Starting phenix.real_space_refine on Fri Mar 15 09:56:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3k_21038/03_2024/6v3k_21038_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3k_21038/03_2024/6v3k_21038.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3k_21038/03_2024/6v3k_21038_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3k_21038/03_2024/6v3k_21038_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3k_21038/03_2024/6v3k_21038_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3k_21038/03_2024/6v3k_21038.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3k_21038/03_2024/6v3k_21038.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3k_21038/03_2024/6v3k_21038_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3k_21038/03_2024/6v3k_21038_updated.pdb" } resolution = 3.4 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= 0.048 sd= 0.590 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 6990 2.51 5 N 2018 2.21 5 O 2188 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 GLU 13": "OE1" <-> "OE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 11": "OE1" <-> "OE2" Residue "B GLU 157": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "G ARG 20": "NH1" <-> "NH2" Residue "G GLU 138": "OE1" <-> "OE2" Residue "G GLU 157": "OE1" <-> "OE2" Residue "G GLU 170": "OE1" <-> "OE2" Residue "G GLU 212": "OE1" <-> "OE2" Residue "G GLU 246": "OE1" <-> "OE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H GLU 11": "OE1" <-> "OE2" Residue "H GLU 157": "OE1" <-> "OE2" Residue "H GLU 170": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11314 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2029 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 9, 'TRANS': 249} Chain breaks: 1 Chain: "B" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1916 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 7, 'TRANS': 234} Chain breaks: 3 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: 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: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, ' ZN': 1, 'QUW': 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: "G" Number of atoms: 2029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2029 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 9, 'TRANS': 249} Chain breaks: 1 Chain: "H" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1916 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 7, 'TRANS': 234} Chain breaks: 3 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: 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: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, ' ZN': 1, 'QUW': 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 319 SG CYS A 40 25.361 45.748 54.194 1.00 56.47 S ATOM 342 SG CYS A 43 29.407 46.677 53.019 1.00 38.77 S ATOM 2348 SG CYS B 40 49.538 123.668 25.141 1.00120.74 S ATOM 2371 SG CYS B 43 46.966 121.780 27.987 1.00 95.82 S ATOM 5976 SG CYS G 40 64.699 88.552 54.194 1.00 56.47 S ATOM 5999 SG CYS G 43 60.653 87.623 53.019 1.00 38.77 S ATOM 8005 SG CYS H 40 40.522 10.632 25.141 1.00120.74 S ATOM 8028 SG CYS H 43 43.094 12.520 27.987 1.00 95.82 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A DA F 21 " occ=0.45 ... (40 atoms not shown) pdb=" C4 B DA F 21 " occ=0.55 residue: pdb=" P A DA L 21 " occ=0.45 ... (40 atoms not shown) pdb=" C4 B DA L 21 " occ=0.55 Time building chain proxies: 6.73, per 1000 atoms: 0.59 Number of scatterers: 11314 At special positions: 0 Unit cell: (90.85, 135.09, 86.11, 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 4 9.00 O 2188 8.00 N 2018 7.00 C 6990 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: 4.99 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 303 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 40 " pdb=" ZN B 500 " pdb="ZN ZN B 500 " - pdb=" NE2 HIS B 12 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 40 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 43 " pdb="ZN ZN B 500 " - pdb=" ND1 HIS B 16 " 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 500 " pdb="ZN ZN H 500 " - pdb=" NE2 HIS H 12 " pdb="ZN ZN H 500 " - pdb=" SG CYS H 40 " pdb="ZN ZN H 500 " - pdb=" SG CYS H 43 " pdb="ZN ZN H 500 " - pdb=" ND1 HIS H 16 " Number of angles added : 4 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 20 sheets defined 40.5% alpha, 20.2% beta 30 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 5.34 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 removed outlier: 4.133A 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 39 removed outlier: 3.505A pdb=" N SER A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 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 132 Processing helix chain 'A' and resid 145 through 168 removed outlier: 5.504A pdb=" N VAL A 150 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU A 152 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ARG A 166 " --> pdb=" O GLY A 163 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASP A 167 " --> pdb=" O GLN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 185 Processing helix chain 'A' and resid 196 through 220 Processing helix chain 'B' and resid 2 through 15 removed outlier: 4.252A pdb=" N ASP B 6 " --> pdb=" O LEU B 2 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 26 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 132 Processing helix chain 'B' and resid 151 through 168 removed outlier: 5.509A pdb=" N ASP B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLN B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 185 Processing helix chain 'B' and resid 196 through 221 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'C' and resid 214 through 220 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: 4.133A 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 39 removed outlier: 3.505A pdb=" N SER G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 107 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 132 Processing helix chain 'G' and resid 145 through 168 removed outlier: 5.504A pdb=" N VAL G 150 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU G 152 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ARG G 166 " --> pdb=" O GLY G 163 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASP G 167 " --> pdb=" O GLN G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 185 Processing helix chain 'G' and resid 196 through 220 Processing helix chain 'H' and resid 2 through 15 removed outlier: 4.252A pdb=" N ASP H 6 " --> pdb=" O LEU H 2 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS H 7 " --> pdb=" O ASP H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 26 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 132 Processing helix chain 'H' and resid 151 through 168 removed outlier: 5.509A pdb=" N ASP H 167 " --> pdb=" O GLY H 163 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLN H 168 " --> pdb=" O GLN H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 185 Processing helix chain 'H' and resid 196 through 221 Processing helix chain 'H' and resid 262 through 264 No H-bonds generated for 'chain 'H' and resid 262 through 264' Processing helix chain 'I' and resid 214 through 220 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 84 through 89 removed outlier: 4.224A pdb=" N VAL A 72 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR A 112 " --> pdb=" O TRP A 61 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU A 63 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N HIS A 114 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N CYS A 65 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYS A 136 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N THR A 115 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU A 138 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 257 through 261 removed outlier: 3.625A pdb=" N TRP A 243 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLN A 252 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU A 241 " --> pdb=" O GLN A 252 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 61 through 68 removed outlier: 4.125A pdb=" N VAL B 72 " --> pdb=" O ILE B 89 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 112 through 114 removed outlier: 6.449A pdb=" N LYS B 136 " --> pdb=" O VAL B 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 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: 6.165A pdb=" N GLN B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.711A 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: 6.623A pdb=" N GLN C 252 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.871A 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: 6.569A pdb=" N GLN D 252 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU D 241 " --> pdb=" O GLN D 252 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 84 through 89 removed outlier: 4.224A pdb=" N VAL G 72 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR G 112 " --> pdb=" O TRP G 61 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU G 63 " --> pdb=" O THR G 112 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N HIS G 114 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N CYS G 65 " --> pdb=" O HIS G 114 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYS G 136 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N THR G 115 " --> pdb=" O LYS G 136 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU G 138 " --> pdb=" O THR G 115 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 257 through 261 removed outlier: 3.625A pdb=" N TRP G 243 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLN G 252 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU G 241 " --> pdb=" O GLN G 252 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 61 through 68 removed outlier: 4.125A pdb=" N VAL H 72 " --> pdb=" O ILE H 89 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 112 through 114 removed outlier: 6.449A pdb=" N LYS H 136 " --> pdb=" O VAL H 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= N 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: 6.165A pdb=" N GLN H 252 " --> pdb=" O LEU H 241 " (cutoff:3.500A) removed outlier: 5.711A 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: 6.623A pdb=" N GLN I 252 " --> pdb=" O LEU I 241 " (cutoff:3.500A) removed outlier: 5.871A 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: 6.569A pdb=" N GLN J 252 " --> pdb=" O LEU J 241 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU J 241 " --> pdb=" O GLN J 252 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 5.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1698 1.30 - 1.43: 3348 1.43 - 1.56: 6452 1.56 - 1.68: 142 1.68 - 1.81: 50 Bond restraints: 11690 Sorted by residual: bond pdb=" C LYS A 127 " pdb=" N ALA A 128 " ideal model delta sigma weight residual 1.335 1.531 -0.196 1.31e-02 5.83e+03 2.24e+02 bond pdb=" C LYS G 127 " pdb=" N ALA G 128 " ideal model delta sigma weight residual 1.335 1.531 -0.196 1.31e-02 5.83e+03 2.24e+02 bond pdb=" C ASP G 116 " pdb=" N ASN G 117 " ideal model delta sigma weight residual 1.335 1.272 0.063 1.39e-02 5.18e+03 2.07e+01 bond pdb=" C ASP A 116 " pdb=" N ASN A 117 " ideal model delta sigma weight residual 1.335 1.272 0.063 1.39e-02 5.18e+03 2.07e+01 bond pdb=" N THR A 122 " pdb=" CA THR A 122 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.33e-02 5.65e+03 6.97e+00 ... (remaining 11685 not shown) Histogram of bond angle deviations from ideal: 85.35 - 95.12: 2 95.12 - 104.89: 416 104.89 - 114.65: 7346 114.65 - 124.42: 7832 124.42 - 134.19: 492 Bond angle restraints: 16088 Sorted by residual: angle pdb=" C3' DC F 20 " pdb=" O3' DC F 20 " pdb=" P A DA F 21 " ideal model delta sigma weight residual 120.20 106.95 13.25 1.50e+00 4.44e-01 7.81e+01 angle pdb=" C3' DC L 20 " pdb=" O3' DC L 20 " pdb=" P A DA L 21 " ideal model delta sigma weight residual 120.20 106.95 13.25 1.50e+00 4.44e-01 7.81e+01 angle pdb=" O3' DC F 20 " pdb=" P A DA F 21 " pdb=" OP2A DA F 21 " ideal model delta sigma weight residual 108.00 134.19 -26.19 3.00e+00 1.11e-01 7.62e+01 angle pdb=" O3' DC L 20 " pdb=" P A DA L 21 " pdb=" OP2A DA L 21 " ideal model delta sigma weight residual 108.00 134.19 -26.19 3.00e+00 1.11e-01 7.62e+01 angle pdb=" O3' DC F 20 " pdb=" P A DA F 21 " pdb=" OP1A DA F 21 " ideal model delta sigma weight residual 108.00 85.35 22.65 3.00e+00 1.11e-01 5.70e+01 ... (remaining 16083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 5594 17.70 - 35.40: 730 35.40 - 53.10: 330 53.10 - 70.79: 126 70.79 - 88.49: 8 Dihedral angle restraints: 6788 sinusoidal: 3278 harmonic: 3510 Sorted by residual: dihedral pdb=" CD ARG J 263 " pdb=" NE ARG J 263 " pdb=" CZ ARG J 263 " pdb=" NH1 ARG J 263 " ideal model delta sinusoidal sigma weight residual 0.00 -49.67 49.67 1 1.00e+01 1.00e-02 3.39e+01 dihedral pdb=" CD ARG D 263 " pdb=" NE ARG D 263 " pdb=" CZ ARG D 263 " pdb=" NH1 ARG D 263 " ideal model delta sinusoidal sigma weight residual 0.00 -49.67 49.67 1 1.00e+01 1.00e-02 3.39e+01 dihedral pdb=" CA TYR A 194 " pdb=" C TYR A 194 " pdb=" N SER A 195 " pdb=" CA SER A 195 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 6785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1202 0.039 - 0.077: 412 0.077 - 0.116: 120 0.116 - 0.155: 20 0.155 - 0.193: 6 Chirality restraints: 1760 Sorted by residual: chirality pdb=" P A DA F 21 " pdb=" OP1A DA F 21 " pdb=" OP2A DA F 21 " pdb=" O5'A DA F 21 " both_signs ideal model delta sigma weight residual True 2.35 -2.54 -0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" P A DA L 21 " pdb=" OP1A DA L 21 " pdb=" OP2A DA L 21 " pdb=" O5'A DA L 21 " both_signs ideal model delta sigma weight residual True 2.35 -2.54 -0.19 2.00e-01 2.50e+01 9.36e-01 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 7.74e-01 ... (remaining 1757 not shown) Planarity restraints: 1774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 263 " -0.834 9.50e-02 1.11e+02 3.74e-01 8.49e+01 pdb=" NE ARG J 263 " 0.050 2.00e-02 2.50e+03 pdb=" CZ ARG J 263 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG J 263 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG J 263 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 263 " 0.834 9.50e-02 1.11e+02 3.74e-01 8.49e+01 pdb=" NE ARG D 263 " -0.050 2.00e-02 2.50e+03 pdb=" CZ ARG D 263 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG D 263 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 263 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER G 57 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO G 58 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO G 58 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 58 " -0.031 5.00e-02 4.00e+02 ... (remaining 1771 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 36 2.31 - 2.96: 5194 2.96 - 3.60: 16206 3.60 - 4.25: 26870 4.25 - 4.90: 43228 Nonbonded interactions: 91534 Sorted by model distance: nonbonded pdb="MG MG A 302 " pdb=" OAE QUW A 304 " model vdw 1.659 2.170 nonbonded pdb="MG MG G 302 " pdb=" OAE QUW G 304 " model vdw 1.659 2.170 nonbonded pdb="MG MG G 301 " pdb=" NAS QUW G 304 " model vdw 1.749 2.250 nonbonded pdb="MG MG A 301 " pdb=" NAS QUW A 304 " model vdw 1.749 2.250 nonbonded pdb="MG MG A 302 " pdb=" OAC QUW A 304 " model vdw 1.763 2.170 ... (remaining 91529 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 1 through 43 or resid 57 through 140 or resid 150 through \ 268 or resid 303)) selection = (chain 'B' and (resid 1 through 227 or resid 237 through 268 or resid 500)) selection = (chain 'G' and (resid 1 through 43 or resid 57 through 140 or resid 150 through \ 268 or resid 303)) selection = (chain 'H' and (resid 1 through 227 or resid 237 through 268 or resid 500)) } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.130 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 40.310 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 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 : 0.006 0.196 11690 Z= 0.332 Angle : 0.729 26.191 16088 Z= 0.394 Chirality : 0.044 0.193 1760 Planarity : 0.013 0.374 1774 Dihedral : 19.801 88.492 4524 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.19 % Allowed : 4.28 % Favored : 95.53 % 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: -2.30 (0.23), residues: 1194 helix: -0.57 (0.20), residues: 504 sheet: -1.88 (0.30), residues: 280 loop : -2.27 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 19 HIS 0.003 0.001 HIS H 12 PHE 0.006 0.001 PHE H 181 TYR 0.016 0.001 TYR B 83 ARG 0.002 0.000 ARG C 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 212 time to evaluate : 1.350 Fit side-chains REVERT: A 27 ASN cc_start: 0.8332 (t0) cc_final: 0.8116 (t0) REVERT: A 226 TYR cc_start: 0.6493 (m-80) cc_final: 0.6232 (m-10) REVERT: C 267 ILE cc_start: 0.9266 (mt) cc_final: 0.9046 (mt) REVERT: G 27 ASN cc_start: 0.8332 (t0) cc_final: 0.8118 (t0) REVERT: G 226 TYR cc_start: 0.6493 (m-80) cc_final: 0.6233 (m-10) REVERT: I 267 ILE cc_start: 0.9264 (mt) cc_final: 0.9046 (mt) outliers start: 2 outliers final: 2 residues processed: 214 average time/residue: 0.2758 time to fit residues: 79.7473 Evaluate side-chains 156 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain G residue 120 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 0.0970 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 0.4980 chunk 110 optimal weight: 1.9990 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 27 ASN A 222 ASN B 9 GLN D 254 ASN G 27 ASN G 222 ASN H 9 GLN J 254 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11690 Z= 0.178 Angle : 0.473 4.647 16088 Z= 0.265 Chirality : 0.041 0.129 1760 Planarity : 0.003 0.043 1774 Dihedral : 22.442 79.014 2134 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.75 % Allowed : 11.67 % Favored : 86.58 % 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: -0.97 (0.25), residues: 1194 helix: 0.74 (0.22), residues: 504 sheet: -1.34 (0.30), residues: 278 loop : -1.78 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 132 HIS 0.003 0.001 HIS A 51 PHE 0.019 0.001 PHE H 26 TYR 0.016 0.001 TYR C 227 ARG 0.005 0.000 ARG H 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 1.332 Fit side-chains REVERT: A 27 ASN cc_start: 0.8351 (t0) cc_final: 0.8070 (t0) REVERT: A 226 TYR cc_start: 0.6444 (m-80) cc_final: 0.6152 (m-10) REVERT: B 227 TYR cc_start: 0.6616 (p90) cc_final: 0.6293 (p90) REVERT: B 252 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7726 (tt0) REVERT: B 253 ASP cc_start: 0.7460 (t0) cc_final: 0.7136 (t0) REVERT: G 27 ASN cc_start: 0.8350 (t0) cc_final: 0.8071 (t0) REVERT: G 226 TYR cc_start: 0.6437 (m-80) cc_final: 0.6152 (m-10) REVERT: H 227 TYR cc_start: 0.6628 (p90) cc_final: 0.6307 (p90) REVERT: H 252 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: H 253 ASP cc_start: 0.7459 (t0) cc_final: 0.7142 (t0) outliers start: 18 outliers final: 12 residues processed: 180 average time/residue: 0.2827 time to fit residues: 68.6548 Evaluate side-chains 174 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain H residue 9 GLN Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain J residue 234 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 0.0070 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11690 Z= 0.243 Angle : 0.498 6.346 16088 Z= 0.277 Chirality : 0.042 0.141 1760 Planarity : 0.003 0.044 1774 Dihedral : 22.380 79.650 2134 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.14 % Allowed : 13.81 % Favored : 84.05 % 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: -0.55 (0.25), residues: 1194 helix: 1.09 (0.22), residues: 506 sheet: -1.12 (0.31), residues: 278 loop : -1.57 (0.33), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 243 HIS 0.003 0.001 HIS A 51 PHE 0.017 0.001 PHE B 26 TYR 0.027 0.002 TYR C 227 ARG 0.006 0.000 ARG H 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 1.687 Fit side-chains REVERT: A 27 ASN cc_start: 0.8363 (t0) cc_final: 0.8075 (t0) REVERT: A 226 TYR cc_start: 0.6427 (m-80) cc_final: 0.6139 (m-10) REVERT: G 27 ASN cc_start: 0.8362 (t0) cc_final: 0.8075 (t0) REVERT: G 226 TYR cc_start: 0.6420 (m-80) cc_final: 0.6141 (m-10) outliers start: 22 outliers final: 14 residues processed: 174 average time/residue: 0.2901 time to fit residues: 68.5427 Evaluate side-chains 170 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain H residue 9 GLN Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 250 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 74 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 98 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN H 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 11690 Z= 0.157 Angle : 0.448 4.729 16088 Z= 0.253 Chirality : 0.041 0.126 1760 Planarity : 0.003 0.041 1774 Dihedral : 22.014 78.246 2130 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.75 % Allowed : 14.20 % Favored : 84.05 % 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 (0.25), residues: 1194 helix: 1.45 (0.23), residues: 508 sheet: -0.85 (0.31), residues: 278 loop : -1.30 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 19 HIS 0.003 0.000 HIS A 51 PHE 0.017 0.001 PHE B 26 TYR 0.012 0.001 TYR I 227 ARG 0.003 0.000 ARG I 262 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ASN cc_start: 0.8351 (t0) cc_final: 0.8062 (t0) REVERT: A 226 TYR cc_start: 0.6258 (m-80) cc_final: 0.5938 (m-10) REVERT: G 27 ASN cc_start: 0.8348 (t0) cc_final: 0.8062 (t0) REVERT: G 226 TYR cc_start: 0.6257 (m-80) cc_final: 0.5937 (m-10) outliers start: 18 outliers final: 14 residues processed: 182 average time/residue: 0.2673 time to fit residues: 67.1180 Evaluate side-chains 180 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 166 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 9 GLN Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 250 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 0.0470 chunk 100 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 0.3980 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN H 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11690 Z= 0.191 Angle : 0.469 4.701 16088 Z= 0.263 Chirality : 0.041 0.129 1760 Planarity : 0.003 0.041 1774 Dihedral : 21.960 78.310 2130 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.95 % Allowed : 15.56 % Favored : 82.49 % 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: 0.11 (0.25), residues: 1194 helix: 1.56 (0.23), residues: 506 sheet: -0.71 (0.31), residues: 278 loop : -1.18 (0.34), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 132 HIS 0.002 0.000 HIS A 51 PHE 0.019 0.001 PHE B 26 TYR 0.029 0.002 TYR I 227 ARG 0.004 0.000 ARG B 262 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ASN cc_start: 0.8345 (t0) cc_final: 0.8053 (t0) REVERT: A 226 TYR cc_start: 0.6193 (m-80) cc_final: 0.5893 (m-10) REVERT: B 35 GLU cc_start: 0.7839 (tp30) cc_final: 0.7595 (tp30) REVERT: G 27 ASN cc_start: 0.8342 (t0) cc_final: 0.8052 (t0) REVERT: G 226 TYR cc_start: 0.6188 (m-80) cc_final: 0.5893 (m-10) REVERT: H 35 GLU cc_start: 0.7831 (tp30) cc_final: 0.7590 (tp30) outliers start: 20 outliers final: 14 residues processed: 180 average time/residue: 0.2683 time to fit residues: 66.3475 Evaluate side-chains 174 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 250 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 0.0980 chunk 118 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 GLN I 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 11690 Z= 0.176 Angle : 0.472 7.274 16088 Z= 0.261 Chirality : 0.041 0.127 1760 Planarity : 0.003 0.040 1774 Dihedral : 21.822 78.108 2130 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.33 % Allowed : 16.15 % Favored : 81.52 % 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: 0.26 (0.26), residues: 1194 helix: 1.69 (0.23), residues: 504 sheet: -0.61 (0.31), residues: 290 loop : -1.11 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 19 HIS 0.002 0.001 HIS H 12 PHE 0.017 0.001 PHE B 26 TYR 0.014 0.001 TYR B 83 ARG 0.005 0.000 ARG H 262 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.141 Fit side-chains REVERT: A 27 ASN cc_start: 0.8362 (t0) cc_final: 0.8081 (t0) REVERT: A 226 TYR cc_start: 0.6102 (m-80) cc_final: 0.5831 (m-10) REVERT: G 27 ASN cc_start: 0.8360 (t0) cc_final: 0.8082 (t0) REVERT: G 226 TYR cc_start: 0.6098 (m-80) cc_final: 0.5830 (m-10) outliers start: 24 outliers final: 16 residues processed: 180 average time/residue: 0.2622 time to fit residues: 65.5735 Evaluate side-chains 168 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 152 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 250 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.7980 chunk 67 optimal weight: 0.0470 chunk 86 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 254 ASN J 254 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11690 Z= 0.177 Angle : 0.479 6.802 16088 Z= 0.266 Chirality : 0.041 0.126 1760 Planarity : 0.003 0.040 1774 Dihedral : 21.795 77.950 2130 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.33 % Allowed : 16.73 % Favored : 80.93 % 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 (0.26), residues: 1194 helix: 1.77 (0.23), residues: 504 sheet: -0.56 (0.31), residues: 290 loop : -1.09 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 132 HIS 0.003 0.000 HIS H 12 PHE 0.017 0.001 PHE B 26 TYR 0.023 0.002 TYR B 83 ARG 0.007 0.000 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 1.322 Fit side-chains REVERT: A 27 ASN cc_start: 0.8378 (t0) cc_final: 0.8101 (t0) REVERT: A 226 TYR cc_start: 0.6048 (m-80) cc_final: 0.5733 (m-10) REVERT: G 27 ASN cc_start: 0.8375 (t0) cc_final: 0.8099 (t0) REVERT: G 226 TYR cc_start: 0.6052 (m-80) cc_final: 0.5740 (m-10) outliers start: 24 outliers final: 20 residues processed: 174 average time/residue: 0.2404 time to fit residues: 59.5827 Evaluate side-chains 176 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 156 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 250 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 254 ASN J 254 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11690 Z= 0.251 Angle : 0.506 6.202 16088 Z= 0.279 Chirality : 0.042 0.132 1760 Planarity : 0.004 0.042 1774 Dihedral : 21.928 79.261 2130 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.24 % Allowed : 17.02 % Favored : 80.74 % 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: 0.29 (0.25), residues: 1194 helix: 1.73 (0.23), residues: 504 sheet: -0.61 (0.31), residues: 290 loop : -1.12 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 132 HIS 0.003 0.001 HIS H 12 PHE 0.016 0.001 PHE B 26 TYR 0.022 0.002 TYR B 83 ARG 0.006 0.000 ARG H 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 1.169 Fit side-chains REVERT: A 27 ASN cc_start: 0.8397 (t0) cc_final: 0.8121 (t0) REVERT: A 226 TYR cc_start: 0.6034 (m-80) cc_final: 0.5731 (m-10) REVERT: G 27 ASN cc_start: 0.8397 (t0) cc_final: 0.8121 (t0) REVERT: G 226 TYR cc_start: 0.6032 (m-80) cc_final: 0.5734 (m-10) outliers start: 23 outliers final: 20 residues processed: 170 average time/residue: 0.2484 time to fit residues: 58.6110 Evaluate side-chains 176 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 156 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 250 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 254 ASN G 222 ASN J 254 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11690 Z= 0.205 Angle : 0.490 5.800 16088 Z= 0.274 Chirality : 0.042 0.129 1760 Planarity : 0.003 0.041 1774 Dihedral : 21.875 78.816 2130 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.04 % Allowed : 17.22 % Favored : 80.74 % 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: 0.37 (0.26), residues: 1194 helix: 1.77 (0.23), residues: 504 sheet: -0.55 (0.31), residues: 290 loop : -1.06 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 132 HIS 0.004 0.001 HIS B 12 PHE 0.019 0.001 PHE B 26 TYR 0.020 0.001 TYR B 83 ARG 0.006 0.000 ARG H 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 1.203 Fit side-chains REVERT: A 27 ASN cc_start: 0.8392 (t0) cc_final: 0.8115 (t0) REVERT: A 226 TYR cc_start: 0.5983 (m-80) cc_final: 0.5707 (m-10) REVERT: B 35 GLU cc_start: 0.7674 (tp30) cc_final: 0.7279 (tm-30) REVERT: G 27 ASN cc_start: 0.8389 (t0) cc_final: 0.8116 (t0) REVERT: G 226 TYR cc_start: 0.5981 (m-80) cc_final: 0.5709 (m-10) REVERT: H 35 GLU cc_start: 0.7668 (tp30) cc_final: 0.7281 (tm-30) outliers start: 21 outliers final: 21 residues processed: 168 average time/residue: 0.2657 time to fit residues: 62.1691 Evaluate side-chains 171 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 250 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.2980 chunk 54 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 254 ASN J 254 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11690 Z= 0.188 Angle : 0.501 6.404 16088 Z= 0.282 Chirality : 0.042 0.154 1760 Planarity : 0.003 0.040 1774 Dihedral : 21.834 78.578 2130 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.95 % Allowed : 17.22 % Favored : 80.84 % 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 (0.26), residues: 1194 helix: 1.72 (0.23), residues: 504 sheet: -0.52 (0.31), residues: 290 loop : -1.02 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 132 HIS 0.002 0.000 HIS B 12 PHE 0.019 0.001 PHE B 26 TYR 0.018 0.001 TYR B 83 ARG 0.006 0.000 ARG H 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 156 time to evaluate : 1.324 Fit side-chains REVERT: A 27 ASN cc_start: 0.8401 (t0) cc_final: 0.8129 (t0) REVERT: A 224 ARG cc_start: 0.8020 (mtp180) cc_final: 0.7715 (mtp180) REVERT: A 226 TYR cc_start: 0.5989 (m-80) cc_final: 0.5601 (m-10) REVERT: B 35 GLU cc_start: 0.7655 (tp30) cc_final: 0.7315 (tm-30) REVERT: G 27 ASN cc_start: 0.8401 (t0) cc_final: 0.8129 (t0) REVERT: G 226 TYR cc_start: 0.5964 (m-80) cc_final: 0.5663 (m-10) REVERT: H 35 GLU cc_start: 0.7655 (tp30) cc_final: 0.7323 (tm-30) outliers start: 20 outliers final: 20 residues processed: 166 average time/residue: 0.2631 time to fit residues: 60.5823 Evaluate side-chains 176 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 156 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 250 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 254 ASN J 254 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.114126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.082628 restraints weight = 15802.187| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.13 r_work: 0.2715 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11690 Z= 0.320 Angle : 0.547 5.717 16088 Z= 0.305 Chirality : 0.044 0.152 1760 Planarity : 0.004 0.043 1774 Dihedral : 22.096 81.125 2130 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.95 % Allowed : 17.51 % Favored : 80.54 % 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: 0.21 (0.26), residues: 1194 helix: 1.57 (0.23), residues: 502 sheet: -0.61 (0.33), residues: 270 loop : -1.03 (0.33), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 132 HIS 0.004 0.001 HIS H 12 PHE 0.019 0.001 PHE B 26 TYR 0.022 0.002 TYR B 83 ARG 0.006 0.000 ARG H 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2676.40 seconds wall clock time: 48 minutes 55.36 seconds (2935.36 seconds total)