Starting phenix.real_space_refine on Fri Jan 19 23:34:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kls_0716/01_2024/6kls_0716_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kls_0716/01_2024/6kls_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_0716/01_2024/6kls_0716.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kls_0716/01_2024/6kls_0716.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kls_0716/01_2024/6kls_0716_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kls_0716/01_2024/6kls_0716_updated.pdb" } resolution = 3.3 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= 0.001 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-1.21-5211/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: 7.61, 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: 6.25 Conformation dependent library (CDL) restraints added in 2.1 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: 2.12 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: 3.06 Time building geometry restraints manager: 6.21 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: 7423 34.29 - 68.58: 241 68.58 - 102.87: 29 102.87 - 137.15: 10 137.15 - 171.44: 6 Dihedral angle restraints: 7709 sinusoidal: 3271 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 7706 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: 0.880 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: 4.130 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 39.170 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.010 ------------------------------------------------------------------------------- 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 : 18.651 171.443 4867 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 % Allowed : 5.44 % Favored : 93.87 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 92 HIS 0.003 0.001 HIS D 138 PHE 0.020 0.002 PHE F 25 TYR 0.013 0.001 TYR E 234 ARG 0.002 0.000 ARG E 308 *********************** 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 : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 ASP cc_start: 0.7669 (t0) cc_final: 0.7435 (t0) REVERT: B 18 ARG cc_start: 0.6919 (mtp180) cc_final: 0.6514 (mmp-170) REVERT: B 250 MET cc_start: 0.8260 (tpp) cc_final: 0.7966 (tpp) REVERT: B 259 MET cc_start: 0.8690 (mmt) cc_final: 0.8081 (mmt) REVERT: B 320 PHE cc_start: 0.7950 (t80) cc_final: 0.7554 (t80) REVERT: B 350 MET cc_start: 0.8999 (mmm) cc_final: 0.8784 (mmp) REVERT: E 12 ASP cc_start: 0.7690 (t0) cc_final: 0.7467 (t0) REVERT: E 18 ARG cc_start: 0.6830 (mtp180) cc_final: 0.6452 (mmp-170) REVERT: E 250 MET cc_start: 0.8231 (tpp) cc_final: 0.7955 (tpp) REVERT: E 259 MET cc_start: 0.8690 (mmt) cc_final: 0.8079 (mmt) REVERT: E 320 PHE cc_start: 0.7969 (t80) cc_final: 0.7546 (t80) outliers start: 9 outliers final: 2 residues processed: 216 average time/residue: 0.2870 time to fit residues: 86.7235 Evaluate side-chains 157 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 155 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain F residue 160 LEU 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: 0.8980 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: 1.3384 ------------------------------------------------------------------------------- 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: 0.7533 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13464 Z= 0.300 Angle : 0.776 15.030 18342 Z= 0.354 Chirality : 0.046 0.161 1914 Planarity : 0.006 0.069 2207 Dihedral : 17.542 179.332 1991 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.13 % Favored : 88.74 % Rotamer: Outliers : 2.07 % Allowed : 10.87 % Favored : 87.06 % 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: -2.57 (0.21), residues: 1510 helix: -0.49 (0.18), residues: 788 sheet: -3.06 (1.08), residues: 20 loop : -3.20 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 183 HIS 0.008 0.001 HIS A 138 PHE 0.023 0.002 PHE C 25 TYR 0.012 0.002 TYR E 141 ARG 0.003 0.000 ARG C 113 *********************** 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 192 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 165 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 ASP cc_start: 0.7800 (t0) cc_final: 0.7557 (t0) REVERT: B 18 ARG cc_start: 0.6987 (mtp180) cc_final: 0.6495 (mmp-170) REVERT: B 250 MET cc_start: 0.8175 (tpp) cc_final: 0.7906 (tpp) REVERT: B 350 MET cc_start: 0.8969 (mmm) cc_final: 0.8752 (tpp) REVERT: C 211 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8386 (ttp) REVERT: E 12 ASP cc_start: 0.7706 (t0) cc_final: 0.7499 (t0) REVERT: E 18 ARG cc_start: 0.6961 (mtp180) cc_final: 0.6474 (mmp-170) REVERT: F 211 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8394 (ttp) outliers start: 27 outliers final: 18 residues processed: 181 average time/residue: 0.2382 time to fit residues: 63.8294 Evaluate side-chains 169 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 182 GLN Chi-restraints excluded: chain F residue 211 MET 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: 2.9990 chunk 113 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 121 optimal weight: 0.4980 chunk 135 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7506 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13464 Z= 0.227 Angle : 0.714 13.243 18342 Z= 0.328 Chirality : 0.045 0.170 1914 Planarity : 0.005 0.066 2207 Dihedral : 16.999 169.966 1991 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.40 % Favored : 89.47 % Rotamer: Outliers : 3.06 % Allowed : 12.17 % Favored : 84.76 % 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: -2.84 (1.06), residues: 20 loop : -3.01 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 183 HIS 0.003 0.001 HIS B 217 PHE 0.020 0.001 PHE F 25 TYR 0.014 0.001 TYR E 249 ARG 0.002 0.000 ARG B 117 *********************** 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 203 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 163 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 ARG cc_start: 0.6957 (mtp180) cc_final: 0.6465 (mmp-170) REVERT: B 350 MET cc_start: 0.8943 (mmm) cc_final: 0.8719 (tpp) REVERT: C 113 ARG cc_start: 0.7850 (ptp90) cc_final: 0.7626 (ptt180) REVERT: E 12 ASP cc_start: 0.7729 (t0) cc_final: 0.7527 (t0) REVERT: E 18 ARG cc_start: 0.6919 (mtp180) cc_final: 0.6443 (mmp-170) REVERT: F 113 ARG cc_start: 0.7854 (ptp90) cc_final: 0.7468 (ptt180) outliers start: 40 outliers final: 23 residues processed: 190 average time/residue: 0.2219 time to fit residues: 64.0328 Evaluate side-chains 173 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 150 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 211 MET 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: 1.9990 chunk 15 optimal weight: 0.0020 chunk 65 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 overall best weight: 0.8190 ------------------------------------------------------------------------------- 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 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1561 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= 0.226 Angle : 0.701 12.622 18342 Z= 0.323 Chirality : 0.045 0.158 1914 Planarity : 0.005 0.057 2207 Dihedral : 16.637 168.037 1987 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.46 % Favored : 89.40 % Rotamer: Outliers : 3.22 % Allowed : 13.94 % Favored : 82.85 % 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: -1.82 (0.22), residues: 1510 helix: 0.16 (0.19), residues: 788 sheet: -2.55 (1.06), residues: 20 loop : -2.90 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 183 HIS 0.003 0.001 HIS B 217 PHE 0.019 0.001 PHE C 25 TYR 0.014 0.001 TYR E 249 ARG 0.002 0.000 ARG B 117 *********************** 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 199 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 157 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 ARG cc_start: 0.6995 (mtp180) cc_final: 0.6480 (mmp-170) REVERT: C 113 ARG cc_start: 0.7848 (ptp90) cc_final: 0.7605 (ptt180) REVERT: E 12 ASP cc_start: 0.7694 (t0) cc_final: 0.7478 (t0) REVERT: E 18 ARG cc_start: 0.6968 (mtp180) cc_final: 0.6472 (mmp-170) REVERT: F 113 ARG cc_start: 0.7838 (ptp90) cc_final: 0.7437 (ptt180) outliers start: 42 outliers final: 27 residues processed: 187 average time/residue: 0.2234 time to fit residues: 63.3041 Evaluate side-chains 182 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 155 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 113 HIS Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 182 GLN Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.5718 > 50: distance: 50 - 56: 29.712 distance: 56 - 57: 42.751 distance: 57 - 58: 21.651 distance: 57 - 60: 34.282 distance: 58 - 59: 20.597 distance: 58 - 65: 44.367 distance: 60 - 61: 16.315 distance: 61 - 62: 21.388 distance: 62 - 63: 8.184 distance: 63 - 64: 41.342 distance: 66 - 67: 39.508 distance: 67 - 68: 44.579 distance: 67 - 74: 48.006 distance: 71 - 72: 13.556 distance: 72 - 73: 41.325 distance: 74 - 75: 48.399 distance: 75 - 76: 40.629 distance: 75 - 78: 38.839 distance: 76 - 77: 39.762 distance: 76 - 83: 28.746 distance: 80 - 81: 15.852 distance: 81 - 82: 34.805 distance: 83 - 84: 34.039 distance: 84 - 85: 20.169 distance: 84 - 87: 56.022 distance: 85 - 86: 36.185 distance: 85 - 91: 31.805 distance: 87 - 88: 48.723 distance: 88 - 89: 30.584 distance: 88 - 90: 27.070 distance: 91 - 92: 12.998 distance: 91 - 97: 28.472 distance: 93 - 94: 40.072 distance: 93 - 98: 11.628 distance: 95 - 96: 39.918 distance: 96 - 97: 14.005 distance: 98 - 99: 38.725 distance: 99 - 100: 30.324 distance: 99 - 102: 39.163 distance: 100 - 101: 13.315 distance: 100 - 106: 28.631 distance: 106 - 107: 17.689 distance: 107 - 108: 55.727 distance: 107 - 110: 17.121 distance: 108 - 109: 51.806 distance: 108 - 115: 44.552 distance: 110 - 111: 51.939 distance: 111 - 112: 35.929 distance: 112 - 113: 27.803 distance: 113 - 114: 10.722 distance: 115 - 116: 41.836 distance: 116 - 117: 36.279 distance: 116 - 119: 17.521 distance: 117 - 126: 39.762 distance: 119 - 120: 18.866 distance: 120 - 122: 32.467 distance: 121 - 123: 42.576 distance: 122 - 124: 42.254 distance: 123 - 125: 31.468 distance: 124 - 125: 11.115 distance: 126 - 127: 54.635 distance: 127 - 128: 3.649 distance: 127 - 130: 37.823 distance: 128 - 129: 13.267 distance: 128 - 133: 39.222 distance: 130 - 132: 40.007 distance: 133 - 134: 38.869 distance: 133 - 139: 53.687 distance: 134 - 135: 12.051 distance: 134 - 137: 38.833 distance: 135 - 136: 27.468 distance: 135 - 140: 28.775 distance: 137 - 138: 39.057 distance: 138 - 139: 39.249