Starting phenix.real_space_refine on Sat Dec 9 13:09:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/12_2023/6puw_20483_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/12_2023/6puw_20483.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/12_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_20483/12_2023/6puw_20483_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/12_2023/6puw_20483_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/12_2023/6puw_20483.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/12_2023/6puw_20483.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/12_2023/6puw_20483_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/12_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-1.21rc1-5172/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: 6.75, per 1000 atoms: 0.61 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: 4.70 Conformation dependent library (CDL) restraints added in 1.8 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: 5.53 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: 4.16 Time building geometry restraints manager: 5.04 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: 5402 17.33 - 34.67: 596 34.67 - 52.00: 312 52.00 - 69.33: 152 69.33 - 86.66: 16 Dihedral angle restraints: 6478 sinusoidal: 3140 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 6475 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: 4.670 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: 0.010 Extract box with map and model: 13.420 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 39.920 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 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:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.120 ------------------------------------------------------------------------------- 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 : 20.009 86.664 4318 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 19 HIS 0.003 0.001 HIS B 183 PHE 0.008 0.001 PHE G 185 TYR 0.009 0.001 TYR A 194 ARG 0.002 0.000 ARG H 224 *********************** 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 : 1.302 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: 1.4893 time to fit residues: 349.3926 Evaluate side-chains 158 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 1.240 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2312 time to fit residues: 2.2407 ------------------------------------------------------------------------------- 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: 0.8637 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11160 Z= 0.266 Angle : 0.869 14.557 15374 Z= 0.455 Chirality : 0.053 0.381 1708 Planarity : 0.009 0.134 1674 Dihedral : 22.615 61.512 2062 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.62 % Allowed : 4.78 % Favored : 94.60 % Rotamer: Outliers : 3.58 % Allowed : 10.63 % Favored : 85.79 % 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: -2.44 (0.22), residues: 1130 helix: -1.30 (0.21), residues: 492 sheet: -1.09 (0.33), residues: 194 loop : -2.07 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.107 0.009 TRP G 61 HIS 0.040 0.004 HIS H 12 PHE 0.089 0.005 PHE G 26 TYR 0.118 0.007 TYR H 99 ARG 0.037 0.001 ARG I 269 *********************** 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 201 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 166 time to evaluate : 1.162 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: 35 outliers final: 7 residues processed: 181 average time/residue: 1.2698 time to fit residues: 248.5392 Evaluate side-chains 150 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 143 time to evaluate : 1.203 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.1851 time to fit residues: 2.4294 ------------------------------------------------------------------------------- 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: 10.0000 chunk 32 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 C 221 GLN G 216 GLN H 164 GLN H 221 GLN I 221 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11160 Z= 0.211 Angle : 0.556 11.797 15374 Z= 0.284 Chirality : 0.041 0.143 1708 Planarity : 0.003 0.050 1674 Dihedral : 22.325 60.796 2062 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.48 % Allowed : 13.50 % Favored : 83.03 % 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: -1.10 (0.23), residues: 1130 helix: 0.08 (0.22), residues: 490 sheet: -0.45 (0.34), residues: 194 loop : -1.70 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 19 HIS 0.003 0.001 HIS H 183 PHE 0.015 0.001 PHE G 121 TYR 0.012 0.001 TYR B 83 ARG 0.003 0.000 ARG G 199 *********************** 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 190 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 156 time to evaluate : 1.092 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: 13 residues processed: 172 average time/residue: 1.2966 time to fit residues: 240.6404 Evaluate side-chains 160 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 6 residues processed: 8 average time/residue: 0.3502 time to fit residues: 5.1971 ------------------------------------------------------------------------------- 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: 0.9990 chunk 79 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 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 C 221 GLN H 117 ASN H 221 GLN I 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11160 Z= 0.203 Angle : 0.543 11.683 15374 Z= 0.276 Chirality : 0.041 0.143 1708 Planarity : 0.003 0.034 1674 Dihedral : 22.226 60.072 2062 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 : 3.17 % Allowed : 14.42 % Favored : 82.41 % 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: -0.46 (0.24), residues: 1130 helix: 0.68 (0.23), residues: 492 sheet: -0.20 (0.34), residues: 194 loop : -1.43 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 19 HIS 0.003 0.001 HIS H 183 PHE 0.012 0.001 PHE G 121 TYR 0.012 0.001 TYR B 83 ARG 0.003 0.000 ARG G 199 *********************** 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 184 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 1.253 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: 31 outliers final: 15 residues processed: 168 average time/residue: 1.2425 time to fit residues: 225.9417 Evaluate side-chains 162 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 147 time to evaluate : 1.245 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 8 residues processed: 7 average time/residue: 0.1223 time to fit residues: 3.1700 ------------------------------------------------------------------------------- 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: 0.2980 chunk 1 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 G 214 GLN H 117 ASN H 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11160 Z= 0.240 Angle : 0.548 11.709 15374 Z= 0.280 Chirality : 0.041 0.142 1708 Planarity : 0.003 0.038 1674 Dihedral : 22.246 60.201 2062 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.97 % Allowed : 16.56 % Favored : 80.47 % 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: -0.20 (0.24), residues: 1130 helix: 0.90 (0.23), residues: 492 sheet: -0.05 (0.34), residues: 194 loop : -1.31 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 131 HIS 0.002 0.001 HIS B 12 PHE 0.013 0.001 PHE G 121 TYR 0.012 0.001 TYR B 83 ARG 0.002 0.000 ARG G 199 *********************** 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 175 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 146 time to evaluate : 1.147 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: 16 residues processed: 161 average time/residue: 1.3129 time to fit residues: 227.7685 Evaluate side-chains 162 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 146 time to evaluate : 1.260 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 10 residues processed: 7 average time/residue: 0.1266 time to fit residues: 3.1499 ------------------------------------------------------------------------------- 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: 0.6980 chunk 100 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 I 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 11160 Z= 0.430 Angle : 0.620 11.805 15374 Z= 0.320 Chirality : 0.045 0.143 1708 Planarity : 0.004 0.041 1674 Dihedral : 22.503 63.119 2062 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.17 % Allowed : 16.97 % Favored : 79.86 % 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: -0.26 (0.24), residues: 1130 helix: 0.80 (0.22), residues: 486 sheet: -0.08 (0.34), residues: 194 loop : -1.24 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP I 235 HIS 0.004 0.001 HIS B 171 PHE 0.018 0.002 PHE G 121 TYR 0.016 0.002 TYR A 194 ARG 0.003 0.000 ARG G 199 *********************** 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 182 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 151 time to evaluate : 1.324 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: 31 outliers final: 15 residues processed: 166 average time/residue: 1.2833 time to fit residues: 230.5017 Evaluate side-chains 157 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 1.192 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 5 average time/residue: 0.1159 time to fit residues: 2.6381 ------------------------------------------------------------------------------- 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: 0.9990 chunk 63 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 0.3980 chunk 62 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN H 117 ASN H 221 GLN I 221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1632 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= 0.181 Angle : 0.542 11.666 15374 Z= 0.278 Chirality : 0.040 0.151 1708 Planarity : 0.003 0.038 1674 Dihedral : 22.257 61.202 2062 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.66 % Allowed : 17.89 % Favored : 79.45 % 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: 0.07 (0.24), residues: 1130 helix: 1.20 (0.23), residues: 488 sheet: 0.05 (0.34), residues: 194 loop : -1.23 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 131 HIS 0.003 0.001 HIS G 171 PHE 0.009 0.001 PHE G 100 TYR 0.010 0.001 TYR B 83 ARG 0.001 0.000 ARG G 166 *********************** 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: 26 poor density : 143 time to evaluate : 1.226 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: 15 residues processed: 158 average time/residue: 1.2815 time to fit residues: 218.9096 Evaluate side-chains 157 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 1.282 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 6 average time/residue: 0.6457 time to fit residues: 6.1469 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.8691 moved from start: 0.1675 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= 0.199 Angle : 0.541 11.668 15374 Z= 0.277 Chirality : 0.041 0.142 1708 Planarity : 0.003 0.037 1674 Dihedral : 22.125 59.950 2062 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 : 2.04 % Allowed : 18.51 % Favored : 79.45 % 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: 0.23 (0.24), residues: 1130 helix: 1.33 (0.23), residues: 488 sheet: 0.17 (0.34), residues: 194 loop : -1.16 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 131 HIS 0.002 0.001 HIS G 12 PHE 0.013 0.001 PHE H 26 TYR 0.011 0.001 TYR B 83 ARG 0.001 0.000 ARG G 199 *********************** 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: 20 poor density : 141 time to evaluate : 1.257 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: 20 outliers final: 13 residues processed: 154 average time/residue: 1.3030 time to fit residues: 216.7476 Evaluate side-chains 151 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 1.206 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.5952 time to fit residues: 3.7327 ------------------------------------------------------------------------------- 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: 0.5980 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 0.1980 chunk 94 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.8671 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11160 Z= 0.173 Angle : 0.530 11.581 15374 Z= 0.272 Chirality : 0.040 0.142 1708 Planarity : 0.003 0.036 1674 Dihedral : 21.974 59.999 2062 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.04 % Allowed : 18.81 % Favored : 79.14 % 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: 0.41 (0.24), residues: 1130 helix: 1.41 (0.23), residues: 492 sheet: 0.33 (0.35), residues: 194 loop : -1.04 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 131 HIS 0.002 0.001 HIS B 183 PHE 0.015 0.001 PHE B 26 TYR 0.010 0.001 TYR B 83 ARG 0.001 0.000 ARG G 199 *********************** 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 167 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 1.130 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: 20 outliers final: 13 residues processed: 159 average time/residue: 1.2948 time to fit residues: 222.4823 Evaluate side-chains 155 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 1.183 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.5708 time to fit residues: 3.5589 ------------------------------------------------------------------------------- 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: 0.3980 chunk 76 optimal weight: 0.5980 chunk 115 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.8680 moved from start: 0.1832 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= 0.192 Angle : 0.534 11.621 15374 Z= 0.274 Chirality : 0.040 0.142 1708 Planarity : 0.003 0.037 1674 Dihedral : 21.969 59.828 2062 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.64 % Allowed : 19.22 % Favored : 79.14 % 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: 0.46 (0.24), residues: 1130 helix: 1.46 (0.23), residues: 488 sheet: 0.42 (0.35), residues: 194 loop : -1.03 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 131 HIS 0.002 0.001 HIS A 183 PHE 0.010 0.001 PHE H 26 TYR 0.011 0.001 TYR B 83 ARG 0.001 0.000 ARG G 199 ********************** 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 158 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 1.279 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: 16 outliers final: 11 residues processed: 154 average time/residue: 1.2766 time to fit residues: 212.2737 Evaluate side-chains 150 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.0979 time to fit residues: 1.6364 ------------------------------------------------------------------------------- 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: 0.9980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.134088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.098143 restraints weight = 17796.726| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.88 r_work: 0.2946 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11160 Z= 0.251 Angle : 0.555 11.696 15374 Z= 0.286 Chirality : 0.042 0.141 1708 Planarity : 0.003 0.037 1674 Dihedral : 22.101 61.333 2062 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.94 % Allowed : 19.33 % Favored : 78.73 % 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: 0.47 (0.24), residues: 1130 helix: 1.45 (0.23), residues: 482 sheet: 0.41 (0.35), residues: 194 loop : -0.95 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 131 HIS 0.002 0.001 HIS H 171 PHE 0.019 0.001 PHE B 26 TYR 0.012 0.001 TYR B 83 ARG 0.002 0.000 ARG G 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4340.96 seconds wall clock time: 77 minutes 53.67 seconds (4673.67 seconds total)