Starting phenix.real_space_refine on Mon Oct 14 16:53:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/10_2024/7una_26618_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/10_2024/7una_26618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/10_2024/7una_26618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/10_2024/7una_26618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/10_2024/7una_26618_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/10_2024/7una_26618_trim.cif" } resolution = 4.0 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= 0.000 sd= 0.002 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 P 8 5.49 5 S 40 5.16 5 C 5918 2.51 5 N 1521 2.21 5 O 1724 1.98 5 H 9203 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 18414 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2286 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain breaks: 4 Chain: "B" Number of atoms: 2266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2266 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain breaks: 4 Chain: "C" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2306 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain breaks: 4 Chain: "D" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2298 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain breaks: 3 Chain: "E" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2249 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 4 Chain: "F" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2277 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain breaks: 4 Chain: "G" Number of atoms: 2271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2271 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain breaks: 4 Chain: "H" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2281 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain breaks: 4 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" C1' 4BW A 401 " occ=0.47 ... (43 atoms not shown) pdb=" PBS 4BW A 401 " occ=0.47 residue: pdb=" C1' 4BW C 401 " occ=0.47 ... (43 atoms not shown) pdb=" PBS 4BW C 401 " occ=0.47 residue: pdb=" C1' 4BW F 401 " occ=0.47 ... (43 atoms not shown) pdb=" PBS 4BW F 401 " occ=0.47 residue: pdb=" C1' 4BW H 401 " occ=0.47 ... (43 atoms not shown) pdb=" PBS 4BW H 401 " occ=0.47 Time building chain proxies: 8.93, per 1000 atoms: 0.48 Number of scatterers: 18414 At special positions: 0 Unit cell: (134.2, 126.5, 171.6, 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) S 40 16.00 P 8 15.00 O 1724 8.00 N 1521 7.00 C 5918 6.00 H 9203 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.40 Conformation dependent library (CDL) restraints added in 1.5 seconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2134 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 51.6% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 154 through 177 Processing helix chain 'A' and resid 206 through 218 Processing helix chain 'A' and resid 262 through 273 removed outlier: 4.276A pdb=" N THR A 266 " --> pdb=" O SER A 262 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU A 269 " --> pdb=" O SER A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 308 Processing helix chain 'B' and resid 154 through 177 Processing helix chain 'B' and resid 206 through 218 Processing helix chain 'B' and resid 262 through 275 removed outlier: 4.293A pdb=" N THR B 266 " --> pdb=" O SER B 262 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B 269 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 308 removed outlier: 3.658A pdb=" N ASN B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 177 Processing helix chain 'C' and resid 206 through 218 Processing helix chain 'C' and resid 263 through 273 removed outlier: 3.964A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU C 269 " --> pdb=" O SER C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 308 removed outlier: 3.578A pdb=" N ASN C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 177 Processing helix chain 'D' and resid 206 through 218 Processing helix chain 'D' and resid 263 through 274 removed outlier: 3.898A pdb=" N ILE D 267 " --> pdb=" O THR D 263 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 308 removed outlier: 3.540A pdb=" N ASN D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 177 Processing helix chain 'E' and resid 206 through 218 Processing helix chain 'E' and resid 262 through 275 removed outlier: 4.289A pdb=" N THR E 266 " --> pdb=" O SER E 262 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE E 267 " --> pdb=" O THR E 263 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL E 268 " --> pdb=" O LEU E 264 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU E 269 " --> pdb=" O SER E 265 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 308 removed outlier: 3.644A pdb=" N ASN E 308 " --> pdb=" O LEU E 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 177 Processing helix chain 'F' and resid 206 through 217 Processing helix chain 'F' and resid 262 through 274 removed outlier: 4.244A pdb=" N THR F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE F 267 " --> pdb=" O THR F 263 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL F 268 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU F 269 " --> pdb=" O SER F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 308 Processing helix chain 'G' and resid 153 through 177 Processing helix chain 'G' and resid 206 through 218 Processing helix chain 'G' and resid 262 through 274 removed outlier: 4.234A pdb=" N THR G 266 " --> pdb=" O SER G 262 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE G 267 " --> pdb=" O THR G 263 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL G 268 " --> pdb=" O LEU G 264 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU G 269 " --> pdb=" O SER G 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 307 removed outlier: 3.861A pdb=" N ARG G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 177 Processing helix chain 'H' and resid 206 through 218 removed outlier: 3.593A pdb=" N TYR H 217 " --> pdb=" O TYR H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 275 removed outlier: 3.845A pdb=" N ILE H 267 " --> pdb=" O THR H 263 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL H 268 " --> pdb=" O LEU H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 308 removed outlier: 3.640A pdb=" N ASN H 308 " --> pdb=" O LEU H 304 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 179 Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 259 removed outlier: 4.032A pdb=" N ASN A 320 " --> pdb=" O ILE A 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 222 Processing sheet with id=AA4, first strand: chain 'B' and resid 220 through 222 removed outlier: 3.767A pdb=" N ASP B 259 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 196 " --> pdb=" O ASP B 259 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL B 193 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU B 318 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL B 195 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AA6, first strand: chain 'C' and resid 254 through 259 Processing sheet with id=AA7, first strand: chain 'D' and resid 220 through 222 removed outlier: 4.099A pdb=" N HIS D 239 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL D 193 " --> pdb=" O ASN D 316 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU D 318 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL D 195 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ASN D 320 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE D 197 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 178 through 179 Processing sheet with id=AA9, first strand: chain 'E' and resid 257 through 259 removed outlier: 3.703A pdb=" N ASP E 259 " --> pdb=" O ASP E 194 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL E 193 " --> pdb=" O ASN E 316 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU E 318 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL E 195 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ASN E 320 " --> pdb=" O VAL E 195 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ILE E 197 " --> pdb=" O ASN E 320 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 220 through 222 Processing sheet with id=AB2, first strand: chain 'F' and resid 220 through 223 removed outlier: 3.594A pdb=" N HIS F 239 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL F 193 " --> pdb=" O ASN F 316 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU F 318 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL F 195 " --> pdb=" O LEU F 318 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASN F 320 " --> pdb=" O VAL F 195 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE F 197 " --> pdb=" O ASN F 320 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 186 through 187 removed outlier: 3.568A pdb=" N VAL G 179 " --> pdb=" O ILE G 186 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 193 through 198 removed outlier: 6.263A pdb=" N VAL G 193 " --> pdb=" O ASN G 316 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU G 318 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL G 195 " --> pdb=" O LEU G 318 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ASN G 320 " --> pdb=" O VAL G 195 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ILE G 197 " --> pdb=" O ASN G 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'H' and resid 220 through 222 removed outlier: 3.791A pdb=" N HIS H 239 " --> pdb=" O LEU H 258 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL H 193 " --> pdb=" O ASN H 316 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU H 318 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL H 195 " --> pdb=" O LEU H 318 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASN H 320 " --> pdb=" O VAL H 195 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE H 197 " --> pdb=" O ASN H 320 " (cutoff:3.500A) 496 hydrogen bonds defined for protein. 1431 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: 6.46 Time building geometry restraints manager: 5.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9179 1.03 - 1.23: 27 1.23 - 1.42: 3844 1.42 - 1.61: 5454 1.61 - 1.81: 80 Bond restraints: 18584 Sorted by residual: bond pdb=" CBI 4BW A 401 " pdb=" CBM 4BW A 401 " ideal model delta sigma weight residual 1.538 1.289 0.249 2.00e-02 2.50e+03 1.54e+02 bond pdb=" CBI 4BW H 401 " pdb=" CBM 4BW H 401 " ideal model delta sigma weight residual 1.538 1.290 0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" CBI 4BW F 401 " pdb=" CBM 4BW F 401 " ideal model delta sigma weight residual 1.538 1.291 0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" CBI 4BW C 401 " pdb=" CBM 4BW C 401 " ideal model delta sigma weight residual 1.538 1.293 0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C4' 4BW C 401 " pdb=" O4' 4BW C 401 " ideal model delta sigma weight residual 1.445 1.656 -0.211 2.00e-02 2.50e+03 1.11e+02 ... (remaining 18579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 33444 3.47 - 6.95: 81 6.95 - 10.42: 48 10.42 - 13.89: 8 13.89 - 17.36: 8 Bond angle restraints: 33589 Sorted by residual: angle pdb=" CA PRO A 237 " pdb=" N PRO A 237 " pdb=" CD PRO A 237 " ideal model delta sigma weight residual 112.00 103.69 8.31 1.40e+00 5.10e-01 3.52e+01 angle pdb=" OAD 4BW C 401 " pdb=" PBR 4BW C 401 " pdb=" OAH 4BW C 401 " ideal model delta sigma weight residual 122.13 104.77 17.36 3.00e+00 1.11e-01 3.35e+01 angle pdb=" OAD 4BW A 401 " pdb=" PBR 4BW A 401 " pdb=" OAH 4BW A 401 " ideal model delta sigma weight residual 122.13 104.79 17.34 3.00e+00 1.11e-01 3.34e+01 angle pdb=" OAD 4BW F 401 " pdb=" PBR 4BW F 401 " pdb=" OAH 4BW F 401 " ideal model delta sigma weight residual 122.13 104.87 17.26 3.00e+00 1.11e-01 3.31e+01 angle pdb=" OAD 4BW H 401 " pdb=" PBR 4BW H 401 " pdb=" OAH 4BW H 401 " ideal model delta sigma weight residual 122.13 104.88 17.25 3.00e+00 1.11e-01 3.31e+01 ... (remaining 33584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.68: 8525 32.68 - 65.36: 268 65.36 - 98.03: 16 98.03 - 130.71: 15 130.71 - 163.39: 13 Dihedral angle restraints: 8837 sinusoidal: 4926 harmonic: 3911 Sorted by residual: dihedral pdb=" CAN 4BW A 401 " pdb=" OAV 4BW A 401 " pdb=" PBR 4BW A 401 " pdb=" OAH 4BW A 401 " ideal model delta sinusoidal sigma weight residual 330.18 166.79 163.39 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" CAN 4BW H 401 " pdb=" OAV 4BW H 401 " pdb=" PBR 4BW H 401 " pdb=" OAH 4BW H 401 " ideal model delta sinusoidal sigma weight residual 330.18 167.73 162.45 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CAN 4BW F 401 " pdb=" OAV 4BW F 401 " pdb=" PBR 4BW F 401 " pdb=" OAH 4BW F 401 " ideal model delta sinusoidal sigma weight residual 330.18 170.25 159.93 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 8834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1185 0.045 - 0.089: 187 0.089 - 0.134: 93 0.134 - 0.178: 15 0.178 - 0.223: 7 Chirality restraints: 1487 Sorted by residual: chirality pdb=" CBI 4BW C 401 " pdb=" CBM 4BW C 401 " pdb=" CBO 4BW C 401 " pdb=" OAG 4BW C 401 " both_signs ideal model delta sigma weight residual False 2.67 2.45 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CBI 4BW H 401 " pdb=" CBM 4BW H 401 " pdb=" CBO 4BW H 401 " pdb=" OAG 4BW H 401 " both_signs ideal model delta sigma weight residual False 2.67 2.47 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CBI 4BW F 401 " pdb=" CBM 4BW F 401 " pdb=" CBO 4BW F 401 " pdb=" OAG 4BW F 401 " both_signs ideal model delta sigma weight residual False 2.67 2.47 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1484 not shown) Planarity restraints: 2581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 236 " 0.077 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO A 237 " -0.191 5.00e-02 4.00e+02 pdb=" CA PRO A 237 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 237 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 163 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.63e+00 pdb=" C ASN A 163 " -0.051 2.00e-02 2.50e+03 pdb=" O ASN A 163 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 164 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 163 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.94e+00 pdb=" C ASN C 163 " -0.046 2.00e-02 2.50e+03 pdb=" O ASN C 163 " 0.017 2.00e-02 2.50e+03 pdb=" N SER C 164 " 0.015 2.00e-02 2.50e+03 ... (remaining 2578 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.20: 1167 2.20 - 2.80: 37925 2.80 - 3.40: 49727 3.40 - 4.00: 62165 4.00 - 4.60: 95811 Nonbonded interactions: 246795 Sorted by model distance: nonbonded pdb=" HG1 THR H 263 " pdb=" O3' 4BW H 401 " model vdw 1.594 2.450 nonbonded pdb=" O GLU F 172 " pdb=" HG SER F 176 " model vdw 1.596 2.450 nonbonded pdb=" OD1 ASN D 308 " pdb=" H ALA D 310 " model vdw 1.599 2.450 nonbonded pdb=" O GLU H 172 " pdb=" HG SER H 176 " model vdw 1.601 2.450 nonbonded pdb=" OD2 ASP G 194 " pdb=" HE2 HIS G 256 " model vdw 1.609 2.450 ... (remaining 246790 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 153 through 225 or (resid 235 and (name N or name CA or na \ me C or name O or name HA2 or name HA3)) or resid 236 through 241 or (resid 253 \ and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or \ name HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or name \ HG22 or name HG23)) or resid 254 through 274 or resid 285 through 321)) selection = (chain 'B' and (resid 153 through 184 or resid 186 through 225 or resid 235 thro \ ugh 241 or (resid 253 and (name N or name CA or name C or name O or name CB or n \ ame CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 \ or name HG21 or name HG22 or name HG23)) or resid 254 through 274 or resid 285 \ through 321)) selection = (chain 'C' and (resid 153 through 180 or (resid 185 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 186 through 225 \ or (resid 235 and (name N or name CA or name C or name O or name HA2 or name HA3 \ )) or resid 236 through 241 or (resid 253 and (name N or name CA or name C or na \ me O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or na \ me HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 254 throu \ gh 274 or (resid 285 and (name N or name CA or name C or name O or name CB or na \ me CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid 286 \ through 321)) selection = (chain 'D' and (resid 153 through 180 or (resid 185 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 186 through 225 \ or (resid 235 and (name N or name CA or name C or name O or name HA2 or name HA3 \ )) or resid 236 through 321)) selection = (chain 'E' and (resid 153 through 225 or resid 235 through 241 or (resid 253 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or na \ me HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG2 \ 2 or name HG23)) or resid 254 through 255 or (resid 256 and (name N or name CA o \ r name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or \ name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or \ name HE2)) or resid 257 through 274 or resid 285 through 321)) selection = (chain 'F' and (resid 153 through 180 or (resid 185 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 186 through 241 \ or (resid 253 and (name N or name CA or name C or name O or name CB or name CG1 \ or name CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or name \ HG21 or name HG22 or name HG23)) or resid 254 through 274 or (resid 285 and (na \ me N or name CA or name C or name O or name CB or name CG or name OD1 or name OD \ 2 or name HA or name HB2 or name HB3)) or resid 286 through 321)) selection = (chain 'G' and (resid 153 through 180 or (resid 185 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 186 through 225 \ or resid 235 through 241 or (resid 253 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name \ HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 254 through \ 255 or (resid 256 and (name N or name CA or name C or name O or name CB or name \ CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name \ HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 257 through 321)) \ selection = (chain 'H' and (resid 153 through 180 or (resid 185 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 186 through 225 \ or (resid 235 and (name N or name CA or name C or name O or name HA2 or name HA3 \ )) or resid 236 through 241 or (resid 253 and (name N or name CA or name C or na \ me O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or na \ me HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 254 throu \ gh 274 or resid 285 through 321)) } 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=0.47 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.160 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: 0.310 Extract box with map and model: 0.780 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 39.570 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.060 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.249 9381 Z= 0.820 Angle : 1.018 17.363 12670 Z= 0.444 Chirality : 0.044 0.223 1487 Planarity : 0.006 0.111 1516 Dihedral : 18.090 163.389 3627 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.26), residues: 1054 helix: 0.94 (0.22), residues: 519 sheet: -2.23 (0.33), residues: 211 loop : -1.96 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 174 PHE 0.019 0.001 PHE C 191 TYR 0.018 0.001 TYR F 162 ARG 0.008 0.001 ARG D 292 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 ASP cc_start: 0.7626 (m-30) cc_final: 0.7347 (m-30) REVERT: A 221 LYS cc_start: 0.6088 (pptt) cc_final: 0.5159 (pptt) REVERT: A 269 GLU cc_start: 0.7889 (mp0) cc_final: 0.7598 (mp0) REVERT: B 273 LEU cc_start: 0.8277 (mm) cc_final: 0.8064 (mm) REVERT: B 320 ASN cc_start: 0.7335 (t0) cc_final: 0.7036 (t0) REVERT: C 171 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8351 (mt-10) REVERT: C 172 GLU cc_start: 0.8089 (tt0) cc_final: 0.7822 (tt0) REVERT: D 172 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7712 (mp0) REVERT: D 292 ARG cc_start: 0.8432 (tpp80) cc_final: 0.8214 (ttm-80) REVERT: F 159 ILE cc_start: 0.8183 (mt) cc_final: 0.7980 (mt) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.4585 time to fit residues: 147.8318 Evaluate side-chains 180 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 ASN B 239 HIS D 316 ASN G 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9381 Z= 0.197 Angle : 0.549 5.001 12670 Z= 0.294 Chirality : 0.041 0.206 1487 Planarity : 0.004 0.051 1516 Dihedral : 20.902 176.114 1449 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.67 % Allowed : 8.64 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.26), residues: 1054 helix: 1.34 (0.22), residues: 522 sheet: -2.20 (0.35), residues: 200 loop : -1.47 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 239 PHE 0.016 0.001 PHE C 191 TYR 0.022 0.001 TYR F 303 ARG 0.005 0.000 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 194 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.6114 (pptt) cc_final: 0.5119 (pptt) REVERT: A 269 GLU cc_start: 0.8177 (mp0) cc_final: 0.7700 (mp0) REVERT: B 292 ARG cc_start: 0.7481 (mmt90) cc_final: 0.7271 (mmt90) REVERT: B 320 ASN cc_start: 0.7254 (t0) cc_final: 0.6740 (t0) REVERT: C 171 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8196 (mt-10) REVERT: C 269 GLU cc_start: 0.8183 (mp0) cc_final: 0.7907 (mp0) REVERT: C 292 ARG cc_start: 0.7703 (mtp85) cc_final: 0.6888 (mmt-90) REVERT: D 172 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7811 (mp0) REVERT: F 159 ILE cc_start: 0.8275 (mt) cc_final: 0.8030 (mt) REVERT: F 194 ASP cc_start: 0.7657 (m-30) cc_final: 0.7416 (t0) REVERT: F 299 LYS cc_start: 0.8383 (ptpp) cc_final: 0.8172 (tptt) REVERT: G 286 MET cc_start: 0.7582 (mmp) cc_final: 0.7212 (mmp) outliers start: 17 outliers final: 12 residues processed: 203 average time/residue: 0.4712 time to fit residues: 135.9033 Evaluate side-chains 187 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 175 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain H residue 202 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 214 ASN D 316 ASN ** F 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9381 Z= 0.301 Angle : 0.592 5.102 12670 Z= 0.323 Chirality : 0.042 0.231 1487 Planarity : 0.004 0.034 1516 Dihedral : 20.796 173.189 1449 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 2.36 % Allowed : 12.37 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.26), residues: 1054 helix: 1.42 (0.22), residues: 522 sheet: -2.10 (0.34), residues: 223 loop : -1.39 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 174 PHE 0.024 0.002 PHE A 191 TYR 0.017 0.002 TYR F 303 ARG 0.013 0.001 ARG D 292 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 180 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.6712 (pptt) cc_final: 0.5748 (pptt) REVERT: A 269 GLU cc_start: 0.8317 (mp0) cc_final: 0.7728 (mp0) REVERT: B 320 ASN cc_start: 0.6917 (t0) cc_final: 0.6560 (t0) REVERT: D 192 ARG cc_start: 0.8285 (pmt170) cc_final: 0.7977 (pmt-80) REVERT: D 290 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: E 291 MET cc_start: 0.7822 (tpt) cc_final: 0.7214 (tpp) REVERT: F 171 GLU cc_start: 0.7402 (tt0) cc_final: 0.7197 (tt0) outliers start: 24 outliers final: 19 residues processed: 193 average time/residue: 0.4564 time to fit residues: 127.6839 Evaluate side-chains 191 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 171 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain G residue 177 GLU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 287 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 ASN B 239 HIS ** F 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9381 Z= 0.303 Angle : 0.586 5.783 12670 Z= 0.320 Chirality : 0.042 0.239 1487 Planarity : 0.004 0.034 1516 Dihedral : 20.900 176.426 1449 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.85 % Allowed : 13.64 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.26), residues: 1054 helix: 1.42 (0.22), residues: 520 sheet: -2.06 (0.34), residues: 228 loop : -1.37 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 239 PHE 0.026 0.002 PHE A 191 TYR 0.016 0.002 TYR F 303 ARG 0.009 0.001 ARG D 292 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 173 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.6695 (pptt) cc_final: 0.5831 (pptt) REVERT: A 269 GLU cc_start: 0.8390 (mp0) cc_final: 0.7715 (mp0) REVERT: B 320 ASN cc_start: 0.7092 (t0) cc_final: 0.6685 (t0) REVERT: C 292 ARG cc_start: 0.7296 (mtp85) cc_final: 0.7037 (mmt-90) REVERT: C 293 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6111 (mp0) REVERT: D 290 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: E 291 MET cc_start: 0.7826 (tpt) cc_final: 0.7286 (tpp) REVERT: F 171 GLU cc_start: 0.7348 (tt0) cc_final: 0.7084 (tt0) REVERT: G 191 PHE cc_start: 0.8132 (t80) cc_final: 0.7599 (t80) REVERT: G 286 MET cc_start: 0.7695 (mmp) cc_final: 0.7452 (mmp) outliers start: 29 outliers final: 24 residues processed: 187 average time/residue: 0.4272 time to fit residues: 115.7289 Evaluate side-chains 192 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 307 ARG Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 188 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 ASN D 316 ASN ** F 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9381 Z= 0.283 Angle : 0.576 6.110 12670 Z= 0.314 Chirality : 0.042 0.247 1487 Planarity : 0.004 0.033 1516 Dihedral : 20.903 176.077 1449 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.24 % Allowed : 15.11 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.26), residues: 1054 helix: 1.47 (0.22), residues: 522 sheet: -2.19 (0.34), residues: 233 loop : -1.22 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 239 PHE 0.021 0.002 PHE A 191 TYR 0.021 0.002 TYR F 303 ARG 0.006 0.001 ARG G 292 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 181 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.6702 (pptt) cc_final: 0.5860 (pptt) REVERT: A 269 GLU cc_start: 0.8504 (mp0) cc_final: 0.7882 (mp0) REVERT: B 307 ARG cc_start: 0.7400 (ttp80) cc_final: 0.6931 (ttm-80) REVERT: B 320 ASN cc_start: 0.6998 (t0) cc_final: 0.6607 (t0) REVERT: C 291 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7772 (ptm) REVERT: C 292 ARG cc_start: 0.7228 (mtp85) cc_final: 0.6715 (mmt-90) REVERT: C 293 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.5866 (mp0) REVERT: D 290 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: E 291 MET cc_start: 0.7811 (tpt) cc_final: 0.7292 (tpp) REVERT: F 171 GLU cc_start: 0.7338 (tt0) cc_final: 0.7052 (tt0) REVERT: G 191 PHE cc_start: 0.8150 (t80) cc_final: 0.7673 (t80) outliers start: 33 outliers final: 23 residues processed: 196 average time/residue: 0.4731 time to fit residues: 131.8728 Evaluate side-chains 196 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 188 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.0020 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 ASN C 204 ASN ** F 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2857 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: