Starting phenix.real_space_refine on Fri Nov 17 12:29:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsl_24674/11_2023/7rsl_24674.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsl_24674/11_2023/7rsl_24674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsl_24674/11_2023/7rsl_24674.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsl_24674/11_2023/7rsl_24674.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsl_24674/11_2023/7rsl_24674.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsl_24674/11_2023/7rsl_24674.pdb" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 12460 2.51 5 N 3120 2.21 5 O 3480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 199": "OE1" <-> "OE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "G GLU 199": "OE1" <-> "OE2" Residue "H GLU 148": "OE1" <-> "OE2" Residue "H GLU 170": "OE1" <-> "OE2" Residue "H GLU 185": "OE1" <-> "OE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E GLU 199": "OE1" <-> "OE2" Residue "F GLU 148": "OE1" <-> "OE2" Residue "F GLU 170": "OE1" <-> "OE2" Residue "F GLU 185": "OE1" <-> "OE2" Residue "I GLU 199": "OE1" <-> "OE2" Residue "I TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J GLU 185": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 185": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 19150 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "G" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "H" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "E" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "F" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "I" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "J" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "C" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "D" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Time building chain proxies: 10.12, per 1000 atoms: 0.53 Number of scatterers: 19150 At special positions: 0 Unit cell: (155.925, 154.275, 85.8, 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 90 16.00 O 3480 8.00 N 3120 7.00 C 12460 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: 7.47 Conformation dependent library (CDL) restraints added in 3.7 seconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4520 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 40 sheets defined 34.7% alpha, 37.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 18 through 45 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'A' and resid 234 through 243 Processing helix chain 'A' and resid 243 through 264 removed outlier: 3.857A pdb=" N ILE A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 45 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 177 through 187 removed outlier: 3.728A pdb=" N LEU B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 264 removed outlier: 3.610A pdb=" N LEU B 246 " --> pdb=" O ARG B 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 45 Proline residue: G 31 - end of helix Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'G' and resid 167 through 174 Processing helix chain 'G' and resid 177 through 186 Processing helix chain 'G' and resid 234 through 243 Processing helix chain 'G' and resid 243 through 264 removed outlier: 3.857A pdb=" N ILE G 252 " --> pdb=" O TYR G 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 45 Proline residue: H 31 - end of helix Processing helix chain 'H' and resid 56 through 58 No H-bonds generated for 'chain 'H' and resid 56 through 58' Processing helix chain 'H' and resid 167 through 174 Processing helix chain 'H' and resid 177 through 187 removed outlier: 3.728A pdb=" N LEU H 187 " --> pdb=" O ASP H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 264 removed outlier: 3.610A pdb=" N LEU H 246 " --> pdb=" O ARG H 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 45 Proline residue: E 31 - end of helix Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 167 through 174 Processing helix chain 'E' and resid 177 through 186 Processing helix chain 'E' and resid 234 through 243 Processing helix chain 'E' and resid 243 through 264 removed outlier: 3.857A pdb=" N ILE E 252 " --> pdb=" O TYR E 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 45 Proline residue: F 31 - end of helix Processing helix chain 'F' and resid 56 through 58 No H-bonds generated for 'chain 'F' and resid 56 through 58' Processing helix chain 'F' and resid 167 through 174 Processing helix chain 'F' and resid 177 through 187 removed outlier: 3.728A pdb=" N LEU F 187 " --> pdb=" O ASP F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 264 removed outlier: 3.610A pdb=" N LEU F 246 " --> pdb=" O ARG F 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 45 Proline residue: I 31 - end of helix Processing helix chain 'I' and resid 56 through 58 No H-bonds generated for 'chain 'I' and resid 56 through 58' Processing helix chain 'I' and resid 167 through 174 Processing helix chain 'I' and resid 177 through 186 Processing helix chain 'I' and resid 234 through 243 Processing helix chain 'I' and resid 243 through 264 removed outlier: 3.856A pdb=" N ILE I 252 " --> pdb=" O TYR I 248 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 45 Proline residue: J 31 - end of helix Processing helix chain 'J' and resid 56 through 58 No H-bonds generated for 'chain 'J' and resid 56 through 58' Processing helix chain 'J' and resid 167 through 174 Processing helix chain 'J' and resid 177 through 187 removed outlier: 3.728A pdb=" N LEU J 187 " --> pdb=" O ASP J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 264 removed outlier: 3.610A pdb=" N LEU J 246 " --> pdb=" O ARG J 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 45 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 167 through 174 Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'C' and resid 234 through 243 Processing helix chain 'C' and resid 243 through 264 removed outlier: 3.856A pdb=" N ILE C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 45 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 177 through 187 removed outlier: 3.729A pdb=" N LEU D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 264 removed outlier: 3.611A pdb=" N LEU D 246 " --> pdb=" O ARG D 242 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 54 removed outlier: 4.666A pdb=" N ILE A 196 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N LEU A 107 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP A 194 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU A 109 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE A 192 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU A 111 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE A 190 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS A 113 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N ASN A 188 " --> pdb=" O CYS A 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 61 removed outlier: 3.617A pdb=" N PHE A 71 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 205 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR A 204 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY A 132 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG A 131 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS A 149 " --> pdb=" O ARG A 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 74 through 77 removed outlier: 3.878A pdb=" N MET A 97 " --> pdb=" O LYS A 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 50 through 54 removed outlier: 7.216A pdb=" N TYR B 103 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE B 196 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU B 105 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP B 194 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 54 Processing sheet with id=AA7, first strand: chain 'B' and resid 59 through 61 removed outlier: 3.569A pdb=" N SER B 206 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG B 131 " --> pdb=" O LYS B 149 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS B 149 " --> pdb=" O ARG B 131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 74 through 76 Processing sheet with id=AA9, first strand: chain 'G' and resid 51 through 54 removed outlier: 4.665A pdb=" N ILE G 196 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N LEU G 107 " --> pdb=" O ASP G 194 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASP G 194 " --> pdb=" O LEU G 107 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU G 109 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE G 192 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU G 111 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE G 190 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS G 113 " --> pdb=" O ASN G 188 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N ASN G 188 " --> pdb=" O CYS G 113 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AB2, first strand: chain 'G' and resid 59 through 61 removed outlier: 3.617A pdb=" N PHE G 71 " --> pdb=" O ASN G 59 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE G 205 " --> pdb=" O GLN G 72 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR G 204 " --> pdb=" O GLY G 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY G 132 " --> pdb=" O THR G 204 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG G 131 " --> pdb=" O LYS G 149 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS G 149 " --> pdb=" O ARG G 131 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 74 through 77 removed outlier: 3.823A pdb=" N MET G 97 " --> pdb=" O LYS G 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 50 through 54 removed outlier: 7.216A pdb=" N TYR H 103 " --> pdb=" O ILE H 196 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE H 196 " --> pdb=" O TYR H 103 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU H 105 " --> pdb=" O ASP H 194 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP H 194 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 50 through 54 Processing sheet with id=AB6, first strand: chain 'H' and resid 59 through 61 removed outlier: 3.569A pdb=" N SER H 206 " --> pdb=" O TYR H 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG H 131 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS H 149 " --> pdb=" O ARG H 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 74 through 76 Processing sheet with id=AB8, first strand: chain 'E' and resid 51 through 54 removed outlier: 4.666A pdb=" N ILE E 196 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N LEU E 107 " --> pdb=" O ASP E 194 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP E 194 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU E 109 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE E 192 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU E 111 " --> pdb=" O ILE E 190 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE E 190 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N CYS E 113 " --> pdb=" O ASN E 188 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N ASN E 188 " --> pdb=" O CYS E 113 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 51 through 54 Processing sheet with id=AC1, first strand: chain 'E' and resid 59 through 61 removed outlier: 3.618A pdb=" N PHE E 71 " --> pdb=" O ASN E 59 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE E 205 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR E 204 " --> pdb=" O GLY E 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY E 132 " --> pdb=" O THR E 204 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG E 131 " --> pdb=" O LYS E 149 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS E 149 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 74 through 77 removed outlier: 3.823A pdb=" N MET E 97 " --> pdb=" O LYS E 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 50 through 54 removed outlier: 7.216A pdb=" N TYR F 103 " --> pdb=" O ILE F 196 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE F 196 " --> pdb=" O TYR F 103 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU F 105 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP F 194 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 50 through 54 Processing sheet with id=AC5, first strand: chain 'F' and resid 59 through 61 removed outlier: 3.569A pdb=" N SER F 206 " --> pdb=" O TYR F 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG F 131 " --> pdb=" O LYS F 149 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS F 149 " --> pdb=" O ARG F 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 74 through 76 Processing sheet with id=AC7, first strand: chain 'I' and resid 51 through 54 removed outlier: 4.666A pdb=" N ILE I 196 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N LEU I 107 " --> pdb=" O ASP I 194 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP I 194 " --> pdb=" O LEU I 107 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU I 109 " --> pdb=" O ILE I 192 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE I 192 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU I 111 " --> pdb=" O ILE I 190 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE I 190 " --> pdb=" O LEU I 111 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS I 113 " --> pdb=" O ASN I 188 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N ASN I 188 " --> pdb=" O CYS I 113 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 51 through 54 Processing sheet with id=AC9, first strand: chain 'I' and resid 59 through 61 removed outlier: 3.617A pdb=" N PHE I 71 " --> pdb=" O ASN I 59 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE I 205 " --> pdb=" O GLN I 72 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR I 204 " --> pdb=" O GLY I 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY I 132 " --> pdb=" O THR I 204 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG I 131 " --> pdb=" O LYS I 149 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS I 149 " --> pdb=" O ARG I 131 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 74 through 77 removed outlier: 3.877A pdb=" N MET I 97 " --> pdb=" O LYS I 75 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 50 through 54 removed outlier: 7.216A pdb=" N TYR J 103 " --> pdb=" O ILE J 196 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE J 196 " --> pdb=" O TYR J 103 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU J 105 " --> pdb=" O ASP J 194 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP J 194 " --> pdb=" O LEU J 105 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 50 through 54 Processing sheet with id=AD4, first strand: chain 'J' and resid 59 through 61 removed outlier: 3.569A pdb=" N SER J 206 " --> pdb=" O TYR J 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG J 131 " --> pdb=" O LYS J 149 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS J 149 " --> pdb=" O ARG J 131 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 74 through 76 Processing sheet with id=AD6, first strand: chain 'C' and resid 51 through 54 removed outlier: 4.666A pdb=" N ILE C 196 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N LEU C 107 " --> pdb=" O ASP C 194 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP C 194 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU C 109 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE C 192 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU C 111 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE C 190 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N CYS C 113 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N ASN C 188 " --> pdb=" O CYS C 113 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 51 through 54 Processing sheet with id=AD8, first strand: chain 'C' and resid 59 through 61 removed outlier: 3.617A pdb=" N PHE C 71 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 205 " --> pdb=" O GLN C 72 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR C 204 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY C 132 " --> pdb=" O THR C 204 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ARG C 131 " --> pdb=" O LYS C 149 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LYS C 149 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 74 through 77 removed outlier: 3.878A pdb=" N MET C 97 " --> pdb=" O LYS C 75 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 50 through 54 removed outlier: 7.215A pdb=" N TYR D 103 " --> pdb=" O ILE D 196 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE D 196 " --> pdb=" O TYR D 103 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU D 105 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP D 194 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 50 through 54 Processing sheet with id=AE3, first strand: chain 'D' and resid 59 through 61 removed outlier: 3.569A pdb=" N SER D 206 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG D 131 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS D 149 " --> pdb=" O ARG D 131 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 74 through 76 1070 hydrogen bonds defined for protein. 2985 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: 6.01 Time building geometry restraints manager: 8.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4854 1.33 - 1.45: 3393 1.45 - 1.57: 11153 1.57 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 19540 Sorted by residual: bond pdb=" N ILE B 150 " pdb=" CA ILE B 150 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.06e-02 8.90e+03 1.26e+01 bond pdb=" N ILE J 150 " pdb=" CA ILE J 150 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.06e-02 8.90e+03 1.26e+01 bond pdb=" N ILE H 150 " pdb=" CA ILE H 150 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.06e-02 8.90e+03 1.26e+01 bond pdb=" N ILE D 150 " pdb=" CA ILE D 150 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.06e-02 8.90e+03 1.25e+01 bond pdb=" N ILE F 150 " pdb=" CA ILE F 150 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.06e-02 8.90e+03 1.24e+01 ... (remaining 19535 not shown) Histogram of bond angle deviations from ideal: 98.79 - 105.82: 441 105.82 - 112.84: 10625 112.84 - 119.87: 6340 119.87 - 126.89: 8910 126.89 - 133.92: 174 Bond angle restraints: 26490 Sorted by residual: angle pdb=" N HIS J 119 " pdb=" CA HIS J 119 " pdb=" C HIS J 119 " ideal model delta sigma weight residual 110.50 100.67 9.83 1.41e+00 5.03e-01 4.86e+01 angle pdb=" N HIS H 119 " pdb=" CA HIS H 119 " pdb=" C HIS H 119 " ideal model delta sigma weight residual 110.50 100.70 9.80 1.41e+00 5.03e-01 4.83e+01 angle pdb=" N HIS B 119 " pdb=" CA HIS B 119 " pdb=" C HIS B 119 " ideal model delta sigma weight residual 110.50 100.73 9.77 1.41e+00 5.03e-01 4.80e+01 angle pdb=" N HIS D 119 " pdb=" CA HIS D 119 " pdb=" C HIS D 119 " ideal model delta sigma weight residual 110.50 100.73 9.77 1.41e+00 5.03e-01 4.80e+01 angle pdb=" N HIS F 119 " pdb=" CA HIS F 119 " pdb=" C HIS F 119 " ideal model delta sigma weight residual 110.50 100.76 9.74 1.41e+00 5.03e-01 4.77e+01 ... (remaining 26485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 10796 17.74 - 35.48: 872 35.48 - 53.22: 119 53.22 - 70.96: 47 70.96 - 88.70: 16 Dihedral angle restraints: 11850 sinusoidal: 4910 harmonic: 6940 Sorted by residual: dihedral pdb=" CA MET J 101 " pdb=" C MET J 101 " pdb=" N GLU J 102 " pdb=" CA GLU J 102 " ideal model delta harmonic sigma weight residual -180.00 -154.71 -25.29 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA MET D 101 " pdb=" C MET D 101 " pdb=" N GLU D 102 " pdb=" CA GLU D 102 " ideal model delta harmonic sigma weight residual -180.00 -154.72 -25.28 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA MET B 101 " pdb=" C MET B 101 " pdb=" N GLU B 102 " pdb=" CA GLU B 102 " ideal model delta harmonic sigma weight residual 180.00 -154.72 -25.28 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 11847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2091 0.041 - 0.082: 623 0.082 - 0.122: 315 0.122 - 0.163: 60 0.163 - 0.204: 21 Chirality restraints: 3110 Sorted by residual: chirality pdb=" CA LEU J 91 " pdb=" N LEU J 91 " pdb=" C LEU J 91 " pdb=" CB LEU J 91 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE G 28 " pdb=" N ILE G 28 " pdb=" C ILE G 28 " pdb=" CB ILE G 28 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CA ILE D 205 " pdb=" N ILE D 205 " pdb=" C ILE D 205 " pdb=" CB ILE D 205 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.71e-01 ... (remaining 3107 not shown) Planarity restraints: 3340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP H 118 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.56e+00 pdb=" CG ASP H 118 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP H 118 " 0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP H 118 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP J 118 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" CG ASP J 118 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP J 118 " -0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP J 118 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 118 " 0.012 2.00e-02 2.50e+03 2.55e-02 6.48e+00 pdb=" CG ASP D 118 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP D 118 " 0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP D 118 " 0.015 2.00e-02 2.50e+03 ... (remaining 3337 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1643 2.74 - 3.28: 19652 3.28 - 3.82: 30021 3.82 - 4.36: 37019 4.36 - 4.90: 64414 Nonbonded interactions: 152749 Sorted by model distance: nonbonded pdb=" OD1 ASP I 194 " pdb=" NH2 ARG I 229 " model vdw 2.200 2.520 nonbonded pdb=" OD1 ASP C 194 " pdb=" NH2 ARG C 229 " model vdw 2.200 2.520 nonbonded pdb=" OD1 ASP A 194 " pdb=" NH2 ARG A 229 " model vdw 2.201 2.520 nonbonded pdb=" OD1 ASP E 194 " pdb=" NH2 ARG E 229 " model vdw 2.201 2.520 nonbonded pdb=" OD1 ASP G 194 " pdb=" NH2 ARG G 229 " model vdw 2.202 2.520 ... (remaining 152744 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.490 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 52.430 Find NCS groups from input model: 1.270 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 19540 Z= 0.454 Angle : 0.818 9.828 26490 Z= 0.528 Chirality : 0.051 0.204 3110 Planarity : 0.005 0.043 3340 Dihedral : 13.619 88.702 7330 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.23 % Allowed : 1.71 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.17), residues: 2310 helix: 0.67 (0.19), residues: 725 sheet: -2.21 (0.18), residues: 735 loop : -1.63 (0.20), residues: 850 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 515 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 515 average time/residue: 0.3146 time to fit residues: 242.1497 Evaluate side-chains 293 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 2.327 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 6.9990 chunk 174 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 93 optimal weight: 30.0000 chunk 180 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN ** G 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 ASN ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 19540 Z= 0.429 Angle : 0.699 11.899 26490 Z= 0.351 Chirality : 0.044 0.142 3110 Planarity : 0.005 0.050 3340 Dihedral : 4.999 23.440 2530 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.85 % Allowed : 12.70 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.18), residues: 2310 helix: 0.93 (0.19), residues: 740 sheet: -1.75 (0.17), residues: 865 loop : -1.29 (0.23), residues: 705 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 280 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 27 residues processed: 297 average time/residue: 0.3194 time to fit residues: 143.3748 Evaluate side-chains 273 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 246 time to evaluate : 2.337 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1680 time to fit residues: 11.5316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 186 optimal weight: 30.0000 chunk 207 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 173 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN G 173 GLN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 ASN ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 19540 Z= 0.201 Angle : 0.589 12.362 26490 Z= 0.291 Chirality : 0.042 0.154 3110 Planarity : 0.004 0.039 3340 Dihedral : 4.564 21.853 2530 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.04 % Allowed : 15.09 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.18), residues: 2310 helix: 1.15 (0.19), residues: 740 sheet: -1.38 (0.17), residues: 845 loop : -0.84 (0.24), residues: 725 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 296 time to evaluate : 2.540 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 305 average time/residue: 0.3258 time to fit residues: 149.5884 Evaluate side-chains 265 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 255 time to evaluate : 2.336 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1830 time to fit residues: 6.6195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 206 optimal weight: 9.9990 chunk 157 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 99 optimal weight: 0.0170 chunk 140 optimal weight: 20.0000 chunk 209 optimal weight: 9.9990 chunk 222 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 chunk 199 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS G 121 ASN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 GLN E 119 HIS E 121 ASN ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 173 GLN ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 119 HIS ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 19540 Z= 0.198 Angle : 0.574 10.213 26490 Z= 0.284 Chirality : 0.042 0.144 3110 Planarity : 0.004 0.037 3340 Dihedral : 4.383 21.795 2530 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.67 % Allowed : 16.49 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.18), residues: 2310 helix: 1.26 (0.19), residues: 740 sheet: -1.13 (0.17), residues: 845 loop : -0.78 (0.24), residues: 725 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 274 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 16 residues processed: 290 average time/residue: 0.3262 time to fit residues: 142.2197 Evaluate side-chains 267 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 251 time to evaluate : 1.777 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1524 time to fit residues: 6.8778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 30.0000 chunk 126 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 189 optimal weight: 8.9990 chunk 153 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 113 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN E 121 ASN ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 HIS ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 HIS C 121 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 19540 Z= 0.359 Angle : 0.639 12.271 26490 Z= 0.313 Chirality : 0.042 0.162 3110 Planarity : 0.004 0.037 3340 Dihedral : 4.537 22.503 2530 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.62 % Allowed : 18.11 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.18), residues: 2310 helix: 1.36 (0.19), residues: 740 sheet: -0.96 (0.17), residues: 870 loop : -0.87 (0.24), residues: 700 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 259 time to evaluate : 2.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 17 residues processed: 275 average time/residue: 0.3202 time to fit residues: 133.7327 Evaluate side-chains 262 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 245 time to evaluate : 2.257 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2110 time to fit residues: 9.1726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 130 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 184 optimal weight: 50.0000 chunk 103 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS A 121 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN ** G 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 ASN E 121 ASN F 72 GLN ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19540 Z= 0.186 Angle : 0.594 11.675 26490 Z= 0.288 Chirality : 0.042 0.143 3110 Planarity : 0.004 0.037 3340 Dihedral : 4.308 22.261 2530 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.86 % Allowed : 19.28 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.18), residues: 2310 helix: 1.45 (0.19), residues: 750 sheet: -0.70 (0.17), residues: 850 loop : -0.73 (0.24), residues: 710 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 289 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 19 outliers final: 5 residues processed: 296 average time/residue: 0.3206 time to fit residues: 144.4866 Evaluate side-chains 264 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 259 time to evaluate : 2.478 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1859 time to fit residues: 5.0050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 0.0030 chunk 25 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 221 optimal weight: 3.9990 chunk 138 optimal weight: 50.0000 chunk 135 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN G 173 GLN H 72 GLN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN D 72 GLN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19540 Z= 0.235 Angle : 0.620 14.444 26490 Z= 0.299 Chirality : 0.042 0.144 3110 Planarity : 0.004 0.037 3340 Dihedral : 4.314 22.489 2530 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.81 % Allowed : 19.32 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.18), residues: 2310 helix: 1.39 (0.19), residues: 750 sheet: -0.56 (0.17), residues: 850 loop : -0.72 (0.24), residues: 710 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 275 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 18 outliers final: 6 residues processed: 284 average time/residue: 0.3246 time to fit residues: 138.9062 Evaluate side-chains 265 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 259 time to evaluate : 2.522 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1940 time to fit residues: 5.3451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 140 optimal weight: 20.0000 chunk 151 optimal weight: 0.0030 chunk 109 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN E 121 ASN ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 ASN ** I 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19540 Z= 0.208 Angle : 0.644 14.250 26490 Z= 0.304 Chirality : 0.042 0.165 3110 Planarity : 0.004 0.038 3340 Dihedral : 4.303 22.389 2530 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.81 % Allowed : 20.54 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.18), residues: 2310 helix: 1.41 (0.19), residues: 750 sheet: -0.50 (0.17), residues: 850 loop : -0.69 (0.24), residues: 710 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 283 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 6 residues processed: 289 average time/residue: 0.3248 time to fit residues: 141.9946 Evaluate side-chains 271 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 265 time to evaluate : 2.204 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1868 time to fit residues: 5.5340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 chunk 193 optimal weight: 8.9990 chunk 206 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 162 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 186 optimal weight: 30.0000 chunk 195 optimal weight: 6.9990 chunk 205 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 GLN H 72 GLN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN E 121 ASN ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.140 19540 Z= 0.433 Angle : 0.741 12.437 26490 Z= 0.356 Chirality : 0.043 0.203 3110 Planarity : 0.004 0.036 3340 Dihedral : 4.645 23.878 2530 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.63 % Allowed : 20.72 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.18), residues: 2310 helix: 1.26 (0.19), residues: 750 sheet: -0.46 (0.18), residues: 800 loop : -0.87 (0.22), residues: 760 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 250 time to evaluate : 2.397 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: 14 outliers final: 6 residues processed: 254 average time/residue: 0.3438 time to fit residues: 131.3340 Evaluate side-chains 247 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 241 time to evaluate : 2.566 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2530 time to fit residues: 5.7732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 8.9990 chunk 218 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 229 optimal weight: 6.9990 chunk 210 optimal weight: 7.9990 chunk 182 optimal weight: 0.0040 chunk 18 optimal weight: 4.9990 chunk 140 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 overall best weight: 5.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 GLN ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 19540 Z= 0.371 Angle : 0.736 13.510 26490 Z= 0.352 Chirality : 0.043 0.210 3110 Planarity : 0.004 0.035 3340 Dihedral : 4.661 24.474 2530 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.50 % Allowed : 21.13 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.18), residues: 2310 helix: 1.26 (0.19), residues: 755 sheet: -0.44 (0.18), residues: 790 loop : -0.95 (0.22), residues: 765 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 241 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 246 average time/residue: 0.3330 time to fit residues: 123.4267 Evaluate side-chains 233 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 230 time to evaluate : 2.430 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1716 time to fit residues: 4.0639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 0.0970 chunk 194 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 168 optimal weight: 0.0020 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.081191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.053964 restraints weight = 72003.766| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 4.77 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19540 Z= 0.180 Angle : 0.708 16.388 26490 Z= 0.334 Chirality : 0.043 0.181 3110 Planarity : 0.004 0.037 3340 Dihedral : 4.464 25.653 2530 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.27 % Allowed : 21.49 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.18), residues: 2310 helix: 1.40 (0.19), residues: 755 sheet: -0.36 (0.18), residues: 760 loop : -0.84 (0.22), residues: 795 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3792.60 seconds wall clock time: 72 minutes 32.29 seconds (4352.29 seconds total)