Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 7 17:17:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckw_16704/07_2023/8ckw_16704.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckw_16704/07_2023/8ckw_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_16704/07_2023/8ckw_16704.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckw_16704/07_2023/8ckw_16704.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckw_16704/07_2023/8ckw_16704.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckw_16704/07_2023/8ckw_16704.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-5013/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: 6.93, per 1000 atoms: 0.50 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: 5.36 Conformation dependent library (CDL) restraints added in 1.9 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: 0.62 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: 3.63 Time building geometry restraints manager: 5.73 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: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 12.670 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 34.860 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.100 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.320 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.668 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 outliers start: 0 outliers final: 0 residues processed: 627 average time/residue: 0.3179 time to fit residues: 270.1582 Evaluate side-chains 503 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 503 time to evaluate : 1.616 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3571 ------------------------------------------------------------------------------- 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: 0.8980 chunk 71 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS B 179 GLN C 192 GLN E 179 GLN F 192 GLN F 219 GLN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2988 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= 0.231 Angle : 0.610 10.136 19205 Z= 0.309 Chirality : 0.043 0.153 2185 Planarity : 0.005 0.034 2490 Dihedral : 4.709 20.139 1890 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer Outliers : 2.40 % 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: 1.40 (0.18), residues: 1745 helix: 1.02 (0.14), residues: 1150 sheet: -2.31 (0.49), residues: 45 loop : 1.38 (0.24), residues: 550 *********************** 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 558 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 522 time to evaluate : 1.615 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 outliers start: 36 outliers final: 17 residues processed: 542 average time/residue: 0.3109 time to fit residues: 229.1883 Evaluate side-chains 487 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 470 time to evaluate : 1.577 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1281 time to fit residues: 6.3877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 128 optimal weight: 0.6980 chunk 105 optimal weight: 0.4980 chunk 42 optimal weight: 8.9990 chunk 154 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 GLN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 219 GLN K 155 GLN N 179 GLN N 183 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 14155 Z= 0.194 Angle : 0.562 10.067 19205 Z= 0.286 Chirality : 0.042 0.151 2185 Planarity : 0.004 0.043 2490 Dihedral : 4.429 19.781 1890 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 1.53 % 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: 1.67 (0.19), residues: 1745 helix: 1.25 (0.14), residues: 1150 sheet: -2.43 (0.46), residues: 45 loop : 1.47 (0.25), residues: 550 *********************** 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 514 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 491 time to evaluate : 1.626 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 outliers start: 23 outliers final: 9 residues processed: 502 average time/residue: 0.3227 time to fit residues: 220.3286 Evaluate side-chains 460 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 451 time to evaluate : 1.662 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1248 time to fit residues: 4.3780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 147 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 GLN C 179 GLN C 183 ASN C 195 ASN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN J 50 GLN K 155 GLN K 193 ASN N 155 GLN O 155 GLN O 179 GLN O 183 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 14155 Z= 0.319 Angle : 0.618 10.688 19205 Z= 0.307 Chirality : 0.044 0.158 2185 Planarity : 0.005 0.040 2490 Dihedral : 4.446 18.706 1890 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 1.07 % 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: 1.40 (0.19), residues: 1745 helix: 1.05 (0.14), residues: 1160 sheet: -2.51 (0.42), residues: 45 loop : 1.34 (0.24), residues: 540 *********************** 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 472 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 456 time to evaluate : 1.696 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 outliers start: 16 outliers final: 6 residues processed: 461 average time/residue: 0.3224 time to fit residues: 200.8186 Evaluate side-chains 449 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 443 time to evaluate : 1.651 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1175 time to fit residues: 3.5879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 0.2980 chunk 140 optimal weight: 0.9980 chunk 113 optimal weight: 0.0050 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- 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** C 195 ASN D 50 GLN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN H 193 ASN I 179 GLN I 183 ASN K 155 GLN L 183 ASN O 183 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 14155 Z= 0.203 Angle : 0.550 9.057 19205 Z= 0.279 Chirality : 0.042 0.162 2185 Planarity : 0.004 0.043 2490 Dihedral : 4.226 18.482 1890 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 1.00 % 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: 1.51 (0.19), residues: 1745 helix: 1.11 (0.15), residues: 1160 sheet: -2.30 (0.48), residues: 45 loop : 1.44 (0.24), residues: 540 *********************** 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 471 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 456 time to evaluate : 1.534 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 outliers start: 15 outliers final: 5 residues processed: 460 average time/residue: 0.3299 time to fit residues: 205.3750 Evaluate side-chains 444 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 439 time to evaluate : 1.594 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1293 time to fit residues: 3.4023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN ** I 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 50 GLN K 155 GLN M 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.074 14155 Z= 0.574 Angle : 0.722 10.183 19205 Z= 0.360 Chirality : 0.049 0.173 2185 Planarity : 0.005 0.042 2490 Dihedral : 4.659 19.542 1890 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 1.87 % 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: 1.03 (0.19), residues: 1745 helix: 0.74 (0.15), residues: 1150 sheet: -2.86 (0.38), residues: 45 loop : 1.28 (0.24), residues: 550 *********************** 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 492 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 464 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 476 average time/residue: 0.3331 time to fit residues: 213.1647 Evaluate side-chains 463 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 446 time to evaluate : 1.733 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1424 time to fit residues: 6.7507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN D 50 GLN G 50 GLN H 179 GLN I 179 GLN I 183 ASN O 183 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 14155 Z= 0.302 Angle : 0.603 12.645 19205 Z= 0.306 Chirality : 0.044 0.199 2185 Planarity : 0.005 0.043 2490 Dihedral : 4.440 18.838 1890 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 0.60 % 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: 1.04 (0.18), residues: 1745 helix: 0.80 (0.14), residues: 1160 sheet: -2.83 (0.39), residues: 45 loop : 1.18 (0.23), residues: 540 *********************** 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 467 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 458 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 464 average time/residue: 0.3284 time to fit residues: 205.3761 Evaluate side-chains 440 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 438 time to evaluate : 1.601 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1151 time to fit residues: 2.6113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN H 179 GLN I 179 GLN I 183 ASN J 50 GLN ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 155 GLN O 179 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 14155 Z= 0.205 Angle : 0.564 9.842 19205 Z= 0.288 Chirality : 0.042 0.170 2185 Planarity : 0.004 0.045 2490 Dihedral : 4.234 17.699 1890 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer Outliers : 0.40 % 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: 1.07 (0.19), residues: 1745 helix: 0.89 (0.14), residues: 1225 sheet: -2.76 (0.41), residues: 45 loop : 0.99 (0.25), residues: 475 *********************** 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 458 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 452 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 456 average time/residue: 0.3226 time to fit residues: 198.3664 Evaluate side-chains 440 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 440 time to evaluate : 1.585 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 0.0050 chunk 144 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 161 optimal weight: 0.8980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 GLN ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN G 50 GLN H 155 GLN I 179 GLN I 183 ASN K 179 GLN ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 155 GLN O 179 GLN O 183 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4331 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= 0.195 Angle : 0.569 9.425 19205 Z= 0.289 Chirality : 0.042 0.166 2185 Planarity : 0.004 0.042 2490 Dihedral : 4.143 17.200 1890 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer Outliers : 0.47 % 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: 1.14 (0.19), residues: 1745 helix: 0.90 (0.14), residues: 1210 sheet: -2.56 (0.43), residues: 45 loop : 1.12 (0.25), residues: 490 *********************** 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 460 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 453 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 456 average time/residue: 0.3368 time to fit residues: 207.3330 Evaluate side-chains 442 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 439 time to evaluate : 1.638 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1234 time to fit residues: 2.9406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 169 optimal weight: 0.0470 chunk 155 optimal weight: 0.0070 chunk 134 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 0.0670 chunk 107 optimal weight: 0.5980 chunk 143 optimal weight: 0.8980 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 ASN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN E 179 GLN H 155 GLN I 183 ASN ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 63 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 14155 Z= 0.165 Angle : 0.563 10.041 19205 Z= 0.286 Chirality : 0.041 0.179 2185 Planarity : 0.004 0.045 2490 Dihedral : 4.071 17.531 1890 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer Outliers : 0.20 % 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: 1.24 (0.19), residues: 1745 helix: 0.99 (0.14), residues: 1225 sheet: -2.26 (0.48), residues: 45 loop : 1.11 (0.26), residues: 475 ********************** 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 448 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 445 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 445 average time/residue: 0.3229 time to fit residues: 194.7008 Evaluate side-chains 429 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 426 time to evaluate : 1.644 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1328 time to fit residues: 3.0185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 0.2980 chunk 135 optimal weight: 0.0670 chunk 56 optimal weight: 1.9990 chunk 138 optimal weight: 0.0370 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN A 179 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN ** F 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN I 179 GLN I 183 ASN K 179 GLN K 193 ASN L 179 GLN L 183 ASN N 179 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.136150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.106118 restraints weight = 21425.199| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.40 r_work: 0.3224 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4626 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= 0.174 Angle : 0.563 9.387 19205 Z= 0.287 Chirality : 0.041 0.161 2185 Planarity : 0.004 0.045 2490 Dihedral : 4.036 23.207 1890 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer Outliers : 0.27 % 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: 1.42 (0.19), residues: 1745 helix: 1.06 (0.15), residues: 1175 sheet: -2.12 (0.51), residues: 45 loop : 1.32 (0.25), residues: 525 =============================================================================== Job complete usr+sys time: 4242.16 seconds wall clock time: 76 minutes 49.61 seconds (4609.61 seconds total)