Starting phenix.real_space_refine on Sat Dec 9 17:03:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/12_2023/6puz_20485_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/12_2023/6puz_20485.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/12_2023/6puz_20485_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/12_2023/6puz_20485_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/12_2023/6puz_20485_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/12_2023/6puz_20485.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/12_2023/6puz_20485.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/12_2023/6puz_20485_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/12_2023/6puz_20485_updated.pdb" } resolution = 2.8 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= -0.007 sd= 1.021 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 36 5.16 5 C 7020 2.51 5 N 2044 2.21 5 O 2518 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 3": "OD1" <-> "OD2" Residue "A GLU 13": "OE1" <-> "OE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B ASP 41": "OD1" <-> "OD2" Residue "B TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 167": "OD1" <-> "OD2" Residue "B ASP 202": "OD1" <-> "OD2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 253": "OD1" <-> "OD2" Residue "B ASP 270": "OD1" <-> "OD2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C ASP 253": "OD1" <-> "OD2" Residue "C ASP 270": "OD1" <-> "OD2" Residue "D TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 229": "OD1" <-> "OD2" Residue "D ASP 232": "OD1" <-> "OD2" Residue "G ASP 3": "OD1" <-> "OD2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "G ARG 20": "NH1" <-> "NH2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G GLU 69": "OE1" <-> "OE2" Residue "G GLU 157": "OE1" <-> "OE2" Residue "G TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 246": "OE1" <-> "OE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H ASP 25": "OD1" <-> "OD2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H ASP 41": "OD1" <-> "OD2" Residue "H TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 167": "OD1" <-> "OD2" Residue "H ASP 202": "OD1" <-> "OD2" Residue "H GLU 212": "OE1" <-> "OE2" Residue "H TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 253": "OD1" <-> "OD2" Residue "H ASP 270": "OD1" <-> "OD2" Residue "I ASP 229": "OD1" <-> "OD2" Residue "I ASP 253": "OD1" <-> "OD2" Residue "I ASP 270": "OD1" <-> "OD2" Residue "J TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 229": "OD1" <-> "OD2" Residue "J ASP 232": "OD1" <-> "OD2" 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: 11702 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2052 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 9, 'TRANS': 252} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Chain: "B" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1901 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 7, 'TRANS': 232} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 534 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "D" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 399 Classifications: {'peptide': 48} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 44} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 39 Unusual residues: {' MG': 2, ' ZN': 1, 'XXJ': 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "G" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2052 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 9, 'TRANS': 252} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Chain: "H" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1901 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 7, 'TRANS': 232} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 534 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "J" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 399 Classifications: {'peptide': 48} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 44} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 39 Unusual residues: {' MG': 2, ' ZN': 1, 'XXJ': 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "J" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "L" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 317 SG CYS A 40 26.691 45.365 55.574 1.00 11.56 S ATOM 338 SG CYS A 43 30.143 46.397 54.077 1.00 5.74 S ATOM 2351 SG CYS B 40 49.793 121.387 26.507 1.00 87.46 S ATOM 2374 SG CYS B 43 48.405 120.462 30.308 1.00 90.05 S ATOM 6168 SG CYS G 40 64.949 87.355 55.574 1.00 11.56 S ATOM 6189 SG CYS G 43 61.497 86.323 54.077 1.00 5.74 S ATOM 8202 SG CYS H 40 41.847 11.333 26.507 1.00 87.46 S ATOM 8225 SG CYS H 43 43.235 12.258 30.308 1.00 90.05 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A DA F 21 " occ=0.40 ... (40 atoms not shown) pdb=" C4 B DA F 21 " occ=0.60 residue: pdb=" P A DA L 21 " occ=0.40 ... (40 atoms not shown) pdb=" C4 B DA L 21 " occ=0.60 Time building chain proxies: 6.92, per 1000 atoms: 0.59 Number of scatterers: 11702 At special positions: 0 Unit cell: (92.43, 133.51, 86.9, 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 36 16.00 P 72 15.00 Mg 4 11.99 F 4 9.00 O 2518 8.00 N 2044 7.00 C 7020 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: 4.98 Conformation dependent library (CDL) restraints added in 2.0 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 40 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 43 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 12 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 40 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 43 " 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 40 " pdb="ZN ZN G 303 " - pdb=" SG CYS G 43 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS H 12 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 40 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 43 " Number of angles added : 2 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2276 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 20 sheets defined 39.5% alpha, 20.5% beta 30 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 5.64 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 removed outlier: 3.797A pdb=" N ASP A 6 " --> pdb=" O LEU A 2 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 31 through 39 Processing helix chain 'A' and resid 94 through 107 removed outlier: 3.613A 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: 5.497A pdb=" N VAL A 150 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 4.219A 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 218 Processing helix chain 'B' and resid 5 through 15 WARNING: missing atoms! Processing helix chain 'B' and resid 19 through 25 Processing helix chain 'B' and resid 30 through 39 Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 94 through 107 Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 151 through 168 removed outlier: 5.338A pdb=" N ASP B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) removed outlier: 5.773A 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: 3.685A pdb=" N ILE B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 222 removed outlier: 3.614A pdb=" N ASN C 222 " --> pdb=" O THR C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' 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: 3.797A pdb=" N ASP G 6 " --> pdb=" O LEU G 2 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'G' and resid 19 through 25 Processing helix chain 'G' and resid 31 through 39 Processing helix chain 'G' and resid 94 through 107 removed outlier: 3.613A 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: 5.497A pdb=" N VAL G 150 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 4.219A 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 218 Processing helix chain 'H' and resid 5 through 15 WARNING: missing atoms! Processing helix chain 'H' and resid 19 through 25 Processing helix chain 'H' and resid 30 through 39 Processing helix chain 'H' and resid 41 through 43 No H-bonds generated for 'chain 'H' and resid 41 through 43' Processing helix chain 'H' and resid 94 through 107 Processing helix chain 'H' and resid 124 through 133 Processing helix chain 'H' and resid 151 through 168 removed outlier: 5.338A pdb=" N ASP H 167 " --> pdb=" O GLY H 163 " (cutoff:3.500A) removed outlier: 5.773A 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: 3.685A pdb=" N ILE H 220 " --> pdb=" O GLN H 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 222 removed outlier: 3.614A pdb=" N ASN I 222 " --> pdb=" O THR I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 262 through 264 No H-bonds generated for 'chain 'I' and resid 262 through 264' 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 86 through 89 removed outlier: 4.222A pdb=" N VAL A 72 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR A 112 " --> pdb=" O TRP A 61 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU A 63 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N HIS A 114 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N CYS A 65 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LYS A 136 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N THR A 115 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU A 138 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 224 through 227 Processing sheet with id= C, first strand: chain 'A' and resid 256 through 261 removed outlier: 6.536A pdb=" N GLN A 252 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N LEU A 241 " --> pdb=" O GLN A 252 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 84 through 89 removed outlier: 4.274A pdb=" N VAL B 72 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N THR B 112 " --> pdb=" O TRP B 61 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU B 63 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N HIS B 114 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N CYS B 65 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LYS B 136 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 223 through 227 Processing sheet with id= F, first strand: chain 'B' and resid 256 through 261 removed outlier: 6.234A pdb=" N GLN B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LEU B 241 " --> pdb=" O GLN B 252 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 224 through 227 Processing sheet with id= H, first strand: chain 'C' and resid 256 through 261 removed outlier: 6.177A pdb=" N GLN C 252 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU C 241 " --> pdb=" O GLN C 252 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 224 through 227 Processing sheet with id= J, first strand: chain 'D' and resid 256 through 261 removed outlier: 6.653A pdb=" N GLN D 252 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU D 241 " --> pdb=" O GLN D 252 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 86 through 89 removed outlier: 4.222A pdb=" N VAL G 72 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR G 112 " --> pdb=" O TRP G 61 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU G 63 " --> pdb=" O THR G 112 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N HIS G 114 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N CYS G 65 " --> pdb=" O HIS G 114 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LYS G 136 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N THR G 115 " --> pdb=" O LYS G 136 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU G 138 " --> pdb=" O THR G 115 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 224 through 227 Processing sheet with id= M, first strand: chain 'G' and resid 256 through 261 removed outlier: 6.536A pdb=" N GLN G 252 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N LEU G 241 " --> pdb=" O GLN G 252 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 84 through 89 removed outlier: 4.274A pdb=" N VAL H 72 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N THR H 112 " --> pdb=" O TRP H 61 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU H 63 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N HIS H 114 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N CYS H 65 " --> pdb=" O HIS H 114 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LYS H 136 " --> pdb=" O VAL H 113 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 223 through 227 Processing sheet with id= P, first strand: chain 'H' and resid 256 through 261 removed outlier: 6.234A pdb=" N GLN H 252 " --> pdb=" O LEU H 241 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LEU H 241 " --> pdb=" O GLN H 252 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 224 through 227 Processing sheet with id= R, first strand: chain 'I' and resid 256 through 261 removed outlier: 6.177A pdb=" N GLN I 252 " --> pdb=" O LEU I 241 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU I 241 " --> pdb=" O GLN I 252 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 224 through 227 Processing sheet with id= T, first strand: chain 'J' and resid 256 through 261 removed outlier: 6.653A pdb=" N GLN J 252 " --> pdb=" O LEU J 241 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU J 241 " --> pdb=" O GLN J 252 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1194 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: 4.06 Time building geometry restraints manager: 5.18 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: 1698 1.31 - 1.43: 3432 1.43 - 1.56: 6418 1.56 - 1.69: 136 1.69 - 1.81: 54 Bond restraints: 11738 Sorted by residual: bond pdb=" O3' DC L 20 " pdb=" P B DA L 21 " ideal model delta sigma weight residual 1.607 1.421 0.186 1.50e-02 4.44e+03 1.54e+02 bond pdb=" O3' DC F 20 " pdb=" P B DA F 21 " ideal model delta sigma weight residual 1.607 1.421 0.186 1.50e-02 4.44e+03 1.54e+02 bond pdb=" C ASP G 116 " pdb=" N ASN G 117 " ideal model delta sigma weight residual 1.334 1.270 0.064 1.24e-02 6.50e+03 2.67e+01 bond pdb=" C ASP A 116 " pdb=" N ASN A 117 " ideal model delta sigma weight residual 1.334 1.270 0.064 1.24e-02 6.50e+03 2.67e+01 bond pdb=" O3' DG F 19 " pdb=" P DC F 20 " ideal model delta sigma weight residual 1.607 1.540 0.067 1.50e-02 4.44e+03 2.01e+01 ... (remaining 11733 not shown) Histogram of bond angle deviations from ideal: 97.41 - 104.73: 428 104.73 - 112.05: 5844 112.05 - 119.37: 4048 119.37 - 126.69: 5390 126.69 - 134.01: 430 Bond angle restraints: 16140 Sorted by residual: angle pdb=" O LYS A 127 " pdb=" C LYS A 127 " pdb=" N ALA A 128 " ideal model delta sigma weight residual 122.15 115.50 6.65 1.14e+00 7.69e-01 3.40e+01 angle pdb=" O LYS G 127 " pdb=" C LYS G 127 " pdb=" N ALA G 128 " ideal model delta sigma weight residual 122.15 115.50 6.65 1.14e+00 7.69e-01 3.40e+01 angle pdb=" C LYS A 127 " pdb=" N ALA A 128 " pdb=" CA ALA A 128 " ideal model delta sigma weight residual 120.29 128.30 -8.01 1.42e+00 4.96e-01 3.19e+01 angle pdb=" C LYS G 127 " pdb=" N ALA G 128 " pdb=" CA ALA G 128 " ideal model delta sigma weight residual 120.29 128.30 -8.01 1.42e+00 4.96e-01 3.19e+01 angle pdb=" N SER A 123 " pdb=" CA SER A 123 " pdb=" C SER A 123 " ideal model delta sigma weight residual 110.41 117.14 -6.73 1.23e+00 6.61e-01 3.00e+01 ... (remaining 16135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.69: 6324 32.69 - 65.37: 486 65.37 - 98.06: 26 98.06 - 130.75: 0 130.75 - 163.43: 2 Dihedral angle restraints: 6838 sinusoidal: 3312 harmonic: 3526 Sorted by residual: 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 -155.53 -24.47 0 5.00e+00 4.00e-02 2.40e+01 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 -155.53 -24.47 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA TYR I 271 " pdb=" C TYR I 271 " pdb=" N GLY I 272 " pdb=" CA GLY I 272 " ideal model delta harmonic sigma weight residual 180.00 155.70 24.30 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 6835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 958 0.037 - 0.074: 518 0.074 - 0.111: 204 0.111 - 0.149: 62 0.149 - 0.186: 22 Chirality restraints: 1764 Sorted by residual: chirality pdb=" CB ILE G 60 " pdb=" CA ILE G 60 " pdb=" CG1 ILE G 60 " pdb=" CG2 ILE G 60 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CB ILE A 60 " pdb=" CA ILE A 60 " pdb=" CG1 ILE A 60 " pdb=" CG2 ILE A 60 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CA ILE A 268 " pdb=" N ILE A 268 " pdb=" C ILE A 268 " pdb=" CB ILE A 268 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.13e-01 ... (remaining 1761 not shown) Planarity restraints: 1768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU G 158 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.03e+00 pdb=" C LEU G 158 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU G 158 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS G 159 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 158 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.03e+00 pdb=" C LEU A 158 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU A 158 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS A 159 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 156 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.77e+00 pdb=" C LYS A 156 " -0.048 2.00e-02 2.50e+03 pdb=" O LYS A 156 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU A 157 " 0.016 2.00e-02 2.50e+03 ... (remaining 1765 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 6 0.98 - 1.96: 2 1.96 - 2.94: 4750 2.94 - 3.92: 32416 3.92 - 4.90: 64492 Warning: very small nonbonded interaction distances. Nonbonded interactions: 101666 Sorted by model distance: nonbonded pdb=" O HOH A 457 " pdb=" O HOH K 113 " model vdw 0.000 2.440 nonbonded pdb=" O HOH A 469 " pdb=" O HOH K 114 " model vdw 0.000 2.440 nonbonded pdb=" O HOH E 114 " pdb=" O HOH G 469 " model vdw 0.000 2.440 nonbonded pdb=" O HOH E 113 " pdb=" O HOH G 457 " model vdw 0.000 2.440 nonbonded pdb=" O HOH A 491 " pdb=" O HOH G 476 " model vdw 0.006 2.440 ... (remaining 101661 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 3 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 44 \ or resid 57 through 139 or resid 150 through 269)) selection = (chain 'B' and (resid 3 through 9 or (resid 10 and (name N or name CA or name C \ or name CB or name CG or name CD or name OE1 or name OE2)) or resid 11 through 2 \ 8 or (resid 29 and (name N or name CA or name C or name CB or name CG or name CD \ )) or resid 30 through 41 or (resid 42 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 43 and (name N or n \ ame CA or name C or name CB or name SG )) or resid 44 through 66 or (resid 67 an \ d (name N or name CA or name C or name CB or name CG or name ND1 or name CD2 or \ name CE1 or name NE2)) or resid 68 through 77 or (resid 78 and (name N or name C \ A or name C or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2)) or resid 79 through 80 or (resid 81 and (name N or name CA or name C or name \ CB or name OG )) or resid 82 through 83 or (resid 84 and (name N or name CA or \ name C or name CB or name CG1 or name CG2 or name CD1)) or resid 85 through 228 \ or resid 236 through 269)) selection = (chain 'G' and (resid 3 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 44 \ or resid 57 through 139 or resid 150 through 269)) selection = (chain 'H' and (resid 3 through 9 or (resid 10 and (name N or name CA or name C \ or name CB or name CG or name CD or name OE1 or name OE2)) or resid 11 through 2 \ 8 or (resid 29 and (name N or name CA or name C or name CB or name CG or name CD \ )) or resid 30 through 41 or (resid 42 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 43 and (name N or n \ ame CA or name C or name CB or name SG )) or resid 44 through 66 or (resid 67 an \ d (name N or name CA or name C or name CB or name CG or name ND1 or name CD2 or \ name CE1 or name NE2)) or resid 68 through 77 or (resid 78 and (name N or name C \ A or name C or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2)) or resid 79 through 80 or (resid 81 and (name N or name CA or name C or name \ CB or name OG )) or resid 82 through 83 or (resid 84 and (name N or name CA or \ name C or name CB or name CG1 or name CG2 or name CD1)) or resid 85 through 228 \ or resid 236 through 269)) } 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: 3.020 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: 12.750 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 39.610 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.070 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:10.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 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 : 0.008 0.186 11738 Z= 0.461 Angle : 0.856 9.784 16140 Z= 0.512 Chirality : 0.054 0.186 1764 Planarity : 0.007 0.053 1768 Dihedral : 19.789 163.433 4562 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.19 % Allowed : 3.09 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.21), residues: 1198 helix: -2.09 (0.17), residues: 488 sheet: -0.71 (0.29), residues: 292 loop : -1.87 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 132 HIS 0.005 0.001 HIS B 12 PHE 0.014 0.003 PHE G 185 TYR 0.015 0.002 TYR H 83 ARG 0.007 0.000 ARG G 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 254 time to evaluate : 1.238 Fit side-chains TARDY: cannot create tardy model for: "GLU A 10 " (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 10 " (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: 254 average time/residue: 1.4564 time to fit residues: 395.8176 Evaluate side-chains 204 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 1.217 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2346 time to fit residues: 2.2926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 63 optimal weight: 0.0070 chunk 50 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 HIS B 164 GLN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 GLN G 27 ASN ** G 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS H 16 HIS H 164 GLN ** H 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 221 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 11738 Z= 0.368 Angle : 1.023 35.056 16140 Z= 0.543 Chirality : 0.056 0.488 1764 Planarity : 0.010 0.095 1768 Dihedral : 22.820 167.140 2138 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.17 % Favored : 96.74 % Rotamer: Outliers : 3.97 % Allowed : 13.06 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.49 (0.21), residues: 1198 helix: -1.66 (0.19), residues: 492 sheet: -0.84 (0.29), residues: 292 loop : -1.95 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.005 TRP H 243 HIS 0.066 0.005 HIS G 171 PHE 0.092 0.005 PHE H 223 TYR 0.135 0.005 TYR J 227 ARG 0.052 0.001 ARG I 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 208 time to evaluate : 1.474 Fit side-chains TARDY: cannot create tardy model for: "GLU A 10 " (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 10 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 41 outliers final: 10 residues processed: 223 average time/residue: 1.3409 time to fit residues: 322.2782 Evaluate side-chains 203 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 193 time to evaluate : 1.368 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 4 residues processed: 7 average time/residue: 1.0766 time to fit residues: 9.9520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 38 optimal weight: 0.0270 chunk 90 optimal weight: 7.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 168 GLN B 216 GLN C 221 GLN G 252 GLN H 216 GLN I 221 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11738 Z= 0.211 Angle : 0.507 5.717 16140 Z= 0.287 Chirality : 0.042 0.130 1764 Planarity : 0.004 0.046 1768 Dihedral : 22.423 164.676 2138 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.90 % Allowed : 14.89 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.23), residues: 1198 helix: -0.05 (0.21), residues: 490 sheet: -0.23 (0.30), residues: 280 loop : -1.44 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 132 HIS 0.005 0.001 HIS G 183 PHE 0.012 0.002 PHE H 26 TYR 0.013 0.001 TYR B 99 ARG 0.002 0.000 ARG J 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 212 time to evaluate : 1.234 Fit side-chains TARDY: cannot create tardy model for: "GLU A 10 " (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 10 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 30 outliers final: 7 residues processed: 220 average time/residue: 1.2329 time to fit residues: 293.4605 Evaluate side-chains 199 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 192 time to evaluate : 1.260 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.8710 time to fit residues: 5.5851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 0.0370 chunk 32 optimal weight: 5.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 GLN C 221 GLN H 216 GLN I 221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11738 Z= 0.188 Angle : 0.481 5.690 16140 Z= 0.273 Chirality : 0.041 0.141 1764 Planarity : 0.004 0.043 1768 Dihedral : 22.317 158.466 2138 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.42 % Allowed : 16.34 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1198 helix: 0.63 (0.22), residues: 494 sheet: 0.07 (0.31), residues: 282 loop : -1.11 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 132 HIS 0.003 0.001 HIS G 183 PHE 0.008 0.001 PHE G 100 TYR 0.016 0.001 TYR A 83 ARG 0.003 0.000 ARG H 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 204 time to evaluate : 1.356 Fit side-chains TARDY: cannot create tardy model for: "GLU A 10 " (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 10 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 25 outliers final: 8 residues processed: 210 average time/residue: 1.2558 time to fit residues: 285.5541 Evaluate side-chains 195 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 187 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.8344 time to fit residues: 5.3426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 216 GLN C 221 GLN G 171 HIS G 252 GLN H 155 ASN H 164 GLN H 216 GLN I 221 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 11738 Z= 0.405 Angle : 0.573 6.033 16140 Z= 0.321 Chirality : 0.046 0.143 1764 Planarity : 0.004 0.042 1768 Dihedral : 22.556 154.275 2138 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.93 % Allowed : 17.31 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.24), residues: 1198 helix: 0.68 (0.22), residues: 490 sheet: -0.04 (0.30), residues: 294 loop : -0.93 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 132 HIS 0.004 0.001 HIS G 16 PHE 0.013 0.002 PHE H 185 TYR 0.014 0.002 TYR A 83 ARG 0.003 0.000 ARG G 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 185 time to evaluate : 1.210 Fit side-chains TARDY: cannot create tardy model for: "GLU A 10 " (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 10 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 20 outliers final: 12 residues processed: 192 average time/residue: 1.1919 time to fit residues: 249.0520 Evaluate side-chains 191 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 179 time to evaluate : 1.192 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 5 residues processed: 7 average time/residue: 0.5054 time to fit residues: 5.8858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 2.9990 chunk 107 optimal weight: 0.0770 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN B 155 ASN B 216 GLN C 221 GLN H 155 ASN H 216 GLN I 221 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11738 Z= 0.176 Angle : 0.479 5.840 16140 Z= 0.271 Chirality : 0.041 0.143 1764 Planarity : 0.004 0.038 1768 Dihedral : 22.324 151.951 2138 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.64 % Allowed : 18.18 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.24), residues: 1198 helix: 1.01 (0.23), residues: 490 sheet: 0.15 (0.30), residues: 294 loop : -0.83 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 132 HIS 0.003 0.001 HIS G 183 PHE 0.010 0.001 PHE G 100 TYR 0.016 0.001 TYR A 83 ARG 0.002 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 190 time to evaluate : 1.264 Fit side-chains TARDY: cannot create tardy model for: "GLU A 10 " (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 10 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 17 outliers final: 9 residues processed: 201 average time/residue: 1.1845 time to fit residues: 259.6060 Evaluate side-chains 192 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 183 time to evaluate : 1.292 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 5 average time/residue: 0.7453 time to fit residues: 5.9045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 0.0980 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN B 216 GLN B 252 GLN C 221 GLN ** G 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 HIS H 164 GLN H 216 GLN I 221 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11738 Z= 0.180 Angle : 0.468 5.853 16140 Z= 0.264 Chirality : 0.041 0.135 1764 Planarity : 0.003 0.037 1768 Dihedral : 22.167 145.654 2138 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.45 % Allowed : 18.67 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.24), residues: 1198 helix: 1.16 (0.23), residues: 492 sheet: 0.37 (0.31), residues: 290 loop : -0.80 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 132 HIS 0.005 0.001 HIS B 171 PHE 0.009 0.001 PHE G 100 TYR 0.018 0.001 TYR A 83 ARG 0.001 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 194 time to evaluate : 1.845 Fit side-chains TARDY: cannot create tardy model for: "GLU A 10 " (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 10 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 15 outliers final: 5 residues processed: 202 average time/residue: 1.1853 time to fit residues: 260.9419 Evaluate side-chains 193 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 188 time to evaluate : 1.219 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.2392 time to fit residues: 1.9688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 216 GLN ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 GLN H 155 ASN H 164 GLN H 216 GLN I 221 GLN J 222 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11738 Z= 0.225 Angle : 0.486 5.960 16140 Z= 0.273 Chirality : 0.042 0.133 1764 Planarity : 0.004 0.037 1768 Dihedral : 22.175 140.982 2138 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.55 % Allowed : 19.15 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1198 helix: 1.13 (0.23), residues: 492 sheet: 0.47 (0.31), residues: 290 loop : -0.75 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 131 HIS 0.005 0.001 HIS H 171 PHE 0.009 0.001 PHE G 100 TYR 0.015 0.001 TYR A 83 ARG 0.001 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 186 time to evaluate : 1.163 Fit side-chains TARDY: cannot create tardy model for: "GLU A 10 " (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 10 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 16 outliers final: 9 residues processed: 191 average time/residue: 1.2840 time to fit residues: 267.3284 Evaluate side-chains 188 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 179 time to evaluate : 1.273 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 5 average time/residue: 0.4843 time to fit residues: 4.5923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 3.9990 chunk 104 optimal weight: 0.3980 chunk 111 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 GLN B 252 GLN C 221 GLN ** G 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 164 GLN H 216 GLN I 221 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11738 Z= 0.175 Angle : 0.465 5.985 16140 Z= 0.262 Chirality : 0.041 0.130 1764 Planarity : 0.003 0.037 1768 Dihedral : 21.977 133.699 2138 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.77 % Allowed : 19.83 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1198 helix: 1.25 (0.23), residues: 490 sheet: 0.58 (0.31), residues: 290 loop : -0.71 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 131 HIS 0.003 0.001 HIS G 183 PHE 0.009 0.001 PHE G 100 TYR 0.019 0.001 TYR A 83 ARG 0.001 0.000 ARG I 269 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 184 time to evaluate : 1.278 Fit side-chains TARDY: cannot create tardy model for: "GLU A 10 " (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 10 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 8 outliers final: 3 residues processed: 187 average time/residue: 1.1864 time to fit residues: 242.9199 Evaluate side-chains 186 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 183 time to evaluate : 1.311 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 1.7722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 4.9990 chunk 71 optimal weight: 0.0870 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 0.4980 chunk 123 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 0.0970 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 GLN B 252 GLN C 221 GLN ** G 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 216 GLN I 221 GLN J 222 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11738 Z= 0.148 Angle : 0.449 5.904 16140 Z= 0.252 Chirality : 0.040 0.126 1764 Planarity : 0.003 0.036 1768 Dihedral : 21.680 119.250 2138 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.87 % Allowed : 19.73 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1198 helix: 1.35 (0.23), residues: 492 sheet: 0.74 (0.31), residues: 290 loop : -0.65 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 131 HIS 0.003 0.001 HIS G 183 PHE 0.009 0.001 PHE G 100 TYR 0.019 0.001 TYR A 83 ARG 0.001 0.000 ARG B 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 190 time to evaluate : 1.691 Fit side-chains TARDY: cannot create tardy model for: "GLU A 10 " (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 10 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 9 outliers final: 4 residues processed: 193 average time/residue: 1.2743 time to fit residues: 267.5889 Evaluate side-chains 188 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 184 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.2253 time to fit residues: 1.9124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 0.0270 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 GLN C 221 GLN H 216 GLN I 221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.139669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.104418 restraints weight = 13163.818| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.51 r_work: 0.2982 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11738 Z= 0.255 Angle : 0.492 6.089 16140 Z= 0.275 Chirality : 0.043 0.129 1764 Planarity : 0.004 0.036 1768 Dihedral : 21.962 122.653 2138 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.87 % Allowed : 19.34 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1198 helix: 1.21 (0.23), residues: 494 sheet: 0.74 (0.31), residues: 290 loop : -0.66 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 131 HIS 0.003 0.001 HIS G 183 PHE 0.009 0.002 PHE H 185 TYR 0.017 0.001 TYR A 83 ARG 0.002 0.000 ARG C 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4965.55 seconds wall clock time: 88 minutes 37.45 seconds (5317.45 seconds total)