Starting phenix.real_space_refine on Wed Nov 15 08:32:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/11_2023/6puw_20483_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/11_2023/6puw_20483.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/11_2023/6puw_20483_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/11_2023/6puw_20483_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/11_2023/6puw_20483_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/11_2023/6puw_20483.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/11_2023/6puw_20483.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/11_2023/6puw_20483_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/11_2023/6puw_20483_updated.pdb" } resolution = 2.9 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= 0.024 sd= 0.693 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: 8 Type Number sf(0) Gaussians Zn 4 6.06 5 P 72 5.49 5 Mg 4 5.21 5 S 34 5.16 5 C 6662 2.51 5 N 1914 2.21 5 O 2420 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 13": "OE1" <-> "OE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 157": "OE1" <-> "OE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "G ARG 20": "NH1" <-> "NH2" Residue "G GLU 157": "OE1" <-> "OE2" Residue "G GLU 170": "OE1" <-> "OE2" Residue "G GLU 212": "OE1" <-> "OE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H GLU 13": "OE1" <-> "OE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 157": "OE1" <-> "OE2" Residue "H GLU 212": "OE1" <-> "OE2" Residue "H ARG 224": "NH1" <-> "NH2" Residue "I GLU 246": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 11116 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1935 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 8, 'TRANS': 240} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "B" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1749 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "C" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 539 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "D" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 388 Classifications: {'peptide': 47} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 43} Chain: "E" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 384 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "F" Number of atoms: 371 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Conformer: "B" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} bond proxies already assigned to first conformer: 369 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 2, ' ZN': 1, 'KLQ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "G" Number of atoms: 1935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1935 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 8, 'TRANS': 240} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "H" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1749 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "I" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 539 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "J" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 388 Classifications: {'peptide': 47} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 43} Chain: "K" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 384 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "L" Number of atoms: 371 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Conformer: "B" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} bond proxies already assigned to first conformer: 369 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 2, ' ZN': 1, 'KLQ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "I" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "J" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "L" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 319 SG CYS A 40 26.812 44.982 52.090 1.00 27.12 S ATOM 342 SG CYS A 43 30.201 46.049 50.522 1.00 13.11 S ATOM 2241 SG CYS B 40 49.179 122.249 23.495 1.00 99.74 S ATOM 2264 SG CYS B 43 47.044 120.689 26.698 1.00107.94 S ATOM 5877 SG CYS G 40 64.828 87.738 52.090 1.00 27.12 S ATOM 5900 SG CYS G 43 61.439 86.671 50.522 1.00 13.11 S ATOM 7799 SG CYS H 40 42.461 10.471 23.495 1.00 99.74 S ATOM 7822 SG CYS H 43 44.596 12.031 26.698 1.00107.94 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A DA F 21 " occ=0.60 ... (40 atoms not shown) pdb=" C4 B DA F 21 " occ=0.40 residue: pdb=" P A DA L 21 " occ=0.60 ... (40 atoms not shown) pdb=" C4 B DA L 21 " occ=0.40 Time building chain proxies: 6.16, per 1000 atoms: 0.55 Number of scatterers: 11116 At special positions: 0 Unit cell: (92.43, 133.51, 83.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 S 34 16.00 P 72 15.00 Mg 4 11.99 F 6 9.00 O 2420 8.00 N 1914 7.00 C 6662 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: 4.55 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 303 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 40 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 12 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 16 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 43 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 40 " pdb=" ZN G 303 " pdb="ZN ZN G 303 " - pdb=" NE2 HIS G 12 " pdb="ZN ZN G 303 " - pdb=" ND1 HIS G 16 " pdb="ZN ZN G 303 " - pdb=" SG CYS G 43 " pdb="ZN ZN G 303 " - pdb=" SG CYS G 40 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS H 12 " pdb="ZN ZN H 301 " - pdb=" ND1 HIS H 16 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 43 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 40 " Number of angles added : 4 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 14 sheets defined 42.2% alpha, 17.8% beta 30 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 4.88 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 removed outlier: 3.920A pdb=" N LYS A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 30 through 38 Processing helix chain 'A' and resid 41 through 43 No H-bonds generated for 'chain 'A' and resid 41 through 43' Processing helix chain 'A' and resid 94 through 107 removed outlier: 3.598A pdb=" N TYR A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 122 No H-bonds generated for 'chain 'A' and resid 119 through 122' Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 145 through 165 removed outlier: 5.563A pdb=" N VAL A 150 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A 152 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 185 Processing helix chain 'A' and resid 196 through 220 removed outlier: 3.623A pdb=" N ILE A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 19 through 26 removed outlier: 3.563A pdb=" N SER B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 39 Processing helix chain 'B' and resid 94 through 107 Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 150 through 168 removed outlier: 5.291A pdb=" N ASP B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLN B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 185 Processing helix chain 'B' and resid 196 through 220 removed outlier: 3.602A pdb=" N ILE B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 222 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 271 through 274 removed outlier: 3.735A pdb=" N GLN C 274 " --> pdb=" O TYR C 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 271 through 274' Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'G' and resid 2 through 15 removed outlier: 3.920A pdb=" N LYS G 14 " --> pdb=" O GLU G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 25 Processing helix chain 'G' and resid 30 through 38 Processing helix chain 'G' and resid 41 through 43 No H-bonds generated for 'chain 'G' and resid 41 through 43' Processing helix chain 'G' and resid 94 through 107 removed outlier: 3.598A pdb=" N TYR G 99 " --> pdb=" O GLN G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 122 No H-bonds generated for 'chain 'G' and resid 119 through 122' Processing helix chain 'G' and resid 124 through 133 Processing helix chain 'G' and resid 145 through 165 removed outlier: 5.563A pdb=" N VAL G 150 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU G 152 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 185 Processing helix chain 'G' and resid 196 through 220 removed outlier: 3.623A pdb=" N ILE G 220 " --> pdb=" O GLN G 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 11 Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.563A pdb=" N SER H 24 " --> pdb=" O ARG H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 39 Processing helix chain 'H' and resid 94 through 107 Processing helix chain 'H' and resid 124 through 133 Processing helix chain 'H' and resid 150 through 168 removed outlier: 5.291A pdb=" N ASP H 167 " --> pdb=" O GLY H 163 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLN H 168 " --> pdb=" O GLN H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 185 Processing helix chain 'H' and resid 196 through 220 removed outlier: 3.602A pdb=" N ILE H 220 " --> pdb=" O GLN H 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 222 Processing helix chain 'I' and resid 262 through 264 No H-bonds generated for 'chain 'I' and resid 262 through 264' Processing helix chain 'I' and resid 271 through 274 removed outlier: 3.735A pdb=" N GLN I 274 " --> pdb=" O TYR I 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 271 through 274' Processing helix chain 'J' and resid 262 through 264 No H-bonds generated for 'chain 'J' and resid 262 through 264' Processing sheet with id= A, first strand: chain 'A' and resid 87 through 89 removed outlier: 4.251A pdb=" N VAL A 72 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR A 112 " --> pdb=" O TRP A 61 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU A 63 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N HIS A 114 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N CYS A 65 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LYS A 136 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N THR A 115 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLU A 138 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 241 through 244 removed outlier: 6.639A pdb=" N VAL A 250 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 84 through 89 removed outlier: 4.086A pdb=" N VAL B 72 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N THR B 112 " --> pdb=" O TRP B 61 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU B 63 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N HIS B 114 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N CYS B 65 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS B 136 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 256 through 258 removed outlier: 3.568A pdb=" N TRP B 243 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLN B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LEU B 241 " --> pdb=" O GLN B 252 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 265 through 268 removed outlier: 6.627A pdb=" N VAL C 250 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LYS C 244 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 224 through 227 removed outlier: 3.849A pdb=" N ARG D 224 " --> pdb=" O ILE D 268 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 256 through 261 removed outlier: 6.527A pdb=" N GLN D 252 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU D 241 " --> pdb=" O GLN D 252 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 87 through 89 removed outlier: 4.251A pdb=" N VAL G 72 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR G 112 " --> pdb=" O TRP G 61 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU G 63 " --> pdb=" O THR G 112 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N HIS G 114 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N CYS G 65 " --> pdb=" O HIS G 114 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LYS G 136 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N THR G 115 " --> pdb=" O LYS G 136 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLU G 138 " --> pdb=" O THR G 115 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 241 through 244 removed outlier: 6.639A pdb=" N VAL G 250 " --> pdb=" O LEU G 242 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 84 through 89 removed outlier: 4.086A pdb=" N VAL H 72 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N THR H 112 " --> pdb=" O TRP H 61 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU H 63 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N HIS H 114 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N CYS H 65 " --> pdb=" O HIS H 114 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS H 136 " --> pdb=" O VAL H 113 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 256 through 258 removed outlier: 3.568A pdb=" N TRP H 243 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLN H 252 " --> pdb=" O LEU H 241 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LEU H 241 " --> pdb=" O GLN H 252 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 265 through 268 removed outlier: 6.627A pdb=" N VAL I 250 " --> pdb=" O LEU I 242 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LYS I 244 " --> pdb=" O ALA I 248 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA I 248 " --> pdb=" O LYS I 244 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'J' and resid 224 through 227 removed outlier: 3.849A pdb=" N ARG J 224 " --> pdb=" O ILE J 268 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'J' and resid 256 through 261 removed outlier: 6.527A pdb=" N GLN J 252 " --> pdb=" O LEU J 241 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU J 241 " --> pdb=" O GLN J 252 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 3.50 Time building geometry restraints manager: 4.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1632 1.31 - 1.43: 3202 1.43 - 1.56: 6130 1.56 - 1.68: 146 1.68 - 1.81: 50 Bond restraints: 11160 Sorted by residual: bond pdb=" CAJ KLQ G 304 " pdb=" CAX KLQ G 304 " ideal model delta sigma weight residual 2.011 1.514 0.497 2.00e-02 2.50e+03 6.19e+02 bond pdb=" CAJ KLQ A 304 " pdb=" CAX KLQ A 304 " ideal model delta sigma weight residual 2.011 1.514 0.497 2.00e-02 2.50e+03 6.19e+02 bond pdb=" CAW KLQ G 304 " pdb=" CBA KLQ G 304 " ideal model delta sigma weight residual 0.990 1.481 -0.491 2.00e-02 2.50e+03 6.03e+02 bond pdb=" CAW KLQ A 304 " pdb=" CBA KLQ A 304 " ideal model delta sigma weight residual 0.990 1.481 -0.491 2.00e-02 2.50e+03 6.03e+02 bond pdb=" CAZ KLQ G 304 " pdb=" NBF KLQ G 304 " ideal model delta sigma weight residual 1.092 1.445 -0.353 2.00e-02 2.50e+03 3.11e+02 ... (remaining 11155 not shown) Histogram of bond angle deviations from ideal: 99.47 - 106.37: 694 106.37 - 113.28: 6110 113.28 - 120.18: 4030 120.18 - 127.09: 4256 127.09 - 133.99: 284 Bond angle restraints: 15374 Sorted by residual: angle pdb=" CAY KLQ A 304 " pdb=" CAV KLQ A 304 " pdb=" FAG KLQ A 304 " ideal model delta sigma weight residual 142.84 119.21 23.63 3.00e+00 1.11e-01 6.21e+01 angle pdb=" CAY KLQ G 304 " pdb=" CAV KLQ G 304 " pdb=" FAG KLQ G 304 " ideal model delta sigma weight residual 142.84 119.21 23.63 3.00e+00 1.11e-01 6.21e+01 angle pdb=" CAI KLQ G 304 " pdb=" CAV KLQ G 304 " pdb=" FAG KLQ G 304 " ideal model delta sigma weight residual 97.12 120.63 -23.51 3.00e+00 1.11e-01 6.14e+01 angle pdb=" CAI KLQ A 304 " pdb=" CAV KLQ A 304 " pdb=" FAG KLQ A 304 " ideal model delta sigma weight residual 97.12 120.63 -23.51 3.00e+00 1.11e-01 6.14e+01 angle pdb=" N SER G 123 " pdb=" CA SER G 123 " pdb=" C SER G 123 " ideal model delta sigma weight residual 110.41 117.17 -6.76 1.23e+00 6.61e-01 3.02e+01 ... (remaining 15369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 5366 17.33 - 34.67: 560 34.67 - 52.00: 308 52.00 - 69.33: 144 69.33 - 86.66: 16 Dihedral angle restraints: 6394 sinusoidal: 3056 harmonic: 3338 Sorted by residual: dihedral pdb=" CA ARG D 228 " pdb=" C ARG D 228 " pdb=" N ASP D 229 " pdb=" CA ASP D 229 " ideal model delta harmonic sigma weight residual -180.00 -155.55 -24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA ARG J 228 " pdb=" C ARG J 228 " pdb=" N ASP J 229 " pdb=" CA ASP J 229 " ideal model delta harmonic sigma weight residual -180.00 -155.55 -24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA TYR G 194 " pdb=" C TYR G 194 " pdb=" N SER G 195 " pdb=" CA SER G 195 " ideal model delta harmonic sigma weight residual 180.00 156.94 23.06 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 6391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1112 0.035 - 0.070: 416 0.070 - 0.105: 132 0.105 - 0.141: 42 0.141 - 0.176: 6 Chirality restraints: 1708 Sorted by residual: chirality pdb=" CA ASN A 120 " pdb=" N ASN A 120 " pdb=" C ASN A 120 " pdb=" CB ASN A 120 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CA ASN G 120 " pdb=" N ASN G 120 " pdb=" C ASN G 120 " pdb=" CB ASN G 120 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CA THR A 122 " pdb=" N THR A 122 " pdb=" C THR A 122 " pdb=" CB THR A 122 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.32e-01 ... (remaining 1705 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS G 127 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C LYS G 127 " 0.040 2.00e-02 2.50e+03 pdb=" O LYS G 127 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA G 128 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 127 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C LYS A 127 " -0.040 2.00e-02 2.50e+03 pdb=" O LYS A 127 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA A 128 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 155 " -0.006 2.00e-02 2.50e+03 1.26e-02 1.60e+00 pdb=" C ASN G 155 " 0.022 2.00e-02 2.50e+03 pdb=" O ASN G 155 " -0.008 2.00e-02 2.50e+03 pdb=" N LYS G 156 " -0.007 2.00e-02 2.50e+03 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 8 0.98 - 1.96: 8 1.96 - 2.94: 4743 2.94 - 3.92: 30808 3.92 - 4.90: 60660 Warning: very small nonbonded interaction distances. Nonbonded interactions: 96227 Sorted by model distance: nonbonded pdb=" O HOH A 464 " pdb=" O HOH G 438 " model vdw 0.000 2.440 nonbonded pdb=" O HOH A 459 " pdb=" O HOH L 109 " model vdw 0.000 2.440 nonbonded pdb=" O HOH A 488 " pdb=" O HOH K 105 " model vdw 0.000 2.440 nonbonded pdb=" O HOH E 105 " pdb=" O HOH G 488 " model vdw 0.000 2.440 nonbonded pdb=" O HOH F 109 " pdb=" O HOH G 459 " model vdw 0.000 2.440 ... (remaining 96222 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name CB or name CG or name CD or name OE1 or name NE2)) or resid 10 through 13 \ or (resid 14 and (name N or name CA or name C or name CB or name CG or name CD \ or name CE or name NZ )) or resid 15 through 44 or resid 57 through 140 or resid \ 150 through 225 or resid 239 through 252 or resid 266)) selection = (chain 'B' and (resid 2 through 79 or (resid 80 and (name N or name CA or name C \ or name CB )) or resid 81 through 84 or (resid 85 and (name N or name CA or nam \ e C or name CB or name CG or name CD or name OE1 or name OE2)) or resid 86 throu \ gh 252 or resid 258)) selection = (chain 'G' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name CB or name CG or name CD or name OE1 or name NE2)) or resid 10 through 13 \ or (resid 14 and (name N or name CA or name C or name CB or name CG or name CD \ or name CE or name NZ )) or resid 15 through 44 or resid 57 through 140 or resid \ 150 through 225 or resid 239 through 252 or resid 266)) selection = (chain 'H' and (resid 2 through 79 or (resid 80 and (name N or name CA or name C \ or name CB )) or resid 81 through 84 or (resid 85 and (name N or name CA or nam \ e C or name CB or name CG or name CD or name OE1 or name OE2)) or resid 86 throu \ gh 252 or resid 258)) } ncs_group { reference = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' } ncs_group { reference = (chain 'F' and resid 5 through 20) selection = (chain 'L' and resid 5 through 20) } 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=0.40 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: 4.710 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: 12.910 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 36.220 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 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 : 0.013 0.497 11160 Z= 0.654 Angle : 0.765 23.633 15374 Z= 0.400 Chirality : 0.043 0.176 1708 Planarity : 0.003 0.026 1674 Dihedral : 19.826 86.664 4234 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.20 % Allowed : 2.66 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.21), residues: 1130 helix: -1.14 (0.20), residues: 494 sheet: -1.04 (0.35), residues: 192 loop : -1.93 (0.25), residues: 444 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 220 time to evaluate : 1.241 Fit side-chains TARDY: cannot create tardy model for: "GLU A 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 2 residues processed: 220 average time/residue: 1.4850 time to fit residues: 348.3831 Evaluate side-chains 158 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 1.171 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2215 time to fit residues: 2.2595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 0.0870 chunk 48 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.0050 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 67 optimal weight: 0.2980 chunk 105 optimal weight: 3.9990 overall best weight: 0.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN C 221 GLN ** G 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 HIS G 214 GLN G 222 ASN H 164 GLN I 221 GLN ** I 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 11160 Z= 0.275 Angle : 0.863 14.455 15374 Z= 0.451 Chirality : 0.053 0.415 1708 Planarity : 0.009 0.149 1674 Dihedral : 22.491 61.456 1978 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.31 % Favored : 94.07 % Rotamer: Outliers : 3.48 % Allowed : 10.63 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.22), residues: 1130 helix: -1.32 (0.21), residues: 492 sheet: -1.07 (0.33), residues: 194 loop : -2.08 (0.27), residues: 444 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 168 time to evaluate : 1.163 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 34 outliers final: 7 residues processed: 182 average time/residue: 1.2589 time to fit residues: 247.4459 Evaluate side-chains 152 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 145 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.1828 time to fit residues: 2.6154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 9.9990 chunk 32 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN G 216 GLN H 164 GLN H 221 GLN I 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11160 Z= 0.209 Angle : 0.557 11.784 15374 Z= 0.286 Chirality : 0.041 0.143 1708 Planarity : 0.003 0.050 1674 Dihedral : 22.221 60.716 1978 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.37 % Allowed : 13.19 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.13 (0.23), residues: 1130 helix: 0.05 (0.22), residues: 488 sheet: -0.46 (0.34), residues: 194 loop : -1.70 (0.27), residues: 448 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 155 time to evaluate : 1.106 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 33 outliers final: 15 residues processed: 170 average time/residue: 1.2487 time to fit residues: 229.3101 Evaluate side-chains 163 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 7 residues processed: 9 average time/residue: 0.2856 time to fit residues: 4.8533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN H 117 ASN H 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11160 Z= 0.167 Angle : 0.532 11.626 15374 Z= 0.270 Chirality : 0.040 0.143 1708 Planarity : 0.003 0.036 1674 Dihedral : 22.046 59.941 1978 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.66 % Allowed : 14.72 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.37 (0.24), residues: 1130 helix: 0.76 (0.23), residues: 492 sheet: -0.09 (0.35), residues: 194 loop : -1.43 (0.28), residues: 444 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 152 time to evaluate : 1.261 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 26 outliers final: 15 residues processed: 163 average time/residue: 1.2187 time to fit residues: 215.5825 Evaluate side-chains 159 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 1.153 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 7 residues processed: 9 average time/residue: 0.1444 time to fit residues: 3.7734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN G 214 GLN H 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11160 Z= 0.238 Angle : 0.546 11.696 15374 Z= 0.279 Chirality : 0.041 0.143 1708 Planarity : 0.003 0.039 1674 Dihedral : 22.156 60.184 1978 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.97 % Allowed : 16.16 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.17 (0.24), residues: 1130 helix: 0.92 (0.23), residues: 492 sheet: 0.01 (0.35), residues: 194 loop : -1.31 (0.27), residues: 444 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 148 time to evaluate : 1.292 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 29 outliers final: 17 residues processed: 162 average time/residue: 1.2298 time to fit residues: 215.7372 Evaluate side-chains 162 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 1.207 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 8 residues processed: 9 average time/residue: 0.4881 time to fit residues: 6.6177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN C 221 GLN H 117 ASN H 221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 11160 Z= 0.290 Angle : 0.566 11.759 15374 Z= 0.291 Chirality : 0.042 0.142 1708 Planarity : 0.003 0.041 1674 Dihedral : 22.276 61.553 1978 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.66 % Allowed : 17.38 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.24), residues: 1130 helix: 1.01 (0.23), residues: 488 sheet: 0.06 (0.34), residues: 194 loop : -1.24 (0.27), residues: 448 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 149 time to evaluate : 1.084 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 26 outliers final: 13 residues processed: 163 average time/residue: 1.3144 time to fit residues: 231.0772 Evaluate side-chains 158 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 1.142 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.1259 time to fit residues: 2.6204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 0.0970 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN C 221 GLN H 117 ASN H 221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11160 Z= 0.176 Angle : 0.536 11.662 15374 Z= 0.273 Chirality : 0.040 0.143 1708 Planarity : 0.003 0.039 1674 Dihedral : 22.095 59.669 1978 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.45 % Allowed : 18.00 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.24 (0.24), residues: 1130 helix: 1.28 (0.23), residues: 490 sheet: 0.19 (0.34), residues: 194 loop : -1.10 (0.28), residues: 446 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 145 time to evaluate : 1.088 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 24 outliers final: 16 residues processed: 158 average time/residue: 1.3226 time to fit residues: 225.4207 Evaluate side-chains 162 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 146 time to evaluate : 1.029 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 8 residues processed: 8 average time/residue: 0.2789 time to fit residues: 4.4416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN C 221 GLN H 117 ASN H 221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11160 Z= 0.202 Angle : 0.537 11.654 15374 Z= 0.275 Chirality : 0.041 0.142 1708 Planarity : 0.003 0.038 1674 Dihedral : 22.068 59.811 1978 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.84 % Allowed : 18.40 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.29 (0.24), residues: 1130 helix: 1.30 (0.23), residues: 492 sheet: 0.25 (0.35), residues: 194 loop : -1.08 (0.28), residues: 444 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 1.329 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 18 outliers final: 12 residues processed: 155 average time/residue: 1.2540 time to fit residues: 210.0070 Evaluate side-chains 153 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 141 time to evaluate : 1.149 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.1881 time to fit residues: 2.3861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 117 ASN H 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11160 Z= 0.190 Angle : 0.530 11.623 15374 Z= 0.271 Chirality : 0.040 0.142 1708 Planarity : 0.003 0.037 1674 Dihedral : 22.020 59.962 1978 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.84 % Allowed : 18.51 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.38 (0.24), residues: 1130 helix: 1.37 (0.23), residues: 492 sheet: 0.31 (0.35), residues: 194 loop : -1.02 (0.28), residues: 444 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 1.185 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 18 outliers final: 14 residues processed: 153 average time/residue: 1.3121 time to fit residues: 216.5062 Evaluate side-chains 153 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 1.068 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 4 average time/residue: 0.1229 time to fit residues: 2.1984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.0070 chunk 76 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 117 ASN H 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11160 Z= 0.173 Angle : 0.530 11.597 15374 Z= 0.271 Chirality : 0.040 0.142 1708 Planarity : 0.003 0.038 1674 Dihedral : 21.947 59.865 1978 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.74 % Allowed : 18.51 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.48 (0.24), residues: 1130 helix: 1.44 (0.23), residues: 492 sheet: 0.40 (0.35), residues: 194 loop : -0.98 (0.28), residues: 444 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 1.185 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 17 outliers final: 13 residues processed: 155 average time/residue: 1.3156 time to fit residues: 220.5563 Evaluate side-chains 156 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 143 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.1574 time to fit residues: 2.4505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 80 optimal weight: 0.0770 chunk 5 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN C 221 GLN H 117 ASN H 221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.137116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.101261 restraints weight = 17971.882| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.90 r_work: 0.2989 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11160 Z= 0.156 Angle : 0.525 11.561 15374 Z= 0.268 Chirality : 0.040 0.142 1708 Planarity : 0.003 0.038 1674 Dihedral : 21.870 59.971 1978 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.74 % Allowed : 18.92 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.60 (0.25), residues: 1130 helix: 1.55 (0.23), residues: 490 sheet: 0.50 (0.35), residues: 194 loop : -0.94 (0.28), residues: 446 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4335.10 seconds wall clock time: 77 minutes 51.16 seconds (4671.16 seconds total)