Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 5 18:07:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/10_2023/6puw_20483_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/10_2023/6puw_20483.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/10_2023/6puw_20483_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/10_2023/6puw_20483_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/10_2023/6puw_20483_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/10_2023/6puw_20483.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/10_2023/6puw_20483.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/10_2023/6puw_20483_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puw_20483/10_2023/6puw_20483_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.024 sd= 0.693 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 4 6.06 5 P 72 5.49 5 Mg 4 5.21 5 S 34 5.16 5 C 6662 2.51 5 N 1914 2.21 5 O 2420 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 13": "OE1" <-> "OE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 157": "OE1" <-> "OE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "G ARG 20": "NH1" <-> "NH2" Residue "G GLU 157": "OE1" <-> "OE2" Residue "G GLU 170": "OE1" <-> "OE2" Residue "G GLU 212": "OE1" <-> "OE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H GLU 13": "OE1" <-> "OE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 157": "OE1" <-> "OE2" Residue "H GLU 212": "OE1" <-> "OE2" Residue "H ARG 224": "NH1" <-> "NH2" Residue "I GLU 246": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 11116 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1935 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 8, 'TRANS': 240} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "B" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1749 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "C" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 539 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "D" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 388 Classifications: {'peptide': 47} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 43} Chain: "E" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 384 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "F" Number of atoms: 371 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Conformer: "B" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} bond proxies already assigned to first conformer: 369 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 2, ' ZN': 1, 'KLQ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "G" Number of atoms: 1935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1935 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 8, 'TRANS': 240} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "H" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1749 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "I" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 539 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "J" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 388 Classifications: {'peptide': 47} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 43} Chain: "K" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 384 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "L" Number of atoms: 371 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Conformer: "B" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} bond proxies already assigned to first conformer: 369 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 2, ' ZN': 1, 'KLQ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "I" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "J" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "L" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 319 SG CYS A 40 26.812 44.982 52.090 1.00 27.12 S ATOM 342 SG CYS A 43 30.201 46.049 50.522 1.00 13.11 S ATOM 2241 SG CYS B 40 49.179 122.249 23.495 1.00 99.74 S ATOM 2264 SG CYS B 43 47.044 120.689 26.698 1.00107.94 S ATOM 5877 SG CYS G 40 64.828 87.738 52.090 1.00 27.12 S ATOM 5900 SG CYS G 43 61.439 86.671 50.522 1.00 13.11 S ATOM 7799 SG CYS H 40 42.461 10.471 23.495 1.00 99.74 S ATOM 7822 SG CYS H 43 44.596 12.031 26.698 1.00107.94 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A DA F 21 " occ=0.60 ... (40 atoms not shown) pdb=" C4 B DA F 21 " occ=0.40 residue: pdb=" P A DA L 21 " occ=0.60 ... (40 atoms not shown) pdb=" C4 B DA L 21 " occ=0.40 Time building chain proxies: 6.55, per 1000 atoms: 0.59 Number of scatterers: 11116 At special positions: 0 Unit cell: (92.43, 133.51, 83.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 S 34 16.00 P 72 15.00 Mg 4 11.99 F 6 9.00 O 2420 8.00 N 1914 7.00 C 6662 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.90 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 303 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 40 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 12 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 16 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 43 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 40 " pdb=" ZN G 303 " pdb="ZN ZN G 303 " - pdb=" NE2 HIS G 12 " pdb="ZN ZN G 303 " - pdb=" ND1 HIS G 16 " pdb="ZN ZN G 303 " - pdb=" SG CYS G 43 " pdb="ZN ZN G 303 " - pdb=" SG CYS G 40 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS H 12 " pdb="ZN ZN H 301 " - pdb=" ND1 HIS H 16 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 43 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 40 " Number of angles added : 4 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 14 sheets defined 42.2% alpha, 17.8% beta 30 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 5.01 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 removed outlier: 3.920A pdb=" N LYS A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 30 through 38 Processing helix chain 'A' and resid 41 through 43 No H-bonds generated for 'chain 'A' and resid 41 through 43' Processing helix chain 'A' and resid 94 through 107 removed outlier: 3.598A pdb=" N TYR A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 122 No H-bonds generated for 'chain 'A' and resid 119 through 122' Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 145 through 165 removed outlier: 5.563A pdb=" N VAL A 150 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A 152 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 185 Processing helix chain 'A' and resid 196 through 220 removed outlier: 3.623A pdb=" N ILE A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 19 through 26 removed outlier: 3.563A pdb=" N SER B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 39 Processing helix chain 'B' and resid 94 through 107 Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 150 through 168 removed outlier: 5.291A pdb=" N ASP B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLN B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 185 Processing helix chain 'B' and resid 196 through 220 removed outlier: 3.602A pdb=" N ILE B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 222 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 271 through 274 removed outlier: 3.735A pdb=" N GLN C 274 " --> pdb=" O TYR C 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 271 through 274' Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'G' and resid 2 through 15 removed outlier: 3.920A pdb=" N LYS G 14 " --> pdb=" O GLU G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 25 Processing helix chain 'G' and resid 30 through 38 Processing helix chain 'G' and resid 41 through 43 No H-bonds generated for 'chain 'G' and resid 41 through 43' Processing helix chain 'G' and resid 94 through 107 removed outlier: 3.598A pdb=" N TYR G 99 " --> pdb=" O GLN G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 122 No H-bonds generated for 'chain 'G' and resid 119 through 122' Processing helix chain 'G' and resid 124 through 133 Processing helix chain 'G' and resid 145 through 165 removed outlier: 5.563A pdb=" N VAL G 150 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU G 152 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 185 Processing helix chain 'G' and resid 196 through 220 removed outlier: 3.623A pdb=" N ILE G 220 " --> pdb=" O GLN G 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 11 Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.563A pdb=" N SER H 24 " --> pdb=" O ARG H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 39 Processing helix chain 'H' and resid 94 through 107 Processing helix chain 'H' and resid 124 through 133 Processing helix chain 'H' and resid 150 through 168 removed outlier: 5.291A pdb=" N ASP H 167 " --> pdb=" O GLY H 163 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLN H 168 " --> pdb=" O GLN H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 185 Processing helix chain 'H' and resid 196 through 220 removed outlier: 3.602A pdb=" N ILE H 220 " --> pdb=" O GLN H 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 222 Processing helix chain 'I' and resid 262 through 264 No H-bonds generated for 'chain 'I' and resid 262 through 264' Processing helix chain 'I' and resid 271 through 274 removed outlier: 3.735A pdb=" N GLN I 274 " --> pdb=" O TYR I 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 271 through 274' Processing helix chain 'J' and resid 262 through 264 No H-bonds generated for 'chain 'J' and resid 262 through 264' Processing sheet with id= A, first strand: chain 'A' and resid 87 through 89 removed outlier: 4.251A pdb=" N VAL A 72 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR A 112 " --> pdb=" O TRP A 61 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU A 63 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N HIS A 114 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N CYS A 65 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LYS A 136 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N THR A 115 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLU A 138 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 241 through 244 removed outlier: 6.639A pdb=" N VAL A 250 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 84 through 89 removed outlier: 4.086A pdb=" N VAL B 72 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N THR B 112 " --> pdb=" O TRP B 61 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU B 63 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N HIS B 114 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N CYS B 65 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS B 136 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 256 through 258 removed outlier: 3.568A pdb=" N TRP B 243 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLN B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LEU B 241 " --> pdb=" O GLN B 252 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 265 through 268 removed outlier: 6.627A pdb=" N VAL C 250 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LYS C 244 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 224 through 227 removed outlier: 3.849A pdb=" N ARG D 224 " --> pdb=" O ILE D 268 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 256 through 261 removed outlier: 6.527A pdb=" N GLN D 252 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU D 241 " --> pdb=" O GLN D 252 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 87 through 89 removed outlier: 4.251A pdb=" N VAL G 72 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR G 112 " --> pdb=" O TRP G 61 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU G 63 " --> pdb=" O THR G 112 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N HIS G 114 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N CYS G 65 " --> pdb=" O HIS G 114 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LYS G 136 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N THR G 115 " --> pdb=" O LYS G 136 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLU G 138 " --> pdb=" O THR G 115 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 241 through 244 removed outlier: 6.639A pdb=" N VAL G 250 " --> pdb=" O LEU G 242 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 84 through 89 removed outlier: 4.086A pdb=" N VAL H 72 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N THR H 112 " --> pdb=" O TRP H 61 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU H 63 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N HIS H 114 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N CYS H 65 " --> pdb=" O HIS H 114 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS H 136 " --> pdb=" O VAL H 113 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 256 through 258 removed outlier: 3.568A pdb=" N TRP H 243 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLN H 252 " --> pdb=" O LEU H 241 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LEU H 241 " --> pdb=" O GLN H 252 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 265 through 268 removed outlier: 6.627A pdb=" N VAL I 250 " --> pdb=" O LEU I 242 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LYS I 244 " --> pdb=" O ALA I 248 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA I 248 " --> pdb=" O LYS I 244 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'J' and resid 224 through 227 removed outlier: 3.849A pdb=" N ARG J 224 " --> pdb=" O ILE J 268 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'J' and resid 256 through 261 removed outlier: 6.527A pdb=" N GLN J 252 " --> pdb=" O LEU J 241 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU J 241 " --> pdb=" O GLN J 252 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 4.17 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: 1632 1.31 - 1.43: 3202 1.43 - 1.56: 6130 1.56 - 1.68: 146 1.68 - 1.81: 50 Bond restraints: 11160 Sorted by residual: bond pdb=" CAJ KLQ G 304 " pdb=" CAX KLQ G 304 " ideal model delta sigma weight residual 2.011 1.514 0.497 2.00e-02 2.50e+03 6.19e+02 bond pdb=" CAJ KLQ A 304 " pdb=" CAX KLQ A 304 " ideal model delta sigma weight residual 2.011 1.514 0.497 2.00e-02 2.50e+03 6.19e+02 bond pdb=" CAW KLQ G 304 " pdb=" CBA KLQ G 304 " ideal model delta sigma weight residual 0.990 1.481 -0.491 2.00e-02 2.50e+03 6.03e+02 bond pdb=" CAW KLQ A 304 " pdb=" CBA KLQ A 304 " ideal model delta sigma weight residual 0.990 1.481 -0.491 2.00e-02 2.50e+03 6.03e+02 bond pdb=" CAZ KLQ G 304 " pdb=" NBF KLQ G 304 " ideal model delta sigma weight residual 1.092 1.445 -0.353 2.00e-02 2.50e+03 3.11e+02 ... (remaining 11155 not shown) Histogram of bond angle deviations from ideal: 99.47 - 106.37: 694 106.37 - 113.28: 6110 113.28 - 120.18: 4030 120.18 - 127.09: 4256 127.09 - 133.99: 284 Bond angle restraints: 15374 Sorted by residual: angle pdb=" CAY KLQ A 304 " pdb=" CAV KLQ A 304 " pdb=" FAG KLQ A 304 " ideal model delta sigma weight residual 142.84 119.21 23.63 3.00e+00 1.11e-01 6.21e+01 angle pdb=" CAY KLQ G 304 " pdb=" CAV KLQ G 304 " pdb=" FAG KLQ G 304 " ideal model delta sigma weight residual 142.84 119.21 23.63 3.00e+00 1.11e-01 6.21e+01 angle pdb=" CAI KLQ G 304 " pdb=" CAV KLQ G 304 " pdb=" FAG KLQ G 304 " ideal model delta sigma weight residual 97.12 120.63 -23.51 3.00e+00 1.11e-01 6.14e+01 angle pdb=" CAI KLQ A 304 " pdb=" CAV KLQ A 304 " pdb=" FAG KLQ A 304 " ideal model delta sigma weight residual 97.12 120.63 -23.51 3.00e+00 1.11e-01 6.14e+01 angle pdb=" N SER G 123 " pdb=" CA SER G 123 " pdb=" C SER G 123 " ideal model delta sigma weight residual 110.41 117.17 -6.76 1.23e+00 6.61e-01 3.02e+01 ... (remaining 15369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 5354 17.33 - 34.67: 556 34.67 - 52.00: 308 52.00 - 69.33: 144 69.33 - 86.66: 16 Dihedral angle restraints: 6378 sinusoidal: 3040 harmonic: 3338 Sorted by residual: dihedral pdb=" CA ARG D 228 " pdb=" C ARG D 228 " pdb=" N ASP D 229 " pdb=" CA ASP D 229 " ideal model delta harmonic sigma weight residual -180.00 -155.55 -24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA ARG J 228 " pdb=" C ARG J 228 " pdb=" N ASP J 229 " pdb=" CA ASP J 229 " ideal model delta harmonic sigma weight residual -180.00 -155.55 -24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA TYR G 194 " pdb=" C TYR G 194 " pdb=" N SER G 195 " pdb=" CA SER G 195 " ideal model delta harmonic sigma weight residual 180.00 156.94 23.06 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 6375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1112 0.035 - 0.070: 416 0.070 - 0.105: 132 0.105 - 0.141: 42 0.141 - 0.176: 6 Chirality restraints: 1708 Sorted by residual: chirality pdb=" CA ASN A 120 " pdb=" N ASN A 120 " pdb=" C ASN A 120 " pdb=" CB ASN A 120 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CA ASN G 120 " pdb=" N ASN G 120 " pdb=" C ASN G 120 " pdb=" CB ASN G 120 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CA THR A 122 " pdb=" N THR A 122 " pdb=" C THR A 122 " pdb=" CB THR A 122 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.32e-01 ... (remaining 1705 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS G 127 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C LYS G 127 " 0.040 2.00e-02 2.50e+03 pdb=" O LYS G 127 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA G 128 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 127 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C LYS A 127 " -0.040 2.00e-02 2.50e+03 pdb=" O LYS A 127 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA A 128 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 155 " -0.006 2.00e-02 2.50e+03 1.26e-02 1.60e+00 pdb=" C ASN G 155 " 0.022 2.00e-02 2.50e+03 pdb=" O ASN G 155 " -0.008 2.00e-02 2.50e+03 pdb=" N LYS G 156 " -0.007 2.00e-02 2.50e+03 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 8 0.98 - 1.96: 8 1.96 - 2.94: 4743 2.94 - 3.92: 30808 3.92 - 4.90: 60660 Warning: very small nonbonded interaction distances. Nonbonded interactions: 96227 Sorted by model distance: nonbonded pdb=" O HOH A 464 " pdb=" O HOH G 438 " model vdw 0.000 2.440 nonbonded pdb=" O HOH A 459 " pdb=" O HOH L 109 " model vdw 0.000 2.440 nonbonded pdb=" O HOH A 488 " pdb=" O HOH K 105 " model vdw 0.000 2.440 nonbonded pdb=" O HOH E 105 " pdb=" O HOH G 488 " model vdw 0.000 2.440 nonbonded pdb=" O HOH F 109 " pdb=" O HOH G 459 " model vdw 0.000 2.440 ... (remaining 96222 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name CB or name CG or name CD or name OE1 or name NE2)) or resid 10 through 13 \ or (resid 14 and (name N or name CA or name C or name CB or name CG or name CD \ or name CE or name NZ )) or resid 15 through 44 or resid 57 through 140 or resid \ 150 through 225 or resid 239 through 252 or resid 266)) selection = (chain 'B' and (resid 2 through 79 or (resid 80 and (name N or name CA or name C \ or name CB )) or resid 81 through 84 or (resid 85 and (name N or name CA or nam \ e C or name CB or name CG or name CD or name OE1 or name OE2)) or resid 86 throu \ gh 252 or resid 258)) selection = (chain 'G' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name CB or name CG or name CD or name OE1 or name NE2)) or resid 10 through 13 \ or (resid 14 and (name N or name CA or name C or name CB or name CG or name CD \ or name CE or name NZ )) or resid 15 through 44 or resid 57 through 140 or resid \ 150 through 225 or resid 239 through 252 or resid 266)) selection = (chain 'H' and (resid 2 through 79 or (resid 80 and (name N or name CA or name C \ or name CB )) or resid 81 through 84 or (resid 85 and (name N or name CA or nam \ e C or name CB or name CG or name CD or name OE1 or name OE2)) or resid 86 throu \ gh 252 or resid 258)) } ncs_group { reference = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' } ncs_group { reference = (chain 'F' and resid 5 through 20) selection = (chain 'L' and resid 5 through 20) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 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: 12.490 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 38.560 Find NCS groups from input model: 0.710 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: 0.010 Load rotamer database and sin/cos tables:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.497 11160 Z= 0.654 Angle : 0.765 23.633 15374 Z= 0.400 Chirality : 0.043 0.176 1708 Planarity : 0.003 0.026 1674 Dihedral : 19.851 86.664 4218 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.20 % Allowed : 2.66 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.21), residues: 1130 helix: -1.14 (0.20), residues: 494 sheet: -1.04 (0.35), residues: 192 loop : -1.93 (0.25), residues: 444 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 220 time to evaluate : 1.167 Fit side-chains TARDY: cannot create tardy model for: "GLU A 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 2 residues processed: 220 average time/residue: 1.4757 time to fit residues: 345.9793 Evaluate side-chains 158 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2362 time to fit residues: 2.2584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 0.0870 chunk 48 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.0050 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 67 optimal weight: 0.2980 chunk 105 optimal weight: 3.9990 overall best weight: 0.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN C 221 GLN ** G 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 HIS G 214 GLN G 222 ASN H 164 GLN I 221 GLN ** I 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 11160 Z= 0.267 Angle : 0.873 14.845 15374 Z= 0.456 Chirality : 0.053 0.412 1708 Planarity : 0.009 0.152 1674 Dihedral : 22.566 61.424 1962 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.71 % Allowed : 5.31 % Favored : 93.98 % Rotamer: Outliers : 3.58 % Allowed : 10.43 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.22), residues: 1130 helix: -1.33 (0.21), residues: 492 sheet: -1.08 (0.33), residues: 194 loop : -2.08 (0.27), residues: 444 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 170 time to evaluate : 1.199 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 35 outliers final: 7 residues processed: 185 average time/residue: 1.2873 time to fit residues: 256.8167 Evaluate side-chains 150 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 143 time to evaluate : 1.222 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.1732 time to fit residues: 2.4468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 87 optimal weight: 0.0980 chunk 71 optimal weight: 0.9990 chunk 29 optimal weight: 0.0870 chunk 105 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN G 216 GLN H 164 GLN H 221 GLN I 221 GLN J 222 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11160 Z= 0.167 Angle : 0.544 11.751 15374 Z= 0.277 Chirality : 0.040 0.143 1708 Planarity : 0.003 0.051 1674 Dihedral : 22.237 60.314 1962 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.17 % Allowed : 13.29 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.24), residues: 1130 helix: 0.14 (0.23), residues: 484 sheet: -0.45 (0.34), residues: 194 loop : -1.65 (0.28), residues: 452 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 158 time to evaluate : 1.209 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 31 outliers final: 12 residues processed: 171 average time/residue: 1.3226 time to fit residues: 243.5159 Evaluate side-chains 161 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 149 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 4 residues processed: 8 average time/residue: 0.3051 time to fit residues: 4.7992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN H 117 ASN H 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11160 Z= 0.234 Angle : 0.552 11.717 15374 Z= 0.281 Chirality : 0.041 0.143 1708 Planarity : 0.003 0.037 1674 Dihedral : 22.264 61.071 1962 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.97 % Allowed : 14.62 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.24), residues: 1130 helix: 0.65 (0.23), residues: 492 sheet: -0.14 (0.34), residues: 194 loop : -1.42 (0.27), residues: 444 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 152 time to evaluate : 1.158 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 29 outliers final: 12 residues processed: 165 average time/residue: 1.2401 time to fit residues: 221.3441 Evaluate side-chains 156 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 5 residues processed: 7 average time/residue: 0.1149 time to fit residues: 2.8650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN G 214 GLN H 117 ASN H 221 GLN I 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 11160 Z= 0.279 Angle : 0.561 11.756 15374 Z= 0.287 Chirality : 0.042 0.143 1708 Planarity : 0.003 0.039 1674 Dihedral : 22.334 61.035 1962 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.76 % Allowed : 16.67 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1130 helix: 0.88 (0.23), residues: 488 sheet: -0.05 (0.34), residues: 194 loop : -1.30 (0.27), residues: 448 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 1.220 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 27 outliers final: 13 residues processed: 162 average time/residue: 1.2274 time to fit residues: 214.9869 Evaluate side-chains 159 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 146 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 6 residues processed: 7 average time/residue: 0.4150 time to fit residues: 5.1700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 58 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN C 221 GLN H 117 ASN H 221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11160 Z= 0.200 Angle : 0.541 11.686 15374 Z= 0.277 Chirality : 0.040 0.144 1708 Planarity : 0.003 0.039 1674 Dihedral : 22.249 59.912 1962 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.25 % Allowed : 17.59 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.24), residues: 1130 helix: 1.09 (0.23), residues: 492 sheet: 0.08 (0.34), residues: 194 loop : -1.19 (0.28), residues: 444 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 148 time to evaluate : 1.199 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 22 outliers final: 13 residues processed: 157 average time/residue: 1.3113 time to fit residues: 222.6432 Evaluate side-chains 159 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 146 time to evaluate : 1.222 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 6 residues processed: 7 average time/residue: 0.1248 time to fit residues: 3.1100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.5980 chunk 63 optimal weight: 0.1980 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN C 221 GLN H 117 ASN H 221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11160 Z= 0.181 Angle : 0.527 11.602 15374 Z= 0.268 Chirality : 0.040 0.143 1708 Planarity : 0.003 0.037 1674 Dihedral : 22.114 59.870 1962 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.25 % Allowed : 17.69 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.24), residues: 1130 helix: 1.28 (0.23), residues: 492 sheet: 0.23 (0.34), residues: 194 loop : -1.10 (0.28), residues: 444 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 149 time to evaluate : 1.190 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 22 outliers final: 12 residues processed: 159 average time/residue: 1.2724 time to fit residues: 218.6450 Evaluate side-chains 158 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 1.252 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 6 residues processed: 6 average time/residue: 0.1239 time to fit residues: 2.8780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 101 optimal weight: 0.4980 chunk 107 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 104 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN H 117 ASN H 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11160 Z= 0.159 Angle : 0.520 11.575 15374 Z= 0.265 Chirality : 0.040 0.142 1708 Planarity : 0.003 0.037 1674 Dihedral : 22.012 59.562 1962 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.74 % Allowed : 18.92 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.24), residues: 1130 helix: 1.40 (0.23), residues: 492 sheet: 0.34 (0.35), residues: 194 loop : -1.03 (0.28), residues: 444 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 1.254 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 17 outliers final: 12 residues processed: 157 average time/residue: 1.3190 time to fit residues: 223.3022 Evaluate side-chains 158 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 0.4243 time to fit residues: 4.1757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.0970 chunk 62 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 67 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: H 117 ASN H 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11160 Z= 0.187 Angle : 0.527 11.601 15374 Z= 0.268 Chirality : 0.040 0.142 1708 Planarity : 0.003 0.036 1674 Dihedral : 22.017 59.673 1962 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.43 % Allowed : 19.02 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.24), residues: 1130 helix: 1.40 (0.23), residues: 492 sheet: 0.42 (0.35), residues: 194 loop : -0.99 (0.28), residues: 444 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 144 time to evaluate : 1.664 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 14 outliers final: 10 residues processed: 153 average time/residue: 1.2813 time to fit residues: 211.7131 Evaluate side-chains 150 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 1.270 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.1438 time to fit residues: 2.3766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 115 optimal weight: 4.9990 chunk 106 optimal weight: 0.2980 chunk 92 optimal weight: 0.6980 chunk 9 optimal weight: 0.0020 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 117 ASN H 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11160 Z= 0.150 Angle : 0.520 11.539 15374 Z= 0.265 Chirality : 0.040 0.142 1708 Planarity : 0.003 0.036 1674 Dihedral : 21.952 59.842 1962 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.12 % Allowed : 19.53 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1130 helix: 1.48 (0.23), residues: 494 sheet: 0.52 (0.35), residues: 194 loop : -0.91 (0.28), residues: 442 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 1.137 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. outliers start: 11 outliers final: 10 residues processed: 158 average time/residue: 1.2737 time to fit residues: 217.4119 Evaluate side-chains 158 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 148 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.1674 time to fit residues: 2.3925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.0870 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN H 117 ASN H 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.136311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.100197 restraints weight = 17932.838| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.90 r_work: 0.2971 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11160 Z= 0.189 Angle : 0.530 11.582 15374 Z= 0.270 Chirality : 0.040 0.142 1708 Planarity : 0.003 0.036 1674 Dihedral : 21.978 59.956 1962 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.53 % Allowed : 19.22 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.24), residues: 1130 helix: 1.50 (0.23), residues: 490 sheet: 0.53 (0.35), residues: 194 loop : -0.91 (0.28), residues: 446 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4399.90 seconds wall clock time: 79 minutes 5.88 seconds (4745.88 seconds total)