Starting phenix.real_space_refine on Wed Mar 20 17:08:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tlj_25989/03_2024/7tlj_25989_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tlj_25989/03_2024/7tlj_25989.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tlj_25989/03_2024/7tlj_25989_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tlj_25989/03_2024/7tlj_25989_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tlj_25989/03_2024/7tlj_25989_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tlj_25989/03_2024/7tlj_25989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tlj_25989/03_2024/7tlj_25989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tlj_25989/03_2024/7tlj_25989_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tlj_25989/03_2024/7tlj_25989_trim_updated.pdb" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.277 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: 7 Type Number sf(0) Gaussians Fe 10 7.16 5 P 2 5.49 5 S 72 5.16 5 C 9378 2.51 5 N 2312 2.21 5 O 2468 1.98 5 H 13511 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 228": "OE1" <-> "OE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A ASP 327": "OD1" <-> "OD2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A GLU 425": "OE1" <-> "OE2" Residue "A GLU 426": "OE1" <-> "OE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B ASP 201": "OD1" <-> "OD2" Residue "C TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C ASP 143": "OD1" <-> "OD2" Residue "E PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 228": "OE1" <-> "OE2" Residue "E ASP 252": "OD1" <-> "OD2" Residue "E GLU 282": "OE1" <-> "OE2" Residue "E TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 425": "OE1" <-> "OE2" Residue "F GLU 60": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G GLU 108": "OE1" <-> "OE2" Residue "G GLU 169": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27753 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 6850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 6850 Classifications: {'peptide': 428} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 399} Chain: "B" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 3794 Classifications: {'peptide': 256} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 235} Chain: "C" Number of atoms: 2648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 2648 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 10, 'TRANS': 168} Chain: "D" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 378 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "E" Number of atoms: 6851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 6851 Classifications: {'peptide': 428} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 399} Chain: "F" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 3794 Classifications: {'peptide': 256} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 235} Chain: "G" Number of atoms: 2648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 2648 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 10, 'TRANS': 168} Chain: "H" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 378 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "A" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 159 Unusual residues: {'HEM': 2, 'LOP': 1, 'PQU': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 159 Unusual residues: {'HEM': 2, 'LOP': 1, 'PQU': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12451 SG CYS C 129 60.107 26.204 68.142 1.00 62.25 S ATOM 12715 SG CYS C 149 56.545 26.275 68.783 1.00 57.81 S ATOM 26122 SG CYS G 129 44.451 88.466 68.175 1.00 69.88 S ATOM 26386 SG CYS G 149 47.890 88.169 69.125 1.00 64.04 S Time building chain proxies: 12.96, per 1000 atoms: 0.47 Number of scatterers: 27753 At special positions: 0 Unit cell: (106.24, 115.37, 106.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 10 26.01 S 72 16.00 P 2 15.00 O 2468 8.00 N 2312 7.00 C 9378 6.00 H 13511 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 169 " distance=2.04 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 151 " distance=2.03 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 169 " distance=2.03 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 151 " distance=2.03 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 24.45 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES C1001 " pdb="FE2 FES C1001 " - pdb=" ND1 HIS C 152 " pdb="FE2 FES C1001 " - pdb=" ND1 HIS C 131 " pdb="FE1 FES C1001 " - pdb=" SG CYS C 149 " pdb="FE1 FES C1001 " - pdb=" SG CYS C 129 " pdb=" FES G1001 " pdb="FE2 FES G1001 " - pdb=" ND1 HIS G 131 " pdb="FE2 FES G1001 " - pdb=" ND1 HIS G 152 " pdb="FE1 FES G1001 " - pdb=" SG CYS G 129 " pdb="FE1 FES G1001 " - pdb=" SG CYS G 149 " Number of angles added : 6 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3224 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 12 sheets defined 51.2% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.28 Creating SS restraints... Processing helix chain 'A' and resid 14 through 20 Processing helix chain 'A' and resid 25 through 33 Processing helix chain 'A' and resid 43 through 67 removed outlier: 4.090A pdb=" N TRP A 47 " --> pdb=" O MET A 44 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY A 48 " --> pdb=" O TRP A 45 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 49 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 61 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 85 Processing helix chain 'A' and resid 90 through 118 removed outlier: 3.807A pdb=" N ALA A 101 " --> pdb=" O HIS A 97 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 147 Processing helix chain 'A' and resid 153 through 168 removed outlier: 3.577A pdb=" N PHE A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 188 through 219 Proline residue: A 202 - end of helix Processing helix chain 'A' and resid 234 through 240 Processing helix chain 'A' and resid 244 through 269 removed outlier: 6.718A pdb=" N ILE A 249 " --> pdb=" O TRP A 245 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 280 Processing helix chain 'A' and resid 296 through 307 Proline residue: A 300 - end of helix Processing helix chain 'A' and resid 313 through 321 Processing helix chain 'A' and resid 328 through 344 removed outlier: 3.887A pdb=" N ILE A 340 " --> pdb=" O MET A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 349 No H-bonds generated for 'chain 'A' and resid 346 through 349' Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 363 through 382 removed outlier: 4.110A pdb=" N ALA A 382 " --> pdb=" O THR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 405 removed outlier: 3.886A pdb=" N PHE A 404 " --> pdb=" O TRP A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 414 removed outlier: 3.718A pdb=" N ALA A 413 " --> pdb=" O PRO A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'B' and resid 22 through 34 Processing helix chain 'B' and resid 36 through 38 No H-bonds generated for 'chain 'B' and resid 36 through 38' Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 60 through 69 removed outlier: 3.610A pdb=" N THR B 68 " --> pdb=" O ARG B 64 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 106 No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 127 through 135 Processing helix chain 'B' and resid 204 through 219 Processing helix chain 'B' and resid 223 through 252 Processing helix chain 'C' and resid 10 through 38 Proline residue: C 33 - end of helix removed outlier: 4.527A pdb=" N MET C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 45 No H-bonds generated for 'chain 'C' and resid 42 through 45' Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 111 through 114 Processing helix chain 'D' and resid 82 through 99 Processing helix chain 'E' and resid 14 through 20 Processing helix chain 'E' and resid 25 through 33 Processing helix chain 'E' and resid 43 through 67 removed outlier: 4.107A pdb=" N TRP E 47 " --> pdb=" O MET E 44 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY E 48 " --> pdb=" O TRP E 45 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL E 49 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR E 61 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA E 66 " --> pdb=" O ILE E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 85 Processing helix chain 'E' and resid 90 through 118 removed outlier: 3.822A pdb=" N ALA E 101 " --> pdb=" O HIS E 97 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 149 Processing helix chain 'E' and resid 153 through 168 Processing helix chain 'E' and resid 173 through 181 Processing helix chain 'E' and resid 188 through 219 Proline residue: E 202 - end of helix Processing helix chain 'E' and resid 234 through 240 Processing helix chain 'E' and resid 244 through 269 removed outlier: 6.709A pdb=" N ILE E 249 " --> pdb=" O TRP E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 280 Processing helix chain 'E' and resid 296 through 307 Proline residue: E 300 - end of helix Processing helix chain 'E' and resid 313 through 321 Processing helix chain 'E' and resid 328 through 349 removed outlier: 3.901A pdb=" N ILE E 340 " --> pdb=" O MET E 336 " (cutoff:3.500A) Proline residue: E 347 - end of helix Processing helix chain 'E' and resid 357 through 359 No H-bonds generated for 'chain 'E' and resid 357 through 359' Processing helix chain 'E' and resid 361 through 382 removed outlier: 3.851A pdb=" N ILE E 365 " --> pdb=" O PRO E 361 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA E 382 " --> pdb=" O THR E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 405 removed outlier: 3.936A pdb=" N PHE E 404 " --> pdb=" O TRP E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 414 removed outlier: 3.681A pdb=" N ALA E 413 " --> pdb=" O PRO E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 428 Processing helix chain 'F' and resid 22 through 34 Processing helix chain 'F' and resid 36 through 38 No H-bonds generated for 'chain 'F' and resid 36 through 38' Processing helix chain 'F' and resid 47 through 50 Processing helix chain 'F' and resid 60 through 69 removed outlier: 3.710A pdb=" N GLN F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 106 No H-bonds generated for 'chain 'F' and resid 103 through 106' Processing helix chain 'F' and resid 118 through 123 Processing helix chain 'F' and resid 127 through 135 Processing helix chain 'F' and resid 144 through 146 No H-bonds generated for 'chain 'F' and resid 144 through 146' Processing helix chain 'F' and resid 167 through 169 No H-bonds generated for 'chain 'F' and resid 167 through 169' Processing helix chain 'F' and resid 204 through 219 Processing helix chain 'F' and resid 223 through 252 Processing helix chain 'G' and resid 12 through 38 removed outlier: 3.774A pdb=" N TYR G 16 " --> pdb=" O ARG G 12 " (cutoff:3.500A) Proline residue: G 33 - end of helix removed outlier: 4.827A pdb=" N MET G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 45 No H-bonds generated for 'chain 'G' and resid 42 through 45' Processing helix chain 'G' and resid 79 through 87 Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'H' and resid 82 through 99 removed outlier: 3.593A pdb=" N PHE H 88 " --> pdb=" O ARG H 84 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 36 through 38 Processing sheet with id= B, first strand: chain 'B' and resid 71 through 73 Processing sheet with id= C, first strand: chain 'B' and resid 155 through 157 Processing sheet with id= D, first strand: chain 'C' and resid 50 through 53 Processing sheet with id= E, first strand: chain 'C' and resid 62 through 67 Processing sheet with id= F, first strand: chain 'C' and resid 147 through 149 Processing sheet with id= G, first strand: chain 'E' and resid 36 through 38 Processing sheet with id= H, first strand: chain 'F' and resid 71 through 73 Processing sheet with id= I, first strand: chain 'F' and resid 155 through 157 Processing sheet with id= J, first strand: chain 'G' and resid 50 through 53 removed outlier: 6.191A pdb=" N GLN G 185 " --> pdb=" O PHE G 178 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N PHE G 178 " --> pdb=" O GLN G 185 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 62 through 67 Processing sheet with id= L, first strand: chain 'G' and resid 147 through 149 639 hydrogen bonds defined for protein. 1755 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.27 Time building geometry restraints manager: 24.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.11: 13509 1.11 - 1.39: 6108 1.39 - 1.66: 8470 1.66 - 1.93: 124 1.93 - 2.21: 32 Bond restraints: 28243 Sorted by residual: bond pdb=" O4 LOP A1004 " pdb=" P1 LOP A1004 " ideal model delta sigma weight residual 1.500 1.720 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" O4 LOP E1004 " pdb=" P1 LOP E1004 " ideal model delta sigma weight residual 1.500 1.720 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" O3 LOP A1004 " pdb=" P1 LOP A1004 " ideal model delta sigma weight residual 1.497 1.714 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" O3 LOP E1004 " pdb=" P1 LOP E1004 " ideal model delta sigma weight residual 1.497 1.714 -0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" O2 LOP A1004 " pdb=" P1 LOP A1004 " ideal model delta sigma weight residual 1.650 1.542 0.108 2.00e-02 2.50e+03 2.90e+01 ... (remaining 28238 not shown) Histogram of bond angle deviations from ideal: 75.45 - 96.08: 28 96.08 - 116.70: 35323 116.70 - 137.32: 15509 137.32 - 157.94: 0 157.94 - 178.56: 12 Bond angle restraints: 50872 Sorted by residual: angle pdb=" C11 PQU A1003 " pdb=" O14 PQU A1003 " pdb=" C15 PQU A1003 " ideal model delta sigma weight residual 109.48 129.01 -19.53 3.00e+00 1.11e-01 4.24e+01 angle pdb=" C11 PQU E1003 " pdb=" O14 PQU E1003 " pdb=" C15 PQU E1003 " ideal model delta sigma weight residual 109.48 128.93 -19.45 3.00e+00 1.11e-01 4.21e+01 angle pdb=" CG ARG G 99 " pdb=" CD ARG G 99 " pdb=" NE ARG G 99 " ideal model delta sigma weight residual 112.00 122.22 -10.22 2.20e+00 2.07e-01 2.16e+01 angle pdb=" O2 LOP A1004 " pdb=" P1 LOP A1004 " pdb=" O3 LOP A1004 " ideal model delta sigma weight residual 110.20 98.39 11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" O2 LOP E1004 " pdb=" P1 LOP E1004 " pdb=" O3 LOP E1004 " ideal model delta sigma weight residual 110.20 99.10 11.10 3.00e+00 1.11e-01 1.37e+01 ... (remaining 50867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 12086 17.98 - 35.97: 804 35.97 - 53.95: 354 53.95 - 71.94: 120 71.94 - 89.92: 13 Dihedral angle restraints: 13377 sinusoidal: 7032 harmonic: 6345 Sorted by residual: dihedral pdb=" CG ARG G 99 " pdb=" CD ARG G 99 " pdb=" NE ARG G 99 " pdb=" CZ ARG G 99 " ideal model delta sinusoidal sigma weight residual 90.00 31.87 58.13 2 1.50e+01 4.44e-03 1.54e+01 dihedral pdb=" C2D HEC F1001 " pdb=" C3D HEC F1001 " pdb=" CAD HEC F1001 " pdb=" CBD HEC F1001 " ideal model delta sinusoidal sigma weight residual 0.00 89.92 -89.92 2 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" C3D HEM A1001 " pdb=" CAD HEM A1001 " pdb=" CBD HEM A1001 " pdb=" CGD HEM A1001 " ideal model delta sinusoidal sigma weight residual 180.00 90.89 89.11 2 2.00e+01 2.50e-03 1.20e+01 ... (remaining 13374 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2046 0.100 - 0.201: 72 0.201 - 0.301: 2 0.301 - 0.401: 1 0.401 - 0.501: 1 Chirality restraints: 2122 Sorted by residual: chirality pdb=" C4 LOP A1004 " pdb=" C3 LOP A1004 " pdb=" C5 LOP A1004 " pdb=" O5 LOP A1004 " both_signs ideal model delta sigma weight residual False -2.34 -1.84 -0.50 2.00e-01 2.50e+01 6.29e+00 chirality pdb=" C4 LOP E1004 " pdb=" C3 LOP E1004 " pdb=" C5 LOP E1004 " pdb=" O5 LOP E1004 " both_signs ideal model delta sigma weight residual False -2.34 -1.98 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" C5 PQU E1003 " pdb=" C6 PQU E1003 " pdb=" C8 PQU E1003 " pdb=" O4 PQU E1003 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 2119 not shown) Planarity restraints: 4192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 LOP E1004 " 0.080 2.00e-02 2.50e+03 1.50e-01 2.24e+02 pdb=" C14 LOP E1004 " -0.196 2.00e-02 2.50e+03 pdb=" C15 LOP E1004 " 0.196 2.00e-02 2.50e+03 pdb=" C16 LOP E1004 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 LOP E1004 " -0.121 2.00e-02 2.50e+03 6.99e-02 4.89e+01 pdb=" C7 LOP E1004 " 0.035 2.00e-02 2.50e+03 pdb=" O5 LOP E1004 " 0.043 2.00e-02 2.50e+03 pdb=" O7 LOP E1004 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC B1001 " 0.008 2.00e-02 2.50e+03 4.33e-02 4.22e+01 pdb=" C2C HEC B1001 " -0.116 2.00e-02 2.50e+03 pdb=" C3C HEC B1001 " 0.039 2.00e-02 2.50e+03 pdb=" C4C HEC B1001 " 0.007 2.00e-02 2.50e+03 pdb=" CAC HEC B1001 " 0.008 2.00e-02 2.50e+03 pdb=" CHC HEC B1001 " 0.022 2.00e-02 2.50e+03 pdb=" CHD HEC B1001 " -0.002 2.00e-02 2.50e+03 pdb=" CMC HEC B1001 " 0.036 2.00e-02 2.50e+03 pdb=" NC HEC B1001 " -0.001 2.00e-02 2.50e+03 ... (remaining 4189 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 3144 2.25 - 2.84: 60479 2.84 - 3.42: 74277 3.42 - 4.01: 102787 4.01 - 4.60: 157878 Nonbonded interactions: 398565 Sorted by model distance: nonbonded pdb="HH12 ARG E 114 " pdb=" O2A HEM E1002 " model vdw 1.662 1.850 nonbonded pdb="HH22 ARG E 85 " pdb=" O ALA F 218 " model vdw 1.677 1.850 nonbonded pdb="HH12 ARG A 114 " pdb=" O2A HEM A1002 " model vdw 1.686 1.850 nonbonded pdb=" O CYS F 169 " pdb=" HG1 THR F 177 " model vdw 1.696 1.850 nonbonded pdb=" O ALA B 65 " pdb=" HG1 THR B 68 " model vdw 1.707 1.850 ... (remaining 398560 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' selection = (chain 'E' and (resid 3 through 96 or (resid 97 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid \ 98 through 430 or resid 1001 through 1004)) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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=1.00 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: 2.070 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: 0.410 Extract box with map and model: 13.110 Check model and map are aligned: 0.470 Set scattering table: 0.280 Process input model: 99.400 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.160 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:11.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 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 : 0.007 0.220 14732 Z= 0.433 Angle : 0.795 19.529 20182 Z= 0.363 Chirality : 0.045 0.501 2122 Planarity : 0.006 0.150 2544 Dihedral : 13.863 89.920 5082 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Rotamer: Outliers : 1.34 % Allowed : 7.55 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 (0.20), residues: 1758 helix: 1.01 (0.17), residues: 926 sheet: -1.76 (0.54), residues: 84 loop : -0.57 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 157 HIS 0.007 0.001 HIS E 111 PHE 0.021 0.002 PHE E 216 TYR 0.010 0.001 TYR E 399 ARG 0.006 0.001 ARG G 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 227 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ASP cc_start: 0.8006 (m-30) cc_final: 0.7745 (m-30) outliers start: 19 outliers final: 3 residues processed: 242 average time/residue: 2.3725 time to fit residues: 636.3684 Evaluate side-chains 153 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 150 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 181 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN B 173 ASN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14732 Z= 0.252 Angle : 0.601 15.266 20182 Z= 0.268 Chirality : 0.040 0.155 2122 Planarity : 0.005 0.047 2544 Dihedral : 10.520 168.464 2060 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.10 % Favored : 97.84 % Rotamer: Outliers : 0.85 % Allowed : 11.85 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.92 (0.20), residues: 1758 helix: 1.44 (0.17), residues: 914 sheet: -1.31 (0.57), residues: 84 loop : -0.09 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 157 HIS 0.007 0.001 HIS E 276 PHE 0.019 0.001 PHE E 216 TYR 0.010 0.001 TYR E 399 ARG 0.003 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 155 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 164 average time/residue: 2.6956 time to fit residues: 490.9606 Evaluate side-chains 146 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 231 PHE Chi-restraints excluded: chain G residue 55 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14732 Z= 0.286 Angle : 0.577 14.008 20182 Z= 0.260 Chirality : 0.040 0.148 2122 Planarity : 0.004 0.040 2544 Dihedral : 9.380 89.877 2053 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.05 % Favored : 97.90 % Rotamer: Outliers : 0.92 % Allowed : 12.06 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.13 (0.21), residues: 1758 helix: 1.56 (0.17), residues: 920 sheet: -1.10 (0.51), residues: 104 loop : 0.09 (0.25), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 157 HIS 0.005 0.001 HIS E 276 PHE 0.021 0.001 PHE E 216 TYR 0.012 0.001 TYR E 399 ARG 0.002 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 140 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8043 (tp30) outliers start: 13 outliers final: 5 residues processed: 158 average time/residue: 2.6408 time to fit residues: 459.5575 Evaluate side-chains 149 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 143 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain F residue 114 MET Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain G residue 89 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 HIS B 173 ASN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 14732 Z= 0.377 Angle : 0.605 14.620 20182 Z= 0.277 Chirality : 0.041 0.144 2122 Planarity : 0.004 0.042 2544 Dihedral : 9.343 89.911 2053 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.45 % Favored : 97.50 % Rotamer: Outliers : 1.06 % Allowed : 12.62 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.09 (0.21), residues: 1758 helix: 1.52 (0.17), residues: 934 sheet: -1.15 (0.51), residues: 104 loop : 0.08 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 157 HIS 0.006 0.001 HIS E 276 PHE 0.023 0.001 PHE E 216 TYR 0.013 0.001 TYR E 399 ARG 0.002 0.000 ARG A 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 2.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8740 (p) REVERT: C 117 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7609 (p0) REVERT: F 140 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8068 (tp30) outliers start: 15 outliers final: 6 residues processed: 154 average time/residue: 2.6621 time to fit residues: 450.8597 Evaluate side-chains 145 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 136 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain F residue 114 MET Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 195 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 41 optimal weight: 0.3980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14732 Z= 0.229 Angle : 0.551 12.537 20182 Z= 0.253 Chirality : 0.039 0.148 2122 Planarity : 0.004 0.041 2544 Dihedral : 9.004 88.663 2052 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.39 % Favored : 97.55 % Rotamer: Outliers : 0.78 % Allowed : 12.76 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.22 (0.21), residues: 1758 helix: 1.62 (0.17), residues: 932 sheet: -1.17 (0.51), residues: 104 loop : 0.15 (0.25), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 157 HIS 0.007 0.001 HIS A 276 PHE 0.022 0.001 PHE A 216 TYR 0.011 0.001 TYR E 399 ARG 0.002 0.000 ARG F 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 148 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 140 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8040 (tp30) outliers start: 11 outliers final: 7 residues processed: 156 average time/residue: 2.7092 time to fit residues: 471.1405 Evaluate side-chains 145 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain G residue 89 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 166 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 HIS B 173 ASN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14732 Z= 0.288 Angle : 0.568 12.980 20182 Z= 0.260 Chirality : 0.040 0.143 2122 Planarity : 0.004 0.042 2544 Dihedral : 8.922 89.918 2052 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.33 % Rotamer: Outliers : 0.78 % Allowed : 13.19 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.22 (0.21), residues: 1758 helix: 1.63 (0.17), residues: 934 sheet: -1.20 (0.51), residues: 104 loop : 0.16 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 157 HIS 0.005 0.001 HIS G 155 PHE 0.023 0.001 PHE A 216 TYR 0.012 0.001 TYR E 399 ARG 0.001 0.000 ARG A 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 VAL cc_start: 0.8914 (OUTLIER) cc_final: 0.8702 (p) REVERT: F 140 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8022 (tp30) outliers start: 11 outliers final: 6 residues processed: 146 average time/residue: 2.5970 time to fit residues: 418.9820 Evaluate side-chains 142 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain G residue 89 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 103 optimal weight: 0.0000 chunk 101 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14732 Z= 0.171 Angle : 0.517 11.008 20182 Z= 0.238 Chirality : 0.039 0.149 2122 Planarity : 0.004 0.039 2544 Dihedral : 8.556 89.929 2052 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.56 % Favored : 97.38 % Rotamer: Outliers : 0.78 % Allowed : 13.19 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.42 (0.21), residues: 1758 helix: 1.77 (0.17), residues: 934 sheet: -1.14 (0.52), residues: 104 loop : 0.27 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 157 HIS 0.007 0.001 HIS E 276 PHE 0.020 0.001 PHE E 216 TYR 0.010 0.001 TYR E 399 ARG 0.001 0.000 ARG F 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 2.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.9097 (t0) cc_final: 0.8827 (t0) REVERT: B 231 PHE cc_start: 0.8379 (m-80) cc_final: 0.7950 (t80) REVERT: C 61 VAL cc_start: 0.8876 (OUTLIER) cc_final: 0.8650 (p) REVERT: E 279 ASN cc_start: 0.9174 (t0) cc_final: 0.8896 (t0) REVERT: F 140 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8036 (tp30) REVERT: H 85 LEU cc_start: 0.8446 (mm) cc_final: 0.8242 (mm) outliers start: 11 outliers final: 4 residues processed: 160 average time/residue: 2.3278 time to fit residues: 414.2298 Evaluate side-chains 146 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 190 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 0.1980 chunk 81 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN F 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14732 Z= 0.274 Angle : 0.558 12.385 20182 Z= 0.255 Chirality : 0.040 0.142 2122 Planarity : 0.004 0.040 2544 Dihedral : 8.437 88.189 2052 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.33 % Rotamer: Outliers : 0.71 % Allowed : 13.82 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.36 (0.21), residues: 1758 helix: 1.77 (0.17), residues: 936 sheet: -1.19 (0.52), residues: 104 loop : 0.18 (0.25), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 157 HIS 0.008 0.001 HIS G 155 PHE 0.022 0.001 PHE E 216 TYR 0.011 0.001 TYR E 399 ARG 0.002 0.000 ARG G 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 141 time to evaluate : 2.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.9129 (t0) cc_final: 0.8862 (t0) REVERT: B 231 PHE cc_start: 0.8412 (m-80) cc_final: 0.7928 (t80) REVERT: C 61 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8673 (p) REVERT: C 117 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7589 (p0) REVERT: E 279 ASN cc_start: 0.9207 (t0) cc_final: 0.8905 (t0) REVERT: F 140 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8053 (tp30) REVERT: H 85 LEU cc_start: 0.8477 (mm) cc_final: 0.8271 (mm) outliers start: 10 outliers final: 5 residues processed: 150 average time/residue: 2.5606 time to fit residues: 427.5067 Evaluate side-chains 146 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 138 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain G residue 72 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 146 optimal weight: 0.3980 chunk 153 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14732 Z= 0.260 Angle : 0.555 12.335 20182 Z= 0.255 Chirality : 0.039 0.144 2122 Planarity : 0.004 0.041 2544 Dihedral : 8.309 88.526 2052 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.33 % Rotamer: Outliers : 0.78 % Allowed : 13.75 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.36 (0.21), residues: 1758 helix: 1.75 (0.17), residues: 938 sheet: -1.18 (0.51), residues: 104 loop : 0.21 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 157 HIS 0.007 0.001 HIS G 155 PHE 0.021 0.001 PHE E 216 TYR 0.011 0.001 TYR E 399 ARG 0.001 0.000 ARG F 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.9125 (t0) cc_final: 0.8848 (t0) REVERT: B 231 PHE cc_start: 0.8409 (m-80) cc_final: 0.7935 (t80) REVERT: C 61 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8654 (p) REVERT: E 279 ASN cc_start: 0.9205 (t0) cc_final: 0.8904 (t0) REVERT: F 140 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8063 (tp30) REVERT: H 85 LEU cc_start: 0.8482 (mm) cc_final: 0.8280 (mm) outliers start: 11 outliers final: 5 residues processed: 149 average time/residue: 2.5049 time to fit residues: 414.0527 Evaluate side-chains 143 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain G residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN F 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14732 Z= 0.231 Angle : 0.539 12.025 20182 Z= 0.248 Chirality : 0.039 0.144 2122 Planarity : 0.004 0.040 2544 Dihedral : 8.206 88.060 2052 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.50 % Favored : 97.44 % Rotamer: Outliers : 0.71 % Allowed : 13.82 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.48 (0.21), residues: 1758 helix: 1.86 (0.17), residues: 926 sheet: -1.16 (0.52), residues: 104 loop : 0.27 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 157 HIS 0.006 0.001 HIS G 155 PHE 0.021 0.001 PHE E 216 TYR 0.011 0.001 TYR E 399 ARG 0.003 0.000 ARG G 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 137 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.9127 (t0) cc_final: 0.8847 (t0) REVERT: B 231 PHE cc_start: 0.8392 (m-80) cc_final: 0.7922 (t80) REVERT: C 61 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8635 (p) REVERT: C 117 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7582 (p0) REVERT: E 279 ASN cc_start: 0.9202 (t0) cc_final: 0.8830 (t160) REVERT: F 140 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8030 (tp30) outliers start: 10 outliers final: 5 residues processed: 144 average time/residue: 2.5178 time to fit residues: 401.6036 Evaluate side-chains 145 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain G residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 0.0770 chunk 125 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 136 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.078541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.067122 restraints weight = 94086.644| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.32 r_work: 0.2804 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14732 Z= 0.190 Angle : 0.530 11.298 20182 Z= 0.243 Chirality : 0.039 0.146 2122 Planarity : 0.004 0.038 2544 Dihedral : 8.049 87.738 2052 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.45 % Favored : 97.50 % Rotamer: Outliers : 0.71 % Allowed : 13.75 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.56 (0.21), residues: 1758 helix: 1.90 (0.17), residues: 928 sheet: -1.10 (0.52), residues: 104 loop : 0.35 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 157 HIS 0.006 0.001 HIS A 276 PHE 0.020 0.001 PHE E 216 TYR 0.010 0.001 TYR E 399 ARG 0.002 0.000 ARG G 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8611.97 seconds wall clock time: 152 minutes 26.98 seconds (9146.98 seconds total)