Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 6 00:29:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/10_2023/6puz_20485_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/10_2023/6puz_20485.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/10_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_20485/10_2023/6puz_20485_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/10_2023/6puz_20485_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/10_2023/6puz_20485.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/10_2023/6puz_20485.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/10_2023/6puz_20485_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/10_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-1.21rc1-5097/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: 6.73, per 1000 atoms: 0.58 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: 5.07 Conformation dependent library (CDL) restraints added in 1.6 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: 5.12 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: 4.25 Time building geometry restraints manager: 5.29 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: 6252 32.69 - 65.37: 474 65.37 - 98.06: 26 98.06 - 130.75: 0 130.75 - 163.43: 2 Dihedral angle restraints: 6754 sinusoidal: 3228 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 6751 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: 2.810 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: 12.600 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 39.070 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.490 ------------------------------------------------------------------------------- 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 : 19.702 163.433 4478 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 *********************** 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 : 1.115 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: 1.4141 time to fit residues: 384.1681 Evaluate side-chains 204 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 1.276 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2411 time to fit residues: 2.3645 ------------------------------------------------------------------------------- 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: 0.8677 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 11738 Z= 0.357 Angle : 0.993 35.065 16140 Z= 0.530 Chirality : 0.055 0.518 1764 Planarity : 0.010 0.100 1768 Dihedral : 22.787 167.388 2054 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 : 3.87 % Allowed : 13.06 % Favored : 83.08 % 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: -2.45 (0.21), residues: 1198 helix: -1.61 (0.19), residues: 490 sheet: -0.86 (0.29), residues: 292 loop : -1.93 (0.28), residues: 416 *********************** 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 248 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 208 time to evaluate : 1.284 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: 40 outliers final: 9 residues processed: 222 average time/residue: 1.3796 time to fit residues: 330.0101 Evaluate side-chains 200 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 191 time to evaluate : 1.218 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 3 residues processed: 6 average time/residue: 0.9493 time to fit residues: 7.9534 ------------------------------------------------------------------------------- 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: 0.8980 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 121 optimal weight: 0.2980 chunk 100 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 38 optimal weight: 0.0980 chunk 90 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 168 GLN H 216 GLN I 221 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1546 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 : 0.493 5.793 16140 Z= 0.280 Chirality : 0.041 0.125 1764 Planarity : 0.004 0.046 1768 Dihedral : 22.447 165.714 2054 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.32 % Allowed : 15.18 % Favored : 82.50 % 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: -0.93 (0.23), residues: 1198 helix: -0.02 (0.21), residues: 492 sheet: -0.20 (0.30), residues: 280 loop : -1.47 (0.29), residues: 426 *********************** 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 228 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 204 time to evaluate : 1.247 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: 24 outliers final: 6 residues processed: 211 average time/residue: 1.2969 time to fit residues: 295.5382 Evaluate side-chains 200 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 194 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 1.0338 time to fit residues: 4.8768 ------------------------------------------------------------------------------- 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: 0.6980 chunk 84 optimal weight: 0.0970 chunk 58 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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: 0.8652 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11738 Z= 0.157 Angle : 0.463 5.684 16140 Z= 0.262 Chirality : 0.041 0.145 1764 Planarity : 0.004 0.042 1768 Dihedral : 22.244 158.402 2054 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: -0.15 (0.24), residues: 1198 helix: 0.73 (0.22), residues: 494 sheet: 0.15 (0.31), residues: 282 loop : -1.17 (0.30), residues: 422 *********************** 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 227 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 202 time to evaluate : 1.185 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: 6 residues processed: 211 average time/residue: 1.2158 time to fit residues: 278.5430 Evaluate side-chains 197 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 191 time to evaluate : 1.301 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.1194 time to fit residues: 2.3206 ------------------------------------------------------------------------------- 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: 0.5980 chunk 49 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 G 171 HIS G 252 GLN H 164 GLN H 216 GLN I 221 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11738 Z= 0.254 Angle : 0.498 5.688 16140 Z= 0.280 Chirality : 0.043 0.130 1764 Planarity : 0.004 0.041 1768 Dihedral : 22.395 153.781 2054 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.13 % Allowed : 16.83 % Favored : 81.04 % 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: 0.07 (0.24), residues: 1198 helix: 0.92 (0.22), residues: 492 sheet: 0.13 (0.31), residues: 294 loop : -0.99 (0.32), residues: 412 *********************** 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 211 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 189 time to evaluate : 1.260 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: 22 outliers final: 9 residues processed: 198 average time/residue: 1.3042 time to fit residues: 280.8656 Evaluate side-chains 200 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 191 time to evaluate : 1.318 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.1087 time to fit residues: 2.3949 ------------------------------------------------------------------------------- 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: 1.9990 chunk 107 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 9 optimal weight: 0.0270 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 H 216 GLN I 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11738 Z= 0.164 Angle : 0.458 5.807 16140 Z= 0.259 Chirality : 0.041 0.138 1764 Planarity : 0.003 0.038 1768 Dihedral : 22.192 149.240 2054 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.55 % Allowed : 16.92 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1198 helix: 1.20 (0.23), residues: 490 sheet: 0.33 (0.31), residues: 290 loop : -0.90 (0.32), residues: 418 *********************** 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 211 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 195 time to evaluate : 1.168 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: 8 residues processed: 204 average time/residue: 1.3169 time to fit residues: 291.3823 Evaluate side-chains 188 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 180 time to evaluate : 1.343 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.9006 time to fit residues: 5.5660 ------------------------------------------------------------------------------- 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: 0.2980 chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 0.0040 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 171 HIS H 164 GLN H 216 GLN I 221 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11738 Z= 0.171 Angle : 0.461 5.797 16140 Z= 0.259 Chirality : 0.041 0.138 1764 Planarity : 0.003 0.036 1768 Dihedral : 22.104 143.784 2054 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.35 % Allowed : 17.79 % Favored : 80.85 % 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: 0.46 (0.25), residues: 1198 helix: 1.26 (0.23), residues: 490 sheet: 0.41 (0.31), residues: 290 loop : -0.84 (0.32), residues: 418 *********************** 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 195 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 181 time to evaluate : 1.197 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: 14 outliers final: 5 residues processed: 191 average time/residue: 1.1702 time to fit residues: 243.5604 Evaluate side-chains 184 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 179 time to evaluate : 1.243 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.1067 time to fit residues: 1.8744 ------------------------------------------------------------------------------- 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: 4.9990 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 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 155 ASN B 216 GLN B 252 GLN C 221 GLN H 155 ASN 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: 0.8743 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 11738 Z= 0.378 Angle : 0.551 6.118 16140 Z= 0.307 Chirality : 0.046 0.136 1764 Planarity : 0.004 0.037 1768 Dihedral : 22.362 144.010 2054 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.84 % Allowed : 17.41 % 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: 0.35 (0.24), residues: 1198 helix: 1.03 (0.22), residues: 486 sheet: 0.37 (0.31), residues: 294 loop : -0.71 (0.32), residues: 418 *********************** 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: 19 poor density : 183 time to evaluate : 1.409 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: 19 outliers final: 9 residues processed: 190 average time/residue: 1.2998 time to fit residues: 267.8187 Evaluate side-chains 187 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 178 time to evaluate : 1.232 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 3 residues processed: 6 average time/residue: 0.4810 time to fit residues: 6.7683 ------------------------------------------------------------------------------- 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: 0.8980 chunk 104 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 GLN B 252 GLN C 221 GLN D 222 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: 0.8689 moved from start: 0.2046 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= 0.189 Angle : 0.474 6.066 16140 Z= 0.267 Chirality : 0.041 0.131 1764 Planarity : 0.003 0.036 1768 Dihedral : 22.130 138.154 2054 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.16 % Allowed : 18.38 % Favored : 80.46 % 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: 0.54 (0.25), residues: 1198 helix: 1.18 (0.23), residues: 490 sheet: 0.70 (0.32), residues: 278 loop : -0.77 (0.31), residues: 430 *********************** 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 202 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 190 time to evaluate : 1.279 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: 12 outliers final: 5 residues processed: 195 average time/residue: 1.2000 time to fit residues: 254.5857 Evaluate side-chains 187 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 182 time to evaluate : 1.231 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.2075 time to fit residues: 2.5090 ------------------------------------------------------------------------------- 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: 5.9990 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 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 216 GLN B 252 GLN C 221 GLN 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: 0.8702 moved from start: 0.2027 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= 0.225 Angle : 0.487 5.985 16140 Z= 0.273 Chirality : 0.042 0.132 1764 Planarity : 0.004 0.036 1768 Dihedral : 22.068 133.695 2054 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.77 % Allowed : 19.25 % Favored : 79.98 % 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: 0.56 (0.25), residues: 1198 helix: 1.18 (0.23), residues: 490 sheet: 0.76 (0.32), residues: 278 loop : -0.77 (0.31), residues: 430 ********************** 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 190 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 182 time to evaluate : 1.237 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: 2 residues processed: 185 average time/residue: 1.1923 time to fit residues: 240.2898 Evaluate side-chains 181 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 179 time to evaluate : 1.305 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.6004 ------------------------------------------------------------------------------- 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: 3.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 H 164 GLN H 216 GLN I 221 GLN J 222 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.136859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.101465 restraints weight = 13277.141| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.51 r_work: 0.2941 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11738 Z= 0.353 Angle : 0.546 6.231 16140 Z= 0.305 Chirality : 0.045 0.134 1764 Planarity : 0.004 0.037 1768 Dihedral : 22.211 135.584 2054 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.77 % Allowed : 19.63 % Favored : 79.59 % 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: 0.45 (0.24), residues: 1198 helix: 1.05 (0.22), residues: 488 sheet: 0.65 (0.32), residues: 282 loop : -0.74 (0.31), residues: 428 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4939.38 seconds wall clock time: 88 minutes 35.51 seconds (5315.51 seconds total)