Starting phenix.real_space_refine on Sat Mar 16 14:52:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckw_16704/03_2024/8ckw_16704.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckw_16704/03_2024/8ckw_16704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckw_16704/03_2024/8ckw_16704.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckw_16704/03_2024/8ckw_16704.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckw_16704/03_2024/8ckw_16704.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckw_16704/03_2024/8ckw_16704.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 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 1045 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: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 8745 2.51 5 N 2390 2.21 5 O 2650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13890 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1612 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "C" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "D" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1612 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "F" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "G" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1612 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "I" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "J" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1612 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "K" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "L" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "M" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1612 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "N" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "O" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Time building chain proxies: 7.11, per 1000 atoms: 0.51 Number of scatterers: 13890 At special positions: 0 Unit cell: (148.8, 153.45, 95.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 2650 8.00 N 2390 7.00 C 8745 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: 5.65 Conformation dependent library (CDL) restraints added in 2.5 seconds 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 5 sheets defined 74.8% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 16 through 30 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 174 Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.254A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 removed outlier: 3.622A pdb=" N ILE A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 160 through 173 Processing helix chain 'B' and resid 178 through 193 removed outlier: 3.555A pdb=" N TRP B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 removed outlier: 3.839A pdb=" N ALA B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 176 removed outlier: 3.609A pdb=" N GLN C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 removed outlier: 4.613A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 removed outlier: 3.609A pdb=" N LEU C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 219 Processing helix chain 'D' and resid 16 through 30 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 62 through 84 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 125 through 145 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 160 through 174 Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.255A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 3.622A pdb=" N ILE D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 160 through 173 Processing helix chain 'E' and resid 178 through 193 removed outlier: 3.555A pdb=" N TRP E 184 " --> pdb=" O GLU E 180 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 removed outlier: 3.839A pdb=" N ALA E 204 " --> pdb=" O THR E 200 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 218 Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'F' and resid 160 through 176 removed outlier: 3.609A pdb=" N GLN F 176 " --> pdb=" O LEU F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 193 removed outlier: 4.613A pdb=" N LEU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 removed outlier: 3.610A pdb=" N LEU F 205 " --> pdb=" O ILE F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 219 Processing helix chain 'G' and resid 16 through 30 Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 57 Processing helix chain 'G' and resid 62 through 84 Processing helix chain 'G' and resid 100 through 105 Processing helix chain 'G' and resid 110 through 120 Processing helix chain 'G' and resid 125 through 145 Processing helix chain 'G' and resid 149 through 153 Processing helix chain 'G' and resid 160 through 174 Processing helix chain 'G' and resid 178 through 193 removed outlier: 4.254A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 205 removed outlier: 3.622A pdb=" N ILE G 201 " --> pdb=" O ASP G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 219 Processing helix chain 'H' and resid 149 through 153 Processing helix chain 'H' and resid 160 through 173 Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.555A pdb=" N TRP H 184 " --> pdb=" O GLU H 180 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU H 190 " --> pdb=" O THR H 186 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL H 191 " --> pdb=" O GLU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 205 removed outlier: 3.839A pdb=" N ALA H 204 " --> pdb=" O THR H 200 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU H 205 " --> pdb=" O ILE H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 218 Processing helix chain 'I' and resid 149 through 153 Processing helix chain 'I' and resid 160 through 176 removed outlier: 3.610A pdb=" N GLN I 176 " --> pdb=" O LEU I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 193 removed outlier: 4.613A pdb=" N LEU I 190 " --> pdb=" O THR I 186 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL I 191 " --> pdb=" O GLU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 removed outlier: 3.609A pdb=" N LEU I 205 " --> pdb=" O ILE I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 219 Processing helix chain 'J' and resid 16 through 30 Processing helix chain 'J' and resid 35 through 44 Processing helix chain 'J' and resid 48 through 57 Processing helix chain 'J' and resid 62 through 84 Processing helix chain 'J' and resid 100 through 105 Processing helix chain 'J' and resid 110 through 120 Processing helix chain 'J' and resid 125 through 145 Processing helix chain 'J' and resid 149 through 153 Processing helix chain 'J' and resid 160 through 174 Processing helix chain 'J' and resid 178 through 193 removed outlier: 4.254A pdb=" N LEU J 190 " --> pdb=" O THR J 186 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL J 191 " --> pdb=" O GLU J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 205 removed outlier: 3.622A pdb=" N ILE J 201 " --> pdb=" O ASP J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 219 Processing helix chain 'K' and resid 149 through 153 Processing helix chain 'K' and resid 160 through 173 Processing helix chain 'K' and resid 178 through 193 removed outlier: 3.555A pdb=" N TRP K 184 " --> pdb=" O GLU K 180 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU K 190 " --> pdb=" O THR K 186 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL K 191 " --> pdb=" O GLU K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 205 removed outlier: 3.839A pdb=" N ALA K 204 " --> pdb=" O THR K 200 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU K 205 " --> pdb=" O ILE K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 218 Processing helix chain 'L' and resid 149 through 153 Processing helix chain 'L' and resid 160 through 176 removed outlier: 3.609A pdb=" N GLN L 176 " --> pdb=" O LEU L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 193 removed outlier: 4.613A pdb=" N LEU L 190 " --> pdb=" O THR L 186 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL L 191 " --> pdb=" O GLU L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 205 removed outlier: 3.609A pdb=" N LEU L 205 " --> pdb=" O ILE L 201 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 219 Processing helix chain 'M' and resid 16 through 30 Processing helix chain 'M' and resid 35 through 44 Processing helix chain 'M' and resid 48 through 57 Processing helix chain 'M' and resid 62 through 84 Processing helix chain 'M' and resid 100 through 105 Processing helix chain 'M' and resid 110 through 120 Processing helix chain 'M' and resid 125 through 145 Processing helix chain 'M' and resid 149 through 153 Processing helix chain 'M' and resid 160 through 174 Processing helix chain 'M' and resid 178 through 193 removed outlier: 4.254A pdb=" N LEU M 190 " --> pdb=" O THR M 186 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL M 191 " --> pdb=" O GLU M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 205 removed outlier: 3.622A pdb=" N ILE M 201 " --> pdb=" O ASP M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 219 Processing helix chain 'N' and resid 149 through 153 Processing helix chain 'N' and resid 160 through 173 Processing helix chain 'N' and resid 178 through 193 removed outlier: 3.555A pdb=" N TRP N 184 " --> pdb=" O GLU N 180 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU N 190 " --> pdb=" O THR N 186 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL N 191 " --> pdb=" O GLU N 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 205 removed outlier: 3.839A pdb=" N ALA N 204 " --> pdb=" O THR N 200 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU N 205 " --> pdb=" O ILE N 201 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 218 Processing helix chain 'O' and resid 149 through 153 Processing helix chain 'O' and resid 160 through 176 removed outlier: 3.609A pdb=" N GLN O 176 " --> pdb=" O LEU O 172 " (cutoff:3.500A) Processing helix chain 'O' and resid 178 through 193 removed outlier: 4.613A pdb=" N LEU O 190 " --> pdb=" O THR O 186 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL O 191 " --> pdb=" O GLU O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 205 removed outlier: 3.609A pdb=" N LEU O 205 " --> pdb=" O ILE O 201 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 219 Processing sheet with id= 1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id= 2, first strand: chain 'D' and resid 2 through 4 Processing sheet with id= 3, first strand: chain 'G' and resid 2 through 4 Processing sheet with id= 4, first strand: chain 'J' and resid 2 through 4 Processing sheet with id= 5, first strand: chain 'M' and resid 2 through 4 860 hydrogen bonds defined for protein. 2490 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.13 Time building geometry restraints manager: 6.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4582 1.34 - 1.46: 1359 1.46 - 1.57: 8034 1.57 - 1.69: 0 1.69 - 1.81: 180 Bond restraints: 14155 Sorted by residual: bond pdb=" N THR F 148 " pdb=" CA THR F 148 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 4.08e+00 bond pdb=" N THR I 148 " pdb=" CA THR I 148 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 3.94e+00 bond pdb=" N THR C 148 " pdb=" CA THR C 148 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 3.94e+00 bond pdb=" N THR L 148 " pdb=" CA THR L 148 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.90e-02 2.77e+03 3.89e+00 bond pdb=" N THR O 148 " pdb=" CA THR O 148 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.90e-02 2.77e+03 3.85e+00 ... (remaining 14150 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.13: 554 106.13 - 113.16: 7538 113.16 - 120.19: 5351 120.19 - 127.23: 5567 127.23 - 134.26: 195 Bond angle restraints: 19205 Sorted by residual: angle pdb=" CB LEU J 83 " pdb=" CG LEU J 83 " pdb=" CD1 LEU J 83 " ideal model delta sigma weight residual 110.70 124.39 -13.69 3.00e+00 1.11e-01 2.08e+01 angle pdb=" CB LEU A 83 " pdb=" CG LEU A 83 " pdb=" CD1 LEU A 83 " ideal model delta sigma weight residual 110.70 124.38 -13.68 3.00e+00 1.11e-01 2.08e+01 angle pdb=" CB LEU M 83 " pdb=" CG LEU M 83 " pdb=" CD1 LEU M 83 " ideal model delta sigma weight residual 110.70 124.37 -13.67 3.00e+00 1.11e-01 2.08e+01 angle pdb=" CB LEU D 83 " pdb=" CG LEU D 83 " pdb=" CD1 LEU D 83 " ideal model delta sigma weight residual 110.70 124.36 -13.66 3.00e+00 1.11e-01 2.07e+01 angle pdb=" CB LEU G 83 " pdb=" CG LEU G 83 " pdb=" CD1 LEU G 83 " ideal model delta sigma weight residual 110.70 124.36 -13.66 3.00e+00 1.11e-01 2.07e+01 ... (remaining 19200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 7907 15.63 - 31.27: 618 31.27 - 46.90: 120 46.90 - 62.54: 35 62.54 - 78.17: 20 Dihedral angle restraints: 8700 sinusoidal: 3535 harmonic: 5165 Sorted by residual: dihedral pdb=" CA THR G 148 " pdb=" C THR G 148 " pdb=" N SER G 149 " pdb=" CA SER G 149 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA THR D 148 " pdb=" C THR D 148 " pdb=" N SER D 149 " pdb=" CA SER D 149 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA THR M 148 " pdb=" C THR M 148 " pdb=" N SER M 149 " pdb=" CA SER M 149 " ideal model delta harmonic sigma weight residual 180.00 159.90 20.10 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 8697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.246: 2180 0.246 - 0.492: 0 0.492 - 0.739: 0 0.739 - 0.985: 0 0.985 - 1.231: 5 Chirality restraints: 2185 Sorted by residual: chirality pdb=" CG LEU M 83 " pdb=" CB LEU M 83 " pdb=" CD1 LEU M 83 " pdb=" CD2 LEU M 83 " both_signs ideal model delta sigma weight residual False -2.59 -1.36 -1.23 2.00e-01 2.50e+01 3.79e+01 chirality pdb=" CG LEU D 83 " pdb=" CB LEU D 83 " pdb=" CD1 LEU D 83 " pdb=" CD2 LEU D 83 " both_signs ideal model delta sigma weight residual False -2.59 -1.36 -1.23 2.00e-01 2.50e+01 3.79e+01 chirality pdb=" CG LEU A 83 " pdb=" CB LEU A 83 " pdb=" CD1 LEU A 83 " pdb=" CD2 LEU A 83 " both_signs ideal model delta sigma weight residual False -2.59 -1.36 -1.23 2.00e-01 2.50e+01 3.79e+01 ... (remaining 2182 not shown) Planarity restraints: 2490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG J 18 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.37e+00 pdb=" C ARG J 18 " -0.044 2.00e-02 2.50e+03 pdb=" O ARG J 18 " 0.016 2.00e-02 2.50e+03 pdb=" N THR J 19 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG M 18 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.36e+00 pdb=" C ARG M 18 " -0.044 2.00e-02 2.50e+03 pdb=" O ARG M 18 " 0.016 2.00e-02 2.50e+03 pdb=" N THR M 19 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 18 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C ARG A 18 " 0.043 2.00e-02 2.50e+03 pdb=" O ARG A 18 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A 19 " -0.015 2.00e-02 2.50e+03 ... (remaining 2487 not shown) Histogram of nonbonded interaction distances: 0.52 - 1.40: 5 1.40 - 2.27: 15 2.27 - 3.15: 12004 3.15 - 4.02: 36391 4.02 - 4.90: 66386 Warning: very small nonbonded interaction distances. Nonbonded interactions: 114801 Sorted by model distance: nonbonded pdb=" CD1 LEU J 20 " pdb=" OE2 GLU M 45 " model vdw 0.523 3.460 nonbonded pdb=" CD1 LEU G 20 " pdb=" OE2 GLU J 45 " model vdw 0.524 3.460 nonbonded pdb=" OE2 GLU A 45 " pdb=" CD1 LEU M 20 " model vdw 0.524 3.460 nonbonded pdb=" CD1 LEU D 20 " pdb=" OE2 GLU G 45 " model vdw 0.524 3.460 nonbonded pdb=" CD1 LEU A 20 " pdb=" OE2 GLU D 45 " model vdw 0.524 3.460 ... (remaining 114796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 12.290 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 36.800 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.110 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 : 0.005 0.076 14155 Z= 0.307 Angle : 0.870 13.695 19205 Z= 0.503 Chirality : 0.075 1.231 2185 Planarity : 0.008 0.083 2490 Dihedral : 12.554 78.172 5340 Min Nonbonded Distance : 0.523 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.70 (0.17), residues: 1745 helix: -0.72 (0.12), residues: 1165 sheet: -2.36 (0.48), residues: 45 loop : 0.86 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.005 TRP J 184 HIS 0.009 0.004 HIS J 12 PHE 0.021 0.003 PHE G 40 TYR 0.026 0.005 TYR G 169 ARG 0.017 0.002 ARG F 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 627 time to evaluate : 1.673 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: A 33 SER cc_start: 0.8725 (t) cc_final: 0.8298 (p) REVERT: A 41 SER cc_start: 0.8852 (t) cc_final: 0.8565 (m) REVERT: A 66 MET cc_start: 0.8883 (tpt) cc_final: 0.8385 (tpt) REVERT: A 170 LYS cc_start: 0.8291 (tttm) cc_final: 0.7983 (ttmt) REVERT: A 186 THR cc_start: 0.8868 (m) cc_final: 0.8589 (p) REVERT: B 179 GLN cc_start: 0.8543 (tp40) cc_final: 0.8254 (tp-100) REVERT: B 183 ASN cc_start: 0.8717 (m-40) cc_final: 0.8420 (m-40) REVERT: B 210 THR cc_start: 0.8823 (p) cc_final: 0.8584 (p) REVERT: C 216 THR cc_start: 0.9468 (m) cc_final: 0.9153 (p) REVERT: D 41 SER cc_start: 0.8806 (t) cc_final: 0.8526 (m) REVERT: D 170 LYS cc_start: 0.8248 (tttm) cc_final: 0.8019 (tptt) REVERT: D 186 THR cc_start: 0.8871 (m) cc_final: 0.8655 (p) REVERT: E 179 GLN cc_start: 0.8503 (tp40) cc_final: 0.7998 (tp-100) REVERT: E 183 ASN cc_start: 0.8718 (m-40) cc_final: 0.8188 (m-40) REVERT: F 185 MET cc_start: 0.8169 (mtm) cc_final: 0.7919 (mtp) REVERT: F 199 LYS cc_start: 0.8964 (tttm) cc_final: 0.8761 (tttt) REVERT: F 216 THR cc_start: 0.9429 (m) cc_final: 0.9067 (p) REVERT: G 37 ILE cc_start: 0.9094 (mt) cc_final: 0.8885 (mm) REVERT: G 41 SER cc_start: 0.8799 (t) cc_final: 0.8545 (m) REVERT: G 170 LYS cc_start: 0.8346 (tttm) cc_final: 0.8094 (tptt) REVERT: H 192 GLN cc_start: 0.8905 (tp40) cc_final: 0.8661 (tp40) REVERT: I 166 ASP cc_start: 0.8215 (m-30) cc_final: 0.7790 (m-30) REVERT: I 216 THR cc_start: 0.9476 (m) cc_final: 0.9123 (p) REVERT: J 41 SER cc_start: 0.8746 (t) cc_final: 0.8487 (m) REVERT: J 170 LYS cc_start: 0.8305 (tttm) cc_final: 0.7982 (ttmt) REVERT: K 210 THR cc_start: 0.8888 (p) cc_final: 0.8538 (p) REVERT: L 170 LYS cc_start: 0.8448 (tttm) cc_final: 0.8135 (ttpp) REVERT: L 185 MET cc_start: 0.8084 (mtm) cc_final: 0.7765 (mtp) REVERT: L 216 THR cc_start: 0.9448 (m) cc_final: 0.9138 (p) REVERT: M 33 SER cc_start: 0.8623 (t) cc_final: 0.8320 (t) REVERT: M 41 SER cc_start: 0.8717 (t) cc_final: 0.8484 (m) REVERT: M 170 LYS cc_start: 0.8219 (tttm) cc_final: 0.7942 (tptt) REVERT: M 221 VAL cc_start: 0.7806 (p) cc_final: 0.7591 (t) REVERT: N 166 ASP cc_start: 0.8072 (m-30) cc_final: 0.7870 (m-30) REVERT: O 170 LYS cc_start: 0.8507 (tttm) cc_final: 0.8151 (ttpp) REVERT: O 216 THR cc_start: 0.9439 (m) cc_final: 0.9102 (p) outliers start: 0 outliers final: 0 residues processed: 627 average time/residue: 0.2999 time to fit residues: 253.1162 Evaluate side-chains 516 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 516 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 3.9990 chunk 128 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS C 192 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 GLN F 219 GLN H 155 GLN H 193 ASN M 219 GLN N 155 GLN N 179 GLN N 183 ASN O 195 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14155 Z= 0.256 Angle : 0.621 10.626 19205 Z= 0.313 Chirality : 0.043 0.166 2185 Planarity : 0.005 0.033 2490 Dihedral : 4.751 19.738 1890 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 2.27 % Allowed : 10.13 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.34 (0.18), residues: 1745 helix: 1.00 (0.14), residues: 1145 sheet: -2.39 (0.47), residues: 45 loop : 1.32 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 184 HIS 0.003 0.001 HIS J 120 PHE 0.009 0.002 PHE G 32 TYR 0.011 0.002 TYR K 169 ARG 0.007 0.001 ARG N 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 525 time to evaluate : 1.645 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: A 66 MET cc_start: 0.8909 (tpt) cc_final: 0.8479 (tpt) REVERT: B 200 THR cc_start: 0.8586 (m) cc_final: 0.8320 (p) REVERT: B 202 LEU cc_start: 0.8973 (mt) cc_final: 0.8760 (mt) REVERT: C 170 LYS cc_start: 0.8536 (ttmm) cc_final: 0.8276 (ttpp) REVERT: C 183 ASN cc_start: 0.9132 (m-40) cc_final: 0.8835 (m-40) REVERT: C 195 ASN cc_start: 0.8259 (m-40) cc_final: 0.8051 (m110) REVERT: D 128 GLU cc_start: 0.7750 (tp30) cc_final: 0.7494 (tp30) REVERT: D 154 ARG cc_start: 0.8208 (mtt-85) cc_final: 0.7947 (mtt-85) REVERT: D 176 GLN cc_start: 0.6579 (pm20) cc_final: 0.6244 (pm20) REVERT: F 170 LYS cc_start: 0.8576 (ttmm) cc_final: 0.8265 (ttpp) REVERT: F 182 LYS cc_start: 0.8827 (mttm) cc_final: 0.8553 (mttp) REVERT: F 183 ASN cc_start: 0.8946 (m-40) cc_final: 0.8671 (m-40) REVERT: F 195 ASN cc_start: 0.8186 (m-40) cc_final: 0.7916 (m110) REVERT: G 176 GLN cc_start: 0.6396 (pm20) cc_final: 0.6100 (pm20) REVERT: H 192 GLN cc_start: 0.8953 (tp40) cc_final: 0.8710 (tp40) REVERT: I 159 GLU cc_start: 0.8320 (tt0) cc_final: 0.8053 (tt0) REVERT: I 166 ASP cc_start: 0.8229 (m-30) cc_final: 0.7804 (m-30) REVERT: I 170 LYS cc_start: 0.8590 (ttmm) cc_final: 0.8348 (ttpp) REVERT: I 183 ASN cc_start: 0.8984 (m-40) cc_final: 0.8707 (m-40) REVERT: I 195 ASN cc_start: 0.8156 (m-40) cc_final: 0.7935 (m110) REVERT: I 216 THR cc_start: 0.9486 (m) cc_final: 0.9285 (p) REVERT: K 200 THR cc_start: 0.8667 (m) cc_final: 0.8405 (p) REVERT: L 170 LYS cc_start: 0.8438 (tttm) cc_final: 0.8213 (ttpp) REVERT: N 200 THR cc_start: 0.8664 (m) cc_final: 0.8367 (p) REVERT: O 195 ASN cc_start: 0.8241 (m-40) cc_final: 0.8019 (m110) REVERT: O 216 THR cc_start: 0.9445 (m) cc_final: 0.9243 (p) outliers start: 34 outliers final: 19 residues processed: 543 average time/residue: 0.3051 time to fit residues: 224.3943 Evaluate side-chains 510 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 491 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain H residue 197 ASP Chi-restraints excluded: chain I residue 152 ASP Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 205 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 chunk 167 optimal weight: 0.0570 chunk 137 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 GLN B 179 GLN G 50 GLN H 179 GLN J 219 GLN K 155 GLN N 179 GLN N 183 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14155 Z= 0.212 Angle : 0.561 10.063 19205 Z= 0.284 Chirality : 0.042 0.151 2185 Planarity : 0.004 0.041 2490 Dihedral : 4.405 19.484 1890 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.60 % Allowed : 12.47 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.74 (0.19), residues: 1745 helix: 1.32 (0.14), residues: 1165 sheet: -2.48 (0.45), residues: 45 loop : 1.47 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 184 HIS 0.002 0.001 HIS J 120 PHE 0.009 0.001 PHE G 32 TYR 0.010 0.001 TYR K 169 ARG 0.007 0.001 ARG H 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 492 time to evaluate : 1.689 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: A 66 MET cc_start: 0.8883 (tpt) cc_final: 0.8363 (tpt) REVERT: A 170 LYS cc_start: 0.8362 (tptt) cc_final: 0.8159 (mmtt) REVERT: A 176 GLN cc_start: 0.6223 (pm20) cc_final: 0.5951 (pm20) REVERT: A 192 GLN cc_start: 0.8720 (tp40) cc_final: 0.8398 (tm-30) REVERT: C 170 LYS cc_start: 0.8569 (ttmm) cc_final: 0.8307 (ttpp) REVERT: C 183 ASN cc_start: 0.8778 (m-40) cc_final: 0.8491 (m-40) REVERT: C 195 ASN cc_start: 0.8273 (m-40) cc_final: 0.8047 (m110) REVERT: D 162 ARG cc_start: 0.8112 (ttp-170) cc_final: 0.7888 (ttt-90) REVERT: F 170 LYS cc_start: 0.8575 (ttmm) cc_final: 0.8279 (ttpp) REVERT: F 182 LYS cc_start: 0.8882 (mttm) cc_final: 0.8626 (mttp) REVERT: F 183 ASN cc_start: 0.8788 (m-40) cc_final: 0.8530 (m-40) REVERT: G 170 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8124 (mmtt) REVERT: I 170 LYS cc_start: 0.8588 (ttmm) cc_final: 0.8353 (ttpp) REVERT: I 203 LYS cc_start: 0.8560 (mtpp) cc_final: 0.8310 (mmtt) REVERT: I 210 THR cc_start: 0.8499 (p) cc_final: 0.7988 (t) REVERT: I 213 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7877 (mt-10) REVERT: J 110 THR cc_start: 0.7863 (p) cc_final: 0.7404 (p) REVERT: J 176 GLN cc_start: 0.6338 (pm20) cc_final: 0.6086 (pm20) REVERT: J 192 GLN cc_start: 0.8726 (tp40) cc_final: 0.8475 (tp40) REVERT: K 200 THR cc_start: 0.8732 (m) cc_final: 0.8478 (p) REVERT: L 213 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7716 (mt-10) REVERT: M 176 GLN cc_start: 0.6718 (pm20) cc_final: 0.6432 (pm20) REVERT: M 192 GLN cc_start: 0.8765 (tp40) cc_final: 0.8473 (tp40) REVERT: O 183 ASN cc_start: 0.8879 (m-40) cc_final: 0.8646 (m-40) REVERT: O 195 ASN cc_start: 0.8321 (m-40) cc_final: 0.8095 (m110) outliers start: 39 outliers final: 16 residues processed: 510 average time/residue: 0.3067 time to fit residues: 212.4837 Evaluate side-chains 487 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 470 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 170 LYS Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 170 LYS Chi-restraints excluded: chain N residue 216 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN D 50 GLN H 155 GLN H 179 GLN H 183 ASN H 193 ASN J 50 GLN K 155 GLN L 183 ASN N 155 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14155 Z= 0.268 Angle : 0.585 9.541 19205 Z= 0.294 Chirality : 0.043 0.159 2185 Planarity : 0.005 0.038 2490 Dihedral : 4.339 18.503 1890 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.20 % Allowed : 14.00 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.71 (0.19), residues: 1745 helix: 1.30 (0.15), residues: 1150 sheet: -2.54 (0.42), residues: 45 loop : 1.44 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 184 HIS 0.002 0.001 HIS G 120 PHE 0.011 0.001 PHE M 32 TYR 0.011 0.002 TYR K 169 ARG 0.008 0.001 ARG H 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 474 time to evaluate : 1.540 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: A 66 MET cc_start: 0.8855 (tpt) cc_final: 0.8346 (tpt) REVERT: A 145 TYR cc_start: 0.8657 (m-80) cc_final: 0.8365 (m-80) REVERT: C 170 LYS cc_start: 0.8580 (ttmm) cc_final: 0.8315 (ttpp) REVERT: C 179 GLN cc_start: 0.8835 (tp40) cc_final: 0.8394 (tp-100) REVERT: C 183 ASN cc_start: 0.8702 (m-40) cc_final: 0.8057 (m-40) REVERT: C 195 ASN cc_start: 0.8319 (m-40) cc_final: 0.7916 (m-40) REVERT: D 176 GLN cc_start: 0.6360 (pm20) cc_final: 0.5833 (pm20) REVERT: F 170 LYS cc_start: 0.8571 (ttmm) cc_final: 0.8253 (ttpp) REVERT: F 179 GLN cc_start: 0.8815 (tp40) cc_final: 0.8554 (tp40) REVERT: F 183 ASN cc_start: 0.8630 (m-40) cc_final: 0.8149 (m-40) REVERT: G 176 GLN cc_start: 0.6422 (pm20) cc_final: 0.6151 (pm20) REVERT: G 192 GLN cc_start: 0.8797 (tp40) cc_final: 0.8292 (tm-30) REVERT: I 166 ASP cc_start: 0.8196 (m-30) cc_final: 0.7791 (m-30) REVERT: I 170 LYS cc_start: 0.8613 (ttmm) cc_final: 0.8345 (ttpp) REVERT: J 110 THR cc_start: 0.7943 (p) cc_final: 0.7683 (p) REVERT: J 176 GLN cc_start: 0.6399 (pm20) cc_final: 0.6116 (pm20) REVERT: L 213 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7762 (mt-10) REVERT: M 176 GLN cc_start: 0.6629 (pm20) cc_final: 0.6371 (pm20) REVERT: M 192 GLN cc_start: 0.8742 (tp40) cc_final: 0.8517 (tp40) REVERT: N 192 GLN cc_start: 0.8806 (tp40) cc_final: 0.8554 (tp40) REVERT: N 200 THR cc_start: 0.8755 (m) cc_final: 0.8481 (p) REVERT: O 195 ASN cc_start: 0.8301 (m-40) cc_final: 0.8033 (m-40) outliers start: 33 outliers final: 20 residues processed: 492 average time/residue: 0.3103 time to fit residues: 206.9706 Evaluate side-chains 473 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 453 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 216 THR Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain N residue 210 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.0270 chunk 93 optimal weight: 8.9990 chunk 2 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 140 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 GLN B 179 GLN C 179 GLN C 183 ASN D 50 GLN F 179 GLN F 183 ASN H 155 GLN I 179 GLN I 183 ASN K 155 GLN ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 193 ASN O 179 GLN O 183 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14155 Z= 0.170 Angle : 0.540 10.082 19205 Z= 0.270 Chirality : 0.041 0.153 2185 Planarity : 0.004 0.040 2490 Dihedral : 4.076 18.122 1890 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.27 % Allowed : 15.93 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.19), residues: 1745 helix: 1.40 (0.15), residues: 1160 sheet: -2.41 (0.45), residues: 45 loop : 1.47 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 184 HIS 0.002 0.001 HIS G 120 PHE 0.010 0.001 PHE I 168 TYR 0.011 0.001 TYR I 164 ARG 0.008 0.001 ARG H 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 467 time to evaluate : 1.690 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: A 66 MET cc_start: 0.8800 (tpt) cc_final: 0.8311 (tpt) REVERT: B 200 THR cc_start: 0.8607 (m) cc_final: 0.8396 (p) REVERT: C 170 LYS cc_start: 0.8547 (ttmm) cc_final: 0.8293 (ttpp) REVERT: C 179 GLN cc_start: 0.8881 (tp-100) cc_final: 0.8631 (tp40) REVERT: C 183 ASN cc_start: 0.8783 (m110) cc_final: 0.8302 (m-40) REVERT: C 195 ASN cc_start: 0.8330 (m-40) cc_final: 0.7912 (m-40) REVERT: D 176 GLN cc_start: 0.6240 (pm20) cc_final: 0.5953 (pm20) REVERT: E 192 GLN cc_start: 0.8690 (tp40) cc_final: 0.8425 (tp40) REVERT: F 170 LYS cc_start: 0.8538 (ttmm) cc_final: 0.8235 (ttpp) REVERT: F 179 GLN cc_start: 0.8893 (tp-100) cc_final: 0.8627 (tp40) REVERT: F 183 ASN cc_start: 0.8708 (m110) cc_final: 0.8118 (m-40) REVERT: G 176 GLN cc_start: 0.6147 (pm20) cc_final: 0.5915 (pm20) REVERT: H 200 THR cc_start: 0.8661 (m) cc_final: 0.8381 (p) REVERT: I 170 LYS cc_start: 0.8588 (ttmm) cc_final: 0.8331 (ttpp) REVERT: I 179 GLN cc_start: 0.8848 (tp-100) cc_final: 0.8629 (tp40) REVERT: I 183 ASN cc_start: 0.8774 (m110) cc_final: 0.8349 (m-40) REVERT: J 110 THR cc_start: 0.7898 (p) cc_final: 0.7620 (p) REVERT: K 200 THR cc_start: 0.8757 (m) cc_final: 0.8536 (p) REVERT: L 213 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7748 (mt-10) REVERT: M 13 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7696 (tt0) REVERT: M 192 GLN cc_start: 0.8705 (tp40) cc_final: 0.8501 (tp40) REVERT: N 192 GLN cc_start: 0.8813 (tp40) cc_final: 0.8587 (tp40) REVERT: N 200 THR cc_start: 0.8731 (m) cc_final: 0.8439 (p) REVERT: O 183 ASN cc_start: 0.8703 (m110) cc_final: 0.8246 (m-40) REVERT: O 195 ASN cc_start: 0.8305 (m-40) cc_final: 0.8050 (m-40) outliers start: 19 outliers final: 11 residues processed: 478 average time/residue: 0.3083 time to fit residues: 199.4923 Evaluate side-chains 469 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 458 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain N residue 210 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN C 179 GLN C 183 ASN E 179 GLN H 155 GLN H 179 GLN H 183 ASN K 155 GLN N 179 GLN O 179 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14155 Z= 0.317 Angle : 0.602 11.299 19205 Z= 0.300 Chirality : 0.043 0.164 2185 Planarity : 0.005 0.039 2490 Dihedral : 4.257 18.301 1890 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.00 % Allowed : 16.27 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.19), residues: 1745 helix: 1.15 (0.15), residues: 1165 sheet: -2.61 (0.40), residues: 45 loop : 1.43 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 184 HIS 0.002 0.001 HIS J 120 PHE 0.012 0.001 PHE M 32 TYR 0.013 0.002 TYR O 169 ARG 0.007 0.001 ARG H 154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 476 time to evaluate : 1.758 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: A 66 MET cc_start: 0.8833 (tpt) cc_final: 0.8350 (tpt) REVERT: A 176 GLN cc_start: 0.6244 (pm20) cc_final: 0.5918 (pm20) REVERT: A 192 GLN cc_start: 0.8772 (tp40) cc_final: 0.8448 (tm-30) REVERT: B 176 GLN cc_start: 0.8095 (mp10) cc_final: 0.7892 (mm-40) REVERT: C 170 LYS cc_start: 0.8569 (ttmm) cc_final: 0.8319 (ttpp) REVERT: C 183 ASN cc_start: 0.8672 (m-40) cc_final: 0.8328 (m-40) REVERT: C 195 ASN cc_start: 0.8300 (m-40) cc_final: 0.7935 (m-40) REVERT: D 176 GLN cc_start: 0.6254 (pm20) cc_final: 0.6006 (pm20) REVERT: E 159 GLU cc_start: 0.8687 (tt0) cc_final: 0.8440 (tt0) REVERT: E 192 GLN cc_start: 0.8673 (tp40) cc_final: 0.8446 (tp40) REVERT: F 170 LYS cc_start: 0.8561 (ttmm) cc_final: 0.8244 (ttpp) REVERT: F 179 GLN cc_start: 0.8936 (tp-100) cc_final: 0.8601 (tp40) REVERT: F 183 ASN cc_start: 0.8627 (m110) cc_final: 0.7985 (m-40) REVERT: G 195 ASN cc_start: 0.8627 (p0) cc_final: 0.8224 (p0) REVERT: H 200 THR cc_start: 0.8765 (m) cc_final: 0.8506 (p) REVERT: I 170 LYS cc_start: 0.8617 (ttmm) cc_final: 0.8345 (ttpp) REVERT: I 179 GLN cc_start: 0.8907 (tp-100) cc_final: 0.8648 (tp40) REVERT: I 183 ASN cc_start: 0.8802 (m110) cc_final: 0.8341 (m-40) REVERT: J 18 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8347 (mtm180) REVERT: J 67 GLN cc_start: 0.8190 (tp40) cc_final: 0.7958 (tp40) REVERT: J 110 THR cc_start: 0.7951 (p) cc_final: 0.7563 (p) REVERT: J 176 GLN cc_start: 0.6447 (pm20) cc_final: 0.6009 (pm20) REVERT: J 192 GLN cc_start: 0.8748 (tp40) cc_final: 0.8519 (tp40) REVERT: K 200 THR cc_start: 0.8831 (m) cc_final: 0.8592 (p) REVERT: L 213 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7753 (mt-10) REVERT: N 192 GLN cc_start: 0.8815 (tp40) cc_final: 0.8572 (tp40) REVERT: N 200 THR cc_start: 0.8796 (m) cc_final: 0.8530 (p) REVERT: O 195 ASN cc_start: 0.8325 (m-40) cc_final: 0.7958 (m110) REVERT: O 215 MET cc_start: 0.8045 (mtm) cc_final: 0.7780 (mtm) outliers start: 30 outliers final: 23 residues processed: 492 average time/residue: 0.3160 time to fit residues: 209.4136 Evaluate side-chains 489 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 465 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain K residue 216 THR Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain O residue 212 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 120 optimal weight: 0.6980 chunk 138 optimal weight: 0.0970 chunk 91 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 99 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 179 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN J 50 GLN O 179 GLN O 183 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14155 Z= 0.204 Angle : 0.562 11.125 19205 Z= 0.282 Chirality : 0.042 0.161 2185 Planarity : 0.004 0.040 2490 Dihedral : 4.121 16.998 1890 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.60 % Allowed : 16.60 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.63 (0.19), residues: 1745 helix: 1.22 (0.15), residues: 1160 sheet: -2.54 (0.43), residues: 45 loop : 1.45 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 184 HIS 0.002 0.001 HIS G 120 PHE 0.008 0.001 PHE G 32 TYR 0.015 0.001 TYR G 145 ARG 0.008 0.001 ARG H 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 471 time to evaluate : 1.686 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: A 50 GLN cc_start: 0.8256 (tt0) cc_final: 0.7937 (tt0) REVERT: A 66 MET cc_start: 0.8807 (tpt) cc_final: 0.8331 (tpt) REVERT: A 176 GLN cc_start: 0.6006 (pm20) cc_final: 0.5705 (pm20) REVERT: A 192 GLN cc_start: 0.8765 (tp40) cc_final: 0.8464 (tm-30) REVERT: C 170 LYS cc_start: 0.8561 (ttmm) cc_final: 0.8305 (ttpp) REVERT: C 183 ASN cc_start: 0.8520 (m-40) cc_final: 0.8313 (m-40) REVERT: C 195 ASN cc_start: 0.8323 (m-40) cc_final: 0.7906 (m-40) REVERT: E 192 GLN cc_start: 0.8651 (tp40) cc_final: 0.8441 (tp40) REVERT: F 170 LYS cc_start: 0.8555 (ttmm) cc_final: 0.8248 (ttpp) REVERT: F 179 GLN cc_start: 0.8902 (tp-100) cc_final: 0.8618 (tp40) REVERT: F 183 ASN cc_start: 0.8540 (m110) cc_final: 0.8066 (m-40) REVERT: F 212 GLU cc_start: 0.8190 (pm20) cc_final: 0.7977 (pm20) REVERT: G 176 GLN cc_start: 0.5568 (pm20) cc_final: 0.5056 (pm20) REVERT: G 195 ASN cc_start: 0.8583 (p0) cc_final: 0.8150 (p0) REVERT: G 203 LYS cc_start: 0.8795 (mmtp) cc_final: 0.8582 (mmtp) REVERT: H 200 THR cc_start: 0.8739 (m) cc_final: 0.8491 (p) REVERT: I 170 LYS cc_start: 0.8597 (ttmm) cc_final: 0.8322 (ttpp) REVERT: I 179 GLN cc_start: 0.8904 (tp-100) cc_final: 0.8654 (tp40) REVERT: I 183 ASN cc_start: 0.8852 (m110) cc_final: 0.8419 (m-40) REVERT: J 67 GLN cc_start: 0.8192 (tp40) cc_final: 0.7957 (tp40) REVERT: J 176 GLN cc_start: 0.6270 (pm20) cc_final: 0.5784 (pm20) REVERT: J 192 GLN cc_start: 0.8746 (tp40) cc_final: 0.8518 (tp40) REVERT: K 200 THR cc_start: 0.8753 (m) cc_final: 0.8550 (p) REVERT: L 195 ASN cc_start: 0.8348 (m-40) cc_final: 0.7949 (m110) REVERT: L 213 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7743 (mt-10) REVERT: M 176 GLN cc_start: 0.6096 (pm20) cc_final: 0.5768 (pm20) REVERT: N 192 GLN cc_start: 0.8811 (tp40) cc_final: 0.8577 (tp40) REVERT: N 200 THR cc_start: 0.8727 (m) cc_final: 0.8461 (p) REVERT: O 195 ASN cc_start: 0.8304 (m-40) cc_final: 0.7960 (m-40) outliers start: 24 outliers final: 16 residues processed: 481 average time/residue: 0.3108 time to fit residues: 201.6619 Evaluate side-chains 478 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 462 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain O residue 212 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 179 GLN O 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 0.044 14155 Z= 0.286 Angle : 0.597 12.530 19205 Z= 0.297 Chirality : 0.043 0.170 2185 Planarity : 0.005 0.039 2490 Dihedral : 4.210 17.358 1890 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.93 % Allowed : 16.20 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.48 (0.19), residues: 1745 helix: 1.09 (0.15), residues: 1165 sheet: -2.61 (0.44), residues: 45 loop : 1.46 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 184 HIS 0.002 0.001 HIS G 120 PHE 0.011 0.001 PHE M 32 TYR 0.018 0.002 TYR A 145 ARG 0.007 0.001 ARG G 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 475 time to evaluate : 1.837 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: A 13 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7705 (tm-30) REVERT: A 50 GLN cc_start: 0.8329 (tt0) cc_final: 0.7994 (tt0) REVERT: A 66 MET cc_start: 0.8829 (tpt) cc_final: 0.8364 (tpt) REVERT: A 176 GLN cc_start: 0.6116 (pm20) cc_final: 0.5849 (pm20) REVERT: A 192 GLN cc_start: 0.8782 (tp40) cc_final: 0.8456 (tm-30) REVERT: B 176 GLN cc_start: 0.8123 (mp10) cc_final: 0.7903 (mm-40) REVERT: C 170 LYS cc_start: 0.8580 (ttmm) cc_final: 0.8320 (ttpp) REVERT: C 195 ASN cc_start: 0.8302 (m-40) cc_final: 0.7922 (m-40) REVERT: F 170 LYS cc_start: 0.8583 (ttmm) cc_final: 0.8278 (ttpp) REVERT: F 179 GLN cc_start: 0.8943 (tp-100) cc_final: 0.8599 (tp40) REVERT: F 183 ASN cc_start: 0.8710 (m110) cc_final: 0.8057 (m-40) REVERT: F 212 GLU cc_start: 0.8265 (pm20) cc_final: 0.8053 (pm20) REVERT: G 176 GLN cc_start: 0.5485 (pm20) cc_final: 0.5151 (pm20) REVERT: G 195 ASN cc_start: 0.8589 (p0) cc_final: 0.8161 (p0) REVERT: H 200 THR cc_start: 0.8761 (m) cc_final: 0.8521 (p) REVERT: I 170 LYS cc_start: 0.8617 (ttmm) cc_final: 0.8345 (ttpp) REVERT: J 67 GLN cc_start: 0.8220 (tp40) cc_final: 0.7992 (tp40) REVERT: J 176 GLN cc_start: 0.6383 (pm20) cc_final: 0.5899 (pm20) REVERT: J 192 GLN cc_start: 0.8736 (tp40) cc_final: 0.8519 (tp40) REVERT: L 213 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7731 (mt-10) REVERT: M 176 GLN cc_start: 0.6107 (pm20) cc_final: 0.5820 (pm20) REVERT: N 192 GLN cc_start: 0.8828 (tp40) cc_final: 0.8600 (tp40) REVERT: N 200 THR cc_start: 0.8751 (m) cc_final: 0.8483 (p) REVERT: O 195 ASN cc_start: 0.8308 (m-40) cc_final: 0.7921 (m110) REVERT: O 215 MET cc_start: 0.7975 (mtm) cc_final: 0.7667 (mtm) outliers start: 29 outliers final: 22 residues processed: 488 average time/residue: 0.3139 time to fit residues: 207.1332 Evaluate side-chains 486 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 464 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 180 GLU Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain O residue 212 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 chunk 144 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 161 optimal weight: 0.2980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 GLN D 50 GLN H 155 GLN J 50 GLN ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14155 Z= 0.180 Angle : 0.560 10.265 19205 Z= 0.281 Chirality : 0.041 0.161 2185 Planarity : 0.004 0.041 2490 Dihedral : 4.084 20.229 1890 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.93 % Allowed : 17.73 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.69 (0.19), residues: 1745 helix: 1.26 (0.15), residues: 1170 sheet: -2.51 (0.46), residues: 45 loop : 1.50 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 184 HIS 0.002 0.000 HIS G 120 PHE 0.008 0.001 PHE K 168 TYR 0.014 0.001 TYR F 164 ARG 0.007 0.001 ARG G 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 467 time to evaluate : 1.561 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: A 13 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7580 (tm-30) REVERT: A 66 MET cc_start: 0.8806 (tpt) cc_final: 0.8283 (tpt) REVERT: A 176 GLN cc_start: 0.5992 (pm20) cc_final: 0.5726 (pm20) REVERT: A 192 GLN cc_start: 0.8772 (tp40) cc_final: 0.8476 (tm-30) REVERT: C 170 LYS cc_start: 0.8540 (ttmm) cc_final: 0.8273 (ttpp) REVERT: C 195 ASN cc_start: 0.8319 (m-40) cc_final: 0.7913 (m-40) REVERT: F 170 LYS cc_start: 0.8565 (ttmm) cc_final: 0.8263 (ttpp) REVERT: F 179 GLN cc_start: 0.8945 (tp-100) cc_final: 0.8645 (tp40) REVERT: F 183 ASN cc_start: 0.8551 (m110) cc_final: 0.8008 (m-40) REVERT: G 176 GLN cc_start: 0.5344 (pm20) cc_final: 0.4948 (pm20) REVERT: H 200 THR cc_start: 0.8729 (m) cc_final: 0.8491 (p) REVERT: I 170 LYS cc_start: 0.8593 (ttmm) cc_final: 0.8320 (ttpp) REVERT: J 67 GLN cc_start: 0.8176 (tp40) cc_final: 0.7955 (tp40) REVERT: J 176 GLN cc_start: 0.6251 (pm20) cc_final: 0.5803 (pm20) REVERT: J 192 GLN cc_start: 0.8729 (tp40) cc_final: 0.8501 (tp40) REVERT: L 195 ASN cc_start: 0.8338 (m-40) cc_final: 0.7969 (m110) REVERT: L 213 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7744 (mt-10) REVERT: M 176 GLN cc_start: 0.6024 (pm20) cc_final: 0.5756 (pm20) REVERT: N 192 GLN cc_start: 0.8795 (tp40) cc_final: 0.8585 (tp40) REVERT: N 200 THR cc_start: 0.8756 (m) cc_final: 0.8497 (p) REVERT: O 195 ASN cc_start: 0.8303 (m-40) cc_final: 0.7987 (m-40) REVERT: O 212 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8059 (pm20) outliers start: 14 outliers final: 12 residues processed: 472 average time/residue: 0.3187 time to fit residues: 203.0548 Evaluate side-chains 463 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 450 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain O residue 212 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 155 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 GLN I 179 GLN I 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14155 Z= 0.233 Angle : 0.588 11.314 19205 Z= 0.293 Chirality : 0.042 0.164 2185 Planarity : 0.005 0.041 2490 Dihedral : 4.143 21.515 1890 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.07 % Allowed : 17.27 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.19), residues: 1745 helix: 1.12 (0.15), residues: 1160 sheet: -2.56 (0.43), residues: 45 loop : 1.52 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 184 HIS 0.002 0.001 HIS G 120 PHE 0.009 0.001 PHE M 32 TYR 0.017 0.002 TYR A 145 ARG 0.009 0.001 ARG J 132 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 464 time to evaluate : 1.445 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: A 66 MET cc_start: 0.8809 (tpt) cc_final: 0.8268 (tpt) REVERT: A 176 GLN cc_start: 0.6052 (pm20) cc_final: 0.5794 (pm20) REVERT: A 192 GLN cc_start: 0.8774 (tp40) cc_final: 0.8472 (tm-30) REVERT: C 170 LYS cc_start: 0.8565 (ttmm) cc_final: 0.8302 (ttpp) REVERT: C 195 ASN cc_start: 0.8309 (m-40) cc_final: 0.7949 (m-40) REVERT: F 170 LYS cc_start: 0.8579 (ttmm) cc_final: 0.8273 (ttpp) REVERT: F 179 GLN cc_start: 0.8947 (tp-100) cc_final: 0.8660 (tp40) REVERT: F 183 ASN cc_start: 0.8472 (m110) cc_final: 0.7954 (m-40) REVERT: G 176 GLN cc_start: 0.5386 (pm20) cc_final: 0.5098 (pm20) REVERT: H 200 THR cc_start: 0.8783 (m) cc_final: 0.8562 (p) REVERT: I 170 LYS cc_start: 0.8600 (ttmm) cc_final: 0.8325 (ttpp) REVERT: J 67 GLN cc_start: 0.8208 (tp40) cc_final: 0.7979 (tp40) REVERT: J 176 GLN cc_start: 0.6356 (pm20) cc_final: 0.5899 (pm20) REVERT: L 195 ASN cc_start: 0.8369 (m-40) cc_final: 0.7995 (m110) REVERT: L 213 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7745 (mt-10) REVERT: M 154 ARG cc_start: 0.8434 (mtt90) cc_final: 0.8148 (mtt90) REVERT: M 176 GLN cc_start: 0.6100 (pm20) cc_final: 0.5840 (pm20) REVERT: N 192 GLN cc_start: 0.8812 (tp40) cc_final: 0.8586 (tp40) REVERT: N 200 THR cc_start: 0.8762 (m) cc_final: 0.8515 (p) REVERT: O 195 ASN cc_start: 0.8319 (m-40) cc_final: 0.7976 (m-40) REVERT: O 212 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7999 (pm20) outliers start: 16 outliers final: 15 residues processed: 469 average time/residue: 0.3143 time to fit residues: 198.6319 Evaluate side-chains 473 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 457 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain O residue 212 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 138 optimal weight: 0.0970 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN I 179 GLN I 183 ASN L 179 GLN L 183 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.133996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.104010 restraints weight = 21473.149| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.39 r_work: 0.3191 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14155 Z= 0.183 Angle : 0.562 10.165 19205 Z= 0.282 Chirality : 0.041 0.159 2185 Planarity : 0.004 0.042 2490 Dihedral : 4.040 19.055 1890 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.87 % Allowed : 18.27 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.63 (0.19), residues: 1745 helix: 1.20 (0.15), residues: 1175 sheet: -2.34 (0.49), residues: 45 loop : 1.52 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 184 HIS 0.002 0.000 HIS G 120 PHE 0.008 0.001 PHE E 168 TYR 0.012 0.001 TYR F 169 ARG 0.007 0.001 ARG G 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4468.61 seconds wall clock time: 80 minutes 5.41 seconds (4805.41 seconds total)