Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 17:53:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kls_0716/04_2023/6kls_0716_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kls_0716/04_2023/6kls_0716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kls_0716/04_2023/6kls_0716.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kls_0716/04_2023/6kls_0716.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kls_0716/04_2023/6kls_0716_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kls_0716/04_2023/6kls_0716_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.007 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: 6 Type Number sf(0) Gaussians Fe 10 7.16 5 P 3 5.49 5 S 56 5.16 5 C 8872 2.51 5 N 1968 2.21 5 O 2102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 30": "NH1" <-> "NH2" Residue "A GLU 34": "OE1" <-> "OE2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B ARG 308": "NH1" <-> "NH2" Residue "C TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 53": "OE1" <-> "OE2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "D ARG 30": "NH1" <-> "NH2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E GLU 19": "OE1" <-> "OE2" Residue "E ARG 22": "NH1" <-> "NH2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E GLU 280": "OE1" <-> "OE2" Residue "E GLU 297": "OE1" <-> "OE2" Residue "E ARG 308": "NH1" <-> "NH2" Residue "F TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F ARG 77": "NH1" <-> "NH2" Residue "F PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 231": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 13011 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1012 Classifications: {'peptide': 134} Link IDs: {'CIS': 2, 'PTRANS': 13, 'TRANS': 118} Chain breaks: 2 Chain: "B" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3226 Classifications: {'peptide': 395} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 367} Chain: "C" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1917 Classifications: {'peptide': 236} Link IDs: {'CIS': 6, 'PTRANS': 15, 'TRANS': 214} Chain: "D" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1012 Classifications: {'peptide': 134} Link IDs: {'CIS': 2, 'PTRANS': 13, 'TRANS': 118} Chain breaks: 2 Chain: "E" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3226 Classifications: {'peptide': 395} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 367} Chain: "F" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1917 Classifications: {'peptide': 236} Link IDs: {'CIS': 6, 'PTRANS': 15, 'TRANS': 214} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 282 Unusual residues: {'DLX': 2, 'HEM': 2, 'PGV': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'DLX': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" 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: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 231 Unusual residues: {'DLX': 2, 'HEM': 2, 'PGV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'DLX': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 626 SG CYS A 111 29.763 32.691 19.945 1.00 1.00 S ATOM 748 SG CYS A 135 31.243 32.795 16.781 1.00 1.00 S ATOM 6781 SG CYS D 111 73.123 70.219 19.957 1.00 1.00 S ATOM 6903 SG CYS D 135 71.643 70.116 16.792 1.00 1.00 S Time building chain proxies: 7.56, per 1000 atoms: 0.58 Number of scatterers: 13011 At special positions: 0 Unit cell: (103.95, 103.95, 105, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 10 26.01 S 56 16.00 P 3 15.00 O 2102 8.00 N 1968 7.00 C 8872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 137 " distance=2.03 Simple disulfide: pdb=" SG CYS D 116 " - pdb=" SG CYS D 137 " 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.40 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 501 " pdb="FE2 FES A 501 " - pdb=" ND1 HIS A 138 " pdb="FE2 FES A 501 " - pdb=" NE2 HIS A 113 " pdb="FE1 FES A 501 " - pdb=" SG CYS A 111 " pdb="FE1 FES A 501 " - pdb=" SG CYS A 135 " pdb=" FES D 501 " pdb="FE2 FES D 501 " - pdb=" ND1 HIS D 138 " pdb="FE1 FES D 501 " - pdb=" SG CYS D 111 " pdb="FE2 FES D 501 " - pdb=" NE2 HIS D 113 " pdb="FE1 FES D 501 " - pdb=" SG CYS D 135 " Number of angles added : 6 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2836 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 6 sheets defined 48.0% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 12 through 32 Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'B' and resid 9 through 15 removed outlier: 3.541A pdb=" N ARG B 14 " --> pdb=" O TRP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 24 removed outlier: 3.621A pdb=" N THR B 23 " --> pdb=" O GLU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 60 removed outlier: 3.664A pdb=" N PHE B 40 " --> pdb=" O PRO B 37 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLY B 41 " --> pdb=" O TYR B 38 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET B 56 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 57 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE B 59 " --> pdb=" O MET B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 79 No H-bonds generated for 'chain 'B' and resid 76 through 79' Processing helix chain 'B' and resid 84 through 111 removed outlier: 3.507A pdb=" N HIS B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 139 Processing helix chain 'B' and resid 147 through 161 removed outlier: 4.140A pdb=" N TRP B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Proline residue: B 160 - end of helix Processing helix chain 'B' and resid 192 through 224 removed outlier: 4.730A pdb=" N TYR B 206 " --> pdb=" O HIS B 202 " (cutoff:3.500A) Proline residue: B 207 - end of helix Processing helix chain 'B' and resid 246 through 249 No H-bonds generated for 'chain 'B' and resid 246 through 249' Processing helix chain 'B' and resid 251 through 271 removed outlier: 3.600A pdb=" N MET B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 298 through 306 removed outlier: 5.148A pdb=" N GLY B 302 " --> pdb=" O TYR B 299 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 327 removed outlier: 4.579A pdb=" N LEU B 327 " --> pdb=" O LEU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 333 No H-bonds generated for 'chain 'B' and resid 330 through 333' Processing helix chain 'B' and resid 345 through 364 removed outlier: 4.189A pdb=" N VAL B 349 " --> pdb=" O PRO B 345 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 389 removed outlier: 3.891A pdb=" N PHE B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 399 Processing helix chain 'C' and resid 4 through 24 removed outlier: 3.631A pdb=" N GLY C 14 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR C 16 " --> pdb=" O PHE C 12 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 22 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 55 No H-bonds generated for 'chain 'C' and resid 53 through 55' Processing helix chain 'C' and resid 58 through 69 Processing helix chain 'C' and resid 146 through 150 Processing helix chain 'C' and resid 152 through 158 Processing helix chain 'C' and resid 162 through 165 No H-bonds generated for 'chain 'C' and resid 162 through 165' Processing helix chain 'C' and resid 184 through 196 Processing helix chain 'C' and resid 204 through 237 removed outlier: 3.678A pdb=" N THR C 209 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS C 235 " --> pdb=" O GLU C 231 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG C 236 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 32 Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'E' and resid 9 through 15 removed outlier: 3.541A pdb=" N ARG E 14 " --> pdb=" O TRP E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 24 removed outlier: 3.620A pdb=" N THR E 23 " --> pdb=" O GLU E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 60 removed outlier: 3.665A pdb=" N PHE E 40 " --> pdb=" O PRO E 37 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLY E 41 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET E 56 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL E 57 " --> pdb=" O SER E 54 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE E 59 " --> pdb=" O MET E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 79 No H-bonds generated for 'chain 'E' and resid 76 through 79' Processing helix chain 'E' and resid 84 through 111 removed outlier: 3.506A pdb=" N HIS E 91 " --> pdb=" O PHE E 87 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 139 Processing helix chain 'E' and resid 147 through 161 removed outlier: 4.140A pdb=" N TRP E 151 " --> pdb=" O GLN E 147 " (cutoff:3.500A) Proline residue: E 160 - end of helix Processing helix chain 'E' and resid 192 through 224 removed outlier: 4.729A pdb=" N TYR E 206 " --> pdb=" O HIS E 202 " (cutoff:3.500A) Proline residue: E 207 - end of helix Processing helix chain 'E' and resid 246 through 249 No H-bonds generated for 'chain 'E' and resid 246 through 249' Processing helix chain 'E' and resid 251 through 271 removed outlier: 3.600A pdb=" N MET E 259 " --> pdb=" O GLY E 255 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE E 268 " --> pdb=" O VAL E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 281 No H-bonds generated for 'chain 'E' and resid 279 through 281' Processing helix chain 'E' and resid 298 through 306 removed outlier: 5.148A pdb=" N GLY E 302 " --> pdb=" O TYR E 299 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU E 305 " --> pdb=" O GLY E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 327 removed outlier: 4.579A pdb=" N LEU E 327 " --> pdb=" O LEU E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 333 No H-bonds generated for 'chain 'E' and resid 330 through 333' Processing helix chain 'E' and resid 345 through 364 removed outlier: 4.190A pdb=" N VAL E 349 " --> pdb=" O PRO E 345 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET E 350 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU E 361 " --> pdb=" O SER E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 389 removed outlier: 3.891A pdb=" N PHE E 388 " --> pdb=" O VAL E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 399 Processing helix chain 'F' and resid 4 through 24 removed outlier: 3.631A pdb=" N GLY F 14 " --> pdb=" O ILE F 10 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR F 16 " --> pdb=" O PHE F 12 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU F 22 " --> pdb=" O VAL F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 55 No H-bonds generated for 'chain 'F' and resid 53 through 55' Processing helix chain 'F' and resid 58 through 69 Processing helix chain 'F' and resid 146 through 150 Processing helix chain 'F' and resid 152 through 158 Processing helix chain 'F' and resid 162 through 165 No H-bonds generated for 'chain 'F' and resid 162 through 165' Processing helix chain 'F' and resid 184 through 196 Processing helix chain 'F' and resid 204 through 237 removed outlier: 3.678A pdb=" N THR F 209 " --> pdb=" O SER F 205 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS F 235 " --> pdb=" O GLU F 231 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG F 236 " --> pdb=" O ASN F 232 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU F 237 " --> pdb=" O LEU F 233 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 56 through 60 removed outlier: 3.838A pdb=" N GLN A 56 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG A 71 " --> pdb=" O GLN A 56 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 133 through 135 removed outlier: 3.613A pdb=" N GLY A 140 " --> pdb=" O CYS A 135 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 101 through 104 removed outlier: 3.577A pdb=" N ARG C 101 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG C 113 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 56 through 60 removed outlier: 3.837A pdb=" N GLN D 56 " --> pdb=" O ARG D 71 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG D 71 " --> pdb=" O GLN D 56 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 133 through 135 removed outlier: 3.613A pdb=" N GLY D 140 " --> pdb=" O CYS D 135 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 101 through 104 removed outlier: 3.576A pdb=" N ARG F 101 " --> pdb=" O PHE F 115 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ARG F 113 " --> pdb=" O VAL F 103 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1308 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: 3.40 Time building geometry restraints manager: 5.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.39: 5244 1.39 - 1.60: 8066 1.60 - 1.81: 120 1.81 - 2.02: 2 2.02 - 2.24: 32 Bond restraints: 13464 Sorted by residual: bond pdb=" C30 DLX B 504 " pdb=" C31 DLX B 504 " ideal model delta sigma weight residual 1.335 1.658 -0.323 2.00e-02 2.50e+03 2.60e+02 bond pdb=" C30 DLX E 504 " pdb=" C31 DLX E 504 " ideal model delta sigma weight residual 1.335 1.658 -0.323 2.00e-02 2.50e+03 2.60e+02 bond pdb=" C30 DLX F 301 " pdb=" C31 DLX F 301 " ideal model delta sigma weight residual 1.335 1.656 -0.321 2.00e-02 2.50e+03 2.57e+02 bond pdb=" C30 DLX C 301 " pdb=" C31 DLX C 301 " ideal model delta sigma weight residual 1.335 1.655 -0.320 2.00e-02 2.50e+03 2.56e+02 bond pdb=" C22 DLX E 504 " pdb=" C23 DLX E 504 " ideal model delta sigma weight residual 1.335 1.597 -0.262 2.00e-02 2.50e+03 1.71e+02 ... (remaining 13459 not shown) Histogram of bond angle deviations from ideal: 87.91 - 106.00: 491 106.00 - 124.09: 17212 124.09 - 142.18: 627 142.18 - 160.27: 0 160.27 - 178.36: 12 Bond angle restraints: 18342 Sorted by residual: angle pdb=" S1 FES A 501 " pdb="FE2 FES A 501 " pdb=" S2 FES A 501 " ideal model delta sigma weight residual 104.33 89.99 14.34 1.14e+00 7.69e-01 1.58e+02 angle pdb=" S1 FES D 501 " pdb="FE2 FES D 501 " pdb=" S2 FES D 501 " ideal model delta sigma weight residual 104.33 90.05 14.28 1.14e+00 7.69e-01 1.57e+02 angle pdb=" S1 FES A 501 " pdb="FE1 FES A 501 " pdb=" S2 FES A 501 " ideal model delta sigma weight residual 104.33 89.99 14.34 1.20e+00 6.94e-01 1.43e+02 angle pdb=" S1 FES D 501 " pdb="FE1 FES D 501 " pdb=" S2 FES D 501 " ideal model delta sigma weight residual 104.33 90.04 14.29 1.20e+00 6.94e-01 1.42e+02 angle pdb="FE1 FES D 501 " pdb=" S2 FES D 501 " pdb="FE2 FES D 501 " ideal model delta sigma weight residual 75.66 88.44 -12.78 1.14e+00 7.69e-01 1.26e+02 ... (remaining 18337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.29: 7393 34.29 - 68.58: 219 68.58 - 102.87: 28 102.87 - 137.15: 9 137.15 - 171.44: 6 Dihedral angle restraints: 7655 sinusoidal: 3217 harmonic: 4438 Sorted by residual: dihedral pdb=" CA GLY D 151 " pdb=" C GLY D 151 " pdb=" N PRO D 152 " pdb=" CA PRO D 152 " ideal model delta harmonic sigma weight residual 180.00 150.29 29.71 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA GLY A 151 " pdb=" C GLY A 151 " pdb=" N PRO A 152 " pdb=" CA PRO A 152 " ideal model delta harmonic sigma weight residual 180.00 150.32 29.68 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA PRO F 140 " pdb=" C PRO F 140 " pdb=" N PRO F 141 " pdb=" CA PRO F 141 " ideal model delta harmonic sigma weight residual 180.00 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 7652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1796 0.093 - 0.187: 105 0.187 - 0.280: 11 0.280 - 0.373: 0 0.373 - 0.467: 2 Chirality restraints: 1914 Sorted by residual: chirality pdb=" CA LEU C 160 " pdb=" N LEU C 160 " pdb=" C LEU C 160 " pdb=" CB LEU C 160 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" CA LEU F 160 " pdb=" N LEU F 160 " pdb=" C LEU F 160 " pdb=" CB LEU F 160 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" C05 PGV B 506 " pdb=" C04 PGV B 506 " pdb=" C06 PGV B 506 " pdb=" O05 PGV B 506 " both_signs ideal model delta sigma weight residual False 2.29 2.55 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1911 not shown) Planarity restraints: 2207 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C25 DLX C 301 " 0.456 2.00e-02 2.50e+03 4.08e-01 2.08e+03 pdb=" C26 DLX C 301 " -0.469 2.00e-02 2.50e+03 pdb=" C27 DLX C 301 " -0.445 2.00e-02 2.50e+03 pdb=" C28 DLX C 301 " 0.006 2.00e-02 2.50e+03 pdb=" C44 DLX C 301 " 0.453 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C25 DLX F 301 " -0.456 2.00e-02 2.50e+03 4.08e-01 2.08e+03 pdb=" C26 DLX F 301 " 0.469 2.00e-02 2.50e+03 pdb=" C27 DLX F 301 " 0.445 2.00e-02 2.50e+03 pdb=" C28 DLX F 301 " -0.006 2.00e-02 2.50e+03 pdb=" C44 DLX F 301 " -0.453 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C25 DLX B 504 " 0.298 2.00e-02 2.50e+03 3.21e-01 1.29e+03 pdb=" C26 DLX B 504 " -0.591 2.00e-02 2.50e+03 pdb=" C27 DLX B 504 " 0.278 2.00e-02 2.50e+03 pdb=" C28 DLX B 504 " 0.015 2.00e-02 2.50e+03 pdb=" C44 DLX B 504 " -0.001 2.00e-02 2.50e+03 ... (remaining 2204 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 100 2.57 - 3.16: 10726 3.16 - 3.74: 19869 3.74 - 4.32: 29579 4.32 - 4.90: 47165 Nonbonded interactions: 107439 Sorted by model distance: nonbonded pdb=" O GLY C 168 " pdb=" CD2 HIS D 138 " model vdw 1.992 3.260 nonbonded pdb=" O PHE B 335 " pdb=" OG SER B 395 " model vdw 2.060 2.440 nonbonded pdb=" O PHE E 335 " pdb=" OG SER E 395 " model vdw 2.060 2.440 nonbonded pdb=" CD2 HIS A 138 " pdb=" O GLY F 168 " model vdw 2.135 3.260 nonbonded pdb=" OE1 GLU A 34 " pdb=" OG SER A 36 " model vdw 2.210 2.440 ... (remaining 107434 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 'D' } ncs_group { reference = (chain 'B' and (resid 7 through 401 or resid 501 through 505)) selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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=0.00 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.740 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 37.250 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 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 : 0.014 0.323 13464 Z= 0.801 Angle : 1.219 17.393 18342 Z= 0.568 Chirality : 0.051 0.467 1914 Planarity : 0.030 0.408 2207 Dihedral : 18.324 171.443 4813 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.66 % Favored : 89.21 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 1.13 % 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: -3.67 (0.19), residues: 1510 helix: -1.53 (0.17), residues: 780 sheet: None (None), residues: 0 loop : -3.57 (0.20), residues: 730 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 211 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 216 average time/residue: 0.2942 time to fit residues: 88.8808 Evaluate side-chains 159 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 157 time to evaluate : 1.474 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1187 time to fit residues: 2.4097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN B 96 ASN B 147 GLN B 373 ASN C 176 ASN C 198 ASN E 51 GLN E 96 ASN E 147 GLN E 373 ASN F 176 ASN F 182 GLN F 198 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 13464 Z= 0.330 Angle : 0.778 12.263 18342 Z= 0.358 Chirality : 0.047 0.161 1914 Planarity : 0.006 0.069 2207 Dihedral : 16.769 179.493 1933 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.93 % Favored : 88.94 % Rotamer Outliers : 2.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 1.13 % 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: -2.63 (0.21), residues: 1510 helix: -0.57 (0.18), residues: 792 sheet: -3.07 (1.08), residues: 20 loop : -3.21 (0.22), residues: 698 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 159 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 18 residues processed: 175 average time/residue: 0.2637 time to fit residues: 68.3420 Evaluate side-chains 162 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 144 time to evaluate : 1.527 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1305 time to fit residues: 6.4456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 13464 Z= 0.245 Angle : 0.713 13.318 18342 Z= 0.329 Chirality : 0.046 0.159 1914 Planarity : 0.005 0.066 2207 Dihedral : 16.213 167.617 1933 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.40 % Favored : 89.47 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 1.13 % 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: -2.13 (0.21), residues: 1510 helix: -0.11 (0.19), residues: 788 sheet: -2.82 (1.07), residues: 20 loop : -3.01 (0.22), residues: 702 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 166 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 6 residues processed: 181 average time/residue: 0.2357 time to fit residues: 64.1481 Evaluate side-chains 152 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 146 time to evaluate : 1.504 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1237 time to fit residues: 3.4214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 65 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 13464 Z= 0.224 Angle : 0.695 12.756 18342 Z= 0.321 Chirality : 0.045 0.169 1914 Planarity : 0.005 0.057 2207 Dihedral : 15.922 167.976 1933 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.79 % Favored : 89.07 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 1.13 % 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: -1.80 (0.22), residues: 1510 helix: 0.17 (0.19), residues: 788 sheet: -2.56 (1.09), residues: 20 loop : -2.88 (0.22), residues: 702 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 173 average time/residue: 0.2678 time to fit residues: 67.6540 Evaluate side-chains 160 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 1.517 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1293 time to fit residues: 4.4015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.6980 chunk 82 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7492 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 13464 Z= 0.225 Angle : 0.680 12.157 18342 Z= 0.318 Chirality : 0.045 0.169 1914 Planarity : 0.005 0.049 2207 Dihedral : 15.677 167.413 1933 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.33 % Favored : 89.54 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 1.13 % 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: -1.59 (0.22), residues: 1510 helix: 0.35 (0.19), residues: 788 sheet: -2.40 (1.09), residues: 20 loop : -2.79 (0.22), residues: 702 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 163 average time/residue: 0.2618 time to fit residues: 62.1507 Evaluate side-chains 159 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 152 time to evaluate : 1.370 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1194 time to fit residues: 3.4440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 145 optimal weight: 0.9990 chunk 120 optimal weight: 0.0870 chunk 67 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 139 optimal weight: 0.5980 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 13464 Z= 0.198 Angle : 0.678 12.433 18342 Z= 0.313 Chirality : 0.044 0.175 1914 Planarity : 0.005 0.047 2207 Dihedral : 15.432 167.795 1933 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.93 % Favored : 89.93 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 1.13 % 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: -1.39 (0.22), residues: 1510 helix: 0.51 (0.19), residues: 798 sheet: -2.09 (1.15), residues: 20 loop : -2.75 (0.23), residues: 692 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 155 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 163 average time/residue: 0.2748 time to fit residues: 64.7592 Evaluate side-chains 153 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 150 time to evaluate : 1.441 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1303 time to fit residues: 2.6584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.3980 chunk 82 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 88 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 13464 Z= 0.298 Angle : 0.726 12.834 18342 Z= 0.334 Chirality : 0.047 0.211 1914 Planarity : 0.005 0.045 2207 Dihedral : 15.481 167.642 1933 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.53 % Favored : 89.34 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 1.13 % 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: -1.44 (0.22), residues: 1510 helix: 0.43 (0.19), residues: 796 sheet: -2.00 (1.14), residues: 20 loop : -2.71 (0.23), residues: 694 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 161 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 173 average time/residue: 0.2727 time to fit residues: 68.4585 Evaluate side-chains 167 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 156 time to evaluate : 1.534 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1312 time to fit residues: 4.7225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 91 optimal weight: 0.0270 chunk 98 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 13464 Z= 0.204 Angle : 0.688 12.699 18342 Z= 0.316 Chirality : 0.044 0.176 1914 Planarity : 0.005 0.044 2207 Dihedral : 15.254 167.963 1933 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.60 % Favored : 90.26 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 1.13 % 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: -1.23 (0.22), residues: 1510 helix: 0.64 (0.19), residues: 796 sheet: -1.83 (1.19), residues: 20 loop : -2.66 (0.23), residues: 694 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 163 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 172 average time/residue: 0.2771 time to fit residues: 68.4640 Evaluate side-chains 156 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 1.456 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1380 time to fit residues: 2.4839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 0.0670 chunk 41 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 88 optimal weight: 0.0670 chunk 142 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 13464 Z= 0.189 Angle : 0.673 12.708 18342 Z= 0.312 Chirality : 0.044 0.168 1914 Planarity : 0.005 0.043 2207 Dihedral : 14.980 167.155 1933 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.20 % Favored : 89.67 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 1.13 % 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: -1.00 (0.23), residues: 1510 helix: 0.84 (0.20), residues: 788 sheet: -1.58 (1.26), residues: 20 loop : -2.53 (0.23), residues: 702 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 155 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 161 average time/residue: 0.2748 time to fit residues: 64.4116 Evaluate side-chains 153 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 150 time to evaluate : 1.401 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1341 time to fit residues: 2.6874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 182 GLN F 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 13464 Z= 0.205 Angle : 0.679 12.687 18342 Z= 0.314 Chirality : 0.044 0.174 1914 Planarity : 0.005 0.041 2207 Dihedral : 14.881 165.704 1933 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.80 % Favored : 90.07 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 1.13 % 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 (0.23), residues: 1510 helix: 0.90 (0.20), residues: 788 sheet: -1.39 (1.30), residues: 20 loop : -2.50 (0.23), residues: 702 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 152 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 157 average time/residue: 0.2709 time to fit residues: 61.9990 Evaluate side-chains 156 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 152 time to evaluate : 1.524 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1596 time to fit residues: 3.1194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.152091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 113)---------------| | r_work = 0.3240 r_free = 0.3240 target = 0.118118 restraints weight = 15620.776| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.44 r_work: 0.3051 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 13464 Z= 0.217 Angle : 0.679 12.754 18342 Z= 0.314 Chirality : 0.045 0.178 1914 Planarity : 0.005 0.041 2207 Dihedral : 14.826 164.738 1933 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.93 % Favored : 89.93 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 1.13 % 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: -0.90 (0.23), residues: 1510 helix: 0.91 (0.19), residues: 788 sheet: -1.41 (1.28), residues: 20 loop : -2.48 (0.23), residues: 702 =============================================================================== Job complete usr+sys time: 2626.06 seconds wall clock time: 48 minutes 45.69 seconds (2925.69 seconds total)