.28 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 178 HIS 0.022 0.001 HIS H 174 PHE 0.032 0.002 PHE B 189 TYR 0.022 0.002 TYR B 159 ARG 0.007 0.001 ARG A 96 *********************** 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 148 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 106 time to evaluate : 1.158 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 189 PHE cc_start: 0.8235 (m-80) cc_final: 0.7989 (t80) REVERT: B 198 ARG cc_start: 0.6587 (mtm110) cc_final: 0.5989 (mmm-85) REVERT: G 127 HIS cc_start: 0.9004 (m-70) cc_final: 0.8752 (m-70) REVERT: G 128 LYS cc_start: 0.9211 (ptmt) cc_final: 0.9001 (pttm) REVERT: C 199 MET cc_start: 0.1383 (mtt) cc_final: 0.0699 (mtt) REVERT: H 103 TYR cc_start: 0.9378 (t80) cc_final: 0.9081 (m-10) REVERT: H 199 MET cc_start: 0.1964 (ptt) cc_final: 0.1460 (ptt) outliers start: 42 outliers final: 33 residues processed: 141 average time/residue: 0.2886 time to fit residues: 56.8253 Evaluate side-chains 127 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 94 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 138 THR 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 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 G residue 8 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 65 MET 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 C residue 184 ASP Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain D residue 14 ARG 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 185 GLN 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: 7.9990 chunk 115 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 75 optimal weight: 40.0000 chunk 31 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 HIS ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5371 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 14041 Z= 0.277 Angle : 0.765 15.313 19659 Z= 0.423 Chirality : 0.043 0.193 2115 Planarity : 0.005 0.049 1934 Dihedral : 25.267 151.829 3243 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 26.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.20 % Favored : 90.72 % Rotamer: Outliers : 5.14 % Allowed : 19.49 % 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: -1.28 (0.24), residues: 1185 helix: -0.30 (0.17), residues: 893 sheet: None (None), residues: 0 loop : -2.27 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 178 HIS 0.019 0.002 HIS H 174 PHE 0.048 0.003 PHE A 93 TYR 0.022 0.003 TYR B 159 ARG 0.027 0.001 ARG D 96 *********************** 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 156 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 104 time to evaluate : 1.208 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: B 189 PHE cc_start: 0.8197 (m-80) cc_final: 0.7939 (t80) REVERT: B 198 ARG cc_start: 0.6721 (mtm110) cc_final: 0.6063 (mmm-85) REVERT: B 199 MET cc_start: 0.4070 (tmm) cc_final: 0.3815 (tmm) REVERT: A 191 PHE cc_start: 0.4484 (OUTLIER) cc_final: 0.4191 (t80) REVERT: G 38 MET cc_start: 0.7924 (ttm) cc_final: 0.7696 (ptm) REVERT: C 199 MET cc_start: 0.1260 (mtt) cc_final: 0.0643 (mtt) REVERT: H 103 TYR cc_start: 0.9364 (t80) cc_final: 0.9099 (m-10) REVERT: H 199 MET cc_start: 0.1690 (ptt) cc_final: 0.1268 (ptt) outliers start: 52 outliers final: 43 residues processed: 143 average time/residue: 0.2995 time to fit residues: 60.7313 Evaluate side-chains 139 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 95 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASP 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 88 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 138 THR 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 A residue 19 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 84 ASP 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 A residue 199 MET Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 92 TYR Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 184 ASP 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 14 ARG 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 175 SER Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 199 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 0.3980 chunk 14 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 128 optimal weight: 30.0000 chunk 80 optimal weight: 8.9990 chunk 78 optimal weight: 50.0000 chunk 59 optimal weight: 0.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- 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** A 101 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5485 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 14041 Z= 0.393 Angle : 0.882 13.084 19659 Z= 0.487 Chirality : 0.047 0.211 2115 Planarity : 0.006 0.075 1934 Dihedral : 25.510 151.959 3243 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 36.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.70 % Favored : 90.04 % Rotamer: Outliers : 5.34 % Allowed : 20.97 % Favored : 73.69 % 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: -1.80 (0.23), residues: 1185 helix: -0.69 (0.16), residues: 884 sheet: None (None), residues: 0 loop : -2.36 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 178 HIS 0.020 0.002 HIS H 174 PHE 0.049 0.003 PHE A 93 TYR 0.031 0.003 TYR A 92 ARG 0.010 0.001 ARG A 96 *********************** 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 154 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 100 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 189 PHE cc_start: 0.8012 (m-80) cc_final: 0.7747 (t80) REVERT: B 198 ARG cc_start: 0.6795 (mtm110) cc_final: 0.6116 (mmm-85) REVERT: A 191 PHE cc_start: 0.4596 (OUTLIER) cc_final: 0.4330 (t80) REVERT: G 38 MET cc_start: 0.7951 (ttm) cc_final: 0.7720 (ptm) REVERT: G 174 HIS cc_start: 0.1246 (OUTLIER) cc_final: 0.0587 (t70) REVERT: C 199 MET cc_start: 0.1104 (mtt) cc_final: 0.0149 (mtt) REVERT: H 103 TYR cc_start: 0.9319 (t80) cc_final: 0.9057 (m-80) REVERT: H 199 MET cc_start: 0.1577 (ptt) cc_final: 0.1028 (ptt) REVERT: D 14 ARG cc_start: 0.2221 (OUTLIER) cc_final: 0.1712 (mtp85) REVERT: D 193 MET cc_start: 0.4282 (mmp) cc_final: 0.3194 (mmp) outliers start: 54 outliers final: 42 residues processed: 140 average time/residue: 0.2744 time to fit residues: 54.8777 Evaluate side-chains 136 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 91 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASP 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 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 138 THR 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 A residue 19 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 84 ASP 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 8 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 92 TYR 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 36 VAL Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 184 ASP 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 14 ARG Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 92 TYR Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 199 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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** A 101 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5348 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14041 Z= 0.228 Angle : 0.729 11.905 19659 Z= 0.404 Chirality : 0.042 0.195 2115 Planarity : 0.005 0.047 1934 Dihedral : 25.386 149.563 3243 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 23.23 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.19 % Favored : 91.56 % Rotamer: Outliers : 3.17 % Allowed : 23.34 % Favored : 73.49 % 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: -1.05 (0.24), residues: 1185 helix: -0.08 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.28 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 178 HIS 0.017 0.001 HIS H 174 PHE 0.052 0.002 PHE A 93 TYR 0.019 0.002 TYR B 159 ARG 0.008 0.001 ARG G 96 *********************** 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 133 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 101 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: symmetry clash REVERT: B 189 PHE cc_start: 0.8203 (m-80) cc_final: 0.7919 (t80) REVERT: A 191 PHE cc_start: 0.4704 (OUTLIER) cc_final: 0.4379 (t80) REVERT: G 38 MET cc_start: 0.7983 (ttm) cc_final: 0.7734 (ptm) REVERT: G 174 HIS cc_start: 0.0891 (OUTLIER) cc_final: 0.0238 (t70) REVERT: C 199 MET cc_start: 0.1094 (mtt) cc_final: 0.0258 (mtt) REVERT: H 103 TYR cc_start: 0.9333 (t80) cc_final: 0.9090 (m-80) REVERT: H 124 GLU cc_start: 0.9622 (mm-30) cc_final: 0.9273 (pp20) REVERT: H 199 MET cc_start: 0.1066 (ptt) cc_final: 0.0685 (ptt) REVERT: D 14 ARG cc_start: 0.1064 (OUTLIER) cc_final: 0.0484 (mtp85) outliers start: 32 outliers final: 25 residues processed: 126 average time/residue: 0.2912 time to fit residues: 52.8215 Evaluate side-chains 118 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 90 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 88 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 138 THR 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 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 92 TYR 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 126 LEU Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 110 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 52 optimal weight: 0.7980 chunk 93 optimal weight: 20.0000 chunk 36 optimal weight: 0.0670 chunk 107 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 overall best weight: 1.1520 ------------------------------------------------------------------------------- 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 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5353 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14041 Z= 0.226 Angle : 0.740 17.119 19659 Z= 0.404 Chirality : 0.041 0.185 2115 Planarity : 0.005 0.048 1934 Dihedral : 25.341 148.451 3243 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 24.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.69 % Favored : 91.14 % 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: -0.83 (0.24), residues: 1185 helix: 0.07 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -2.16 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 178 HIS 0.017 0.001 HIS H 174 PHE 0.024 0.002 PHE A 93 TYR 0.018 0.002 TYR B 159 ARG 0.011 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 130 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 95 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 189 PHE cc_start: 0.8238 (m-80) cc_final: 0.7956 (t80) REVERT: B 198 ARG cc_start: 0.6614 (mtm110) cc_final: 0.5870 (mmm-85) REVERT: A 191 PHE cc_start: 0.4628 (OUTLIER) cc_final: 0.4300 (t80) REVERT: G 38 MET cc_start: 0.7992 (ttm) cc_final: 0.7741 (ptm) REVERT: G 105 LEU cc_start: 0.5511 (OUTLIER) cc_final: 0.5221 (tp) REVERT: G 174 HIS cc_start: 0.0980 (OUTLIER) cc_final: 0.0551 (t70) REVERT: C 199 MET cc_start: 0.0863 (mtt) cc_final: 0.0156 (mtt) REVERT: H 103 TYR cc_start: 0.9317 (t80) cc_final: 0.9069 (m-80) REVERT: H 199 MET cc_start: 0.1015 (ptt) cc_final: 0.0669 (ptt) REVERT: D 14 ARG cc_start: 0.0857 (OUTLIER) cc_final: 0.0275 (mtp85) REVERT: D 127 HIS cc_start: 0.9058 (OUTLIER) cc_final: 0.8687 (m90) outliers start: 35 outliers final: 28 residues processed: 123 average time/residue: 0.2779 time to fit residues: 49.0416 Evaluate side-chains 121 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 88 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 88 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 138 THR 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 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 170 VAL 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 92 TYR 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 126 LEU Chi-restraints excluded: chain D residue 14 ARG 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 127 HIS 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: 0.8980 chunk 87 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 121 optimal weight: 30.0000 chunk 105 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- 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** A 101 GLN ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5550 moved from start: 0.6193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.114 14041 Z= 0.517 Angle : 1.006 13.619 19659 Z= 0.550 Chirality : 0.054 0.533 2115 Planarity : 0.008 0.149 1934 Dihedral : 25.614 149.926 3243 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 44.14 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.72 % Favored : 88.95 % Rotamer: Outliers : 3.76 % Allowed : 24.23 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.24), residues: 1185 helix: -0.78 (0.16), residues: 889 sheet: None (None), residues: 0 loop : -2.12 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 178 HIS 0.019 0.003 HIS H 174 PHE 0.041 0.004 PHE A 93 TYR 0.041 0.004 TYR A 92 ARG 0.016 0.001 ARG B 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 126 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 88 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 189 PHE cc_start: 0.7955 (m-80) cc_final: 0.7714 (t80) REVERT: B 198 ARG cc_start: 0.6983 (mtm110) cc_final: 0.6109 (mmm-85) REVERT: G 38 MET cc_start: 0.7911 (ttm) cc_final: 0.7682 (ptm) REVERT: G 174 HIS cc_start: 0.1424 (OUTLIER) cc_final: 0.0756 (t70) REVERT: C 199 MET cc_start: 0.0746 (mtt) cc_final: -0.0192 (mtt) REVERT: H 103 TYR cc_start: 0.9281 (t80) cc_final: 0.9023 (m-80) REVERT: H 199 MET cc_start: 0.1184 (ptt) cc_final: 0.0579 (ptt) outliers start: 38 outliers final: 36 residues processed: 119 average time/residue: 0.2620 time to fit residues: 45.6486 Evaluate side-chains 121 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 84 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 119 VAL Chi-restraints excluded: chain B residue 138 THR 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 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 170 VAL Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 92 TYR 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 66 LEU 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 92 TYR Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 199 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 92 optimal weight: 0.4980 chunk 6 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 GLN ** A 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.159307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.142286 restraints weight = 104559.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.143238 restraints weight = 63197.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.143536 restraints weight = 41748.298| |-----------------------------------------------------------------------------| r_work (final): 0.4761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5301 moved from start: 0.6128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 14041 Z= 0.231 Angle : 0.772 12.123 19659 Z= 0.424 Chirality : 0.043 0.257 2115 Planarity : 0.005 0.051 1934 Dihedral : 25.479 147.509 3243 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 24.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.35 % Favored : 91.39 % Rotamer: Outliers : 3.36 % Allowed : 25.22 % Favored : 71.41 % 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: -1.26 (0.24), residues: 1185 helix: -0.33 (0.17), residues: 887 sheet: None (None), residues: 0 loop : -2.08 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 178 HIS 0.016 0.001 HIS H 174 PHE 0.028 0.002 PHE A 93 TYR 0.024 0.002 TYR A 159 ARG 0.012 0.001 ARG A 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3196.45 seconds wall clock time: 58 minutes 13.31 seconds (3493.31 seconds total)