Starting phenix.real_space_refine on Tue Feb 13 23:12:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orv_20179/02_2024/6orv_20179_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orv_20179/02_2024/6orv_20179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orv_20179/02_2024/6orv_20179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orv_20179/02_2024/6orv_20179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orv_20179/02_2024/6orv_20179_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orv_20179/02_2024/6orv_20179_updated.pdb" } resolution = 3.0 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= 0.003 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: 5 Type Number sf(0) Gaussians S 47 5.16 5 Cl 2 4.86 5 C 5138 2.51 5 N 1390 2.21 5 O 1464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "AP ARG 42": "NH1" <-> "NH2" Residue "AP GLU 209": "OE1" <-> "OE2" Residue "BP ARG 129": "NH1" <-> "NH2" Residue "BP GLU 215": "OE1" <-> "OE2" Residue "GP GLU 58": "OE1" <-> "OE2" Residue "NP ARG 19": "NH1" <-> "NH2" Residue "RP TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "RP ARG 376": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8041 Number of models: 1 Model: "" Number of chains: 5 Chain: "AP" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1654 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain breaks: 4 Chain: "BP" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "GP" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "NP" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "RP" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2390 Unusual residues: {'N2V': 1} Classifications: {'peptide': 281, 'undetermined': 1} Link IDs: {'PTRANS': 4, 'TRANS': 276, None: 1} Not linked: pdbres="GLURP 423 " pdbres="N2VRP 501 " Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ALARP 209 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALARP 209 " occ=0.00 residue: pdb=" N GLNRP 210 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLNRP 210 " occ=0.00 residue: pdb=" N GLNRP 211 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLNRP 211 " occ=0.00 residue: pdb=" N HISRP 212 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HISRP 212 " occ=0.00 residue: pdb=" N ASPRP 372 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASPRP 372 " occ=0.00 residue: pdb=" N GLURP 373 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLURP 373 " occ=0.00 residue: pdb=" N HISRP 374 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HISRP 374 " occ=0.00 residue: pdb=" N ALARP 375 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALARP 375 " occ=0.00 residue: pdb=" N ARGRP 376 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARGRP 376 " occ=0.00 residue: pdb=" N GLYRP 377 " occ=0.00 ... (2 atoms not shown) pdb=" O GLYRP 377 " occ=0.00 residue: pdb=" N THRRP 378 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THRRP 378 " occ=0.00 residue: pdb=" N LEURP 379 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEURP 379 " occ=0.00 Time building chain proxies: 4.76, per 1000 atoms: 0.59 Number of scatterers: 8041 At special positions: 0 Unit cell: (84.252, 95.816, 131.334, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 47 16.00 O 1464 8.00 N 1390 7.00 C 5138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYSNP 22 " - pdb=" SG CYSNP 96 " distance=2.03 Simple disulfide: pdb=" SG CYSNP 99 " - pdb=" SG CYSNP 107 " distance=2.02 Simple disulfide: pdb=" SG CYSRP 226 " - pdb=" SG CYSRP 296 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.4 seconds 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1878 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 11 sheets defined 32.0% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'AP' and resid 19 through 24 Processing helix chain 'AP' and resid 29 through 37 Processing helix chain 'AP' and resid 235 through 239 removed outlier: 3.883A pdb=" N ASNAP 239 " --> pdb=" O GLNAP 236 " (cutoff:3.500A) Processing helix chain 'AP' and resid 267 through 278 removed outlier: 3.513A pdb=" N SERAP 275 " --> pdb=" O LYSAP 271 " (cutoff:3.500A) Processing helix chain 'AP' and resid 313 through 315 No H-bonds generated for 'chain 'AP' and resid 313 through 315' Processing helix chain 'AP' and resid 332 through 335 No H-bonds generated for 'chain 'AP' and resid 332 through 335' Processing helix chain 'AP' and resid 338 through 349 removed outlier: 3.876A pdb=" N ILEAP 348 " --> pdb=" O GLUAP 344 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SERAP 349 " --> pdb=" O PHEAP 345 " (cutoff:3.500A) Processing helix chain 'AP' and resid 372 through 390 removed outlier: 3.518A pdb=" N ASPAP 381 " --> pdb=" O ASNAP 377 " (cutoff:3.500A) Processing helix chain 'BP' and resid 5 through 23 removed outlier: 4.014A pdb=" N GLNBP 9 " --> pdb=" O ASPBP 5 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLUBP 10 " --> pdb=" O GLNBP 6 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLNBP 17 " --> pdb=" O GLNBP 13 " (cutoff:3.500A) Processing helix chain 'BP' and resid 30 through 33 No H-bonds generated for 'chain 'BP' and resid 30 through 33' Processing helix chain 'GP' and resid 7 through 21 removed outlier: 3.971A pdb=" N ALAGP 12 " --> pdb=" O SERGP 8 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VALGP 16 " --> pdb=" O ALAGP 12 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLNGP 18 " --> pdb=" O LYSGP 14 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEUGP 19 " --> pdb=" O LEUGP 15 " (cutoff:3.500A) Processing helix chain 'GP' and resid 30 through 43 removed outlier: 3.588A pdb=" N ALAGP 35 " --> pdb=" O SERGP 31 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASPGP 36 " --> pdb=" O LYSGP 32 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYSGP 41 " --> pdb=" O LEUGP 37 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLUGP 42 " --> pdb=" O METGP 38 " (cutoff:3.500A) Processing helix chain 'GP' and resid 45 through 47 No H-bonds generated for 'chain 'GP' and resid 45 through 47' Processing helix chain 'NP' and resid 29 through 31 No H-bonds generated for 'chain 'NP' and resid 29 through 31' Processing helix chain 'NP' and resid 62 through 64 No H-bonds generated for 'chain 'NP' and resid 62 through 64' Processing helix chain 'NP' and resid 88 through 90 No H-bonds generated for 'chain 'NP' and resid 88 through 90' Processing helix chain 'RP' and resid 138 through 168 removed outlier: 4.530A pdb=" N PHERP 143 " --> pdb=" O GLURP 139 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILERP 147 " --> pdb=" O PHERP 143 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VALRP 160 " --> pdb=" O PHERP 156 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILERP 161 " --> pdb=" O SERRP 157 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SERRP 163 " --> pdb=" O LEURP 159 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEURP 167 " --> pdb=" O SERRP 163 " (cutoff:3.500A) Processing helix chain 'RP' and resid 170 through 172 No H-bonds generated for 'chain 'RP' and resid 170 through 172' Processing helix chain 'RP' and resid 177 through 206 removed outlier: 3.626A pdb=" N SERRP 186 " --> pdb=" O ASNRP 182 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEURP 189 " --> pdb=" O ALARP 185 " (cutoff:3.500A) Processing helix chain 'RP' and resid 215 through 221 Processing helix chain 'RP' and resid 224 through 241 removed outlier: 4.156A pdb=" N ASNRP 240 " --> pdb=" O CYSRP 236 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYRRP 241 " --> pdb=" O VALRP 237 " (cutoff:3.500A) Processing helix chain 'RP' and resid 248 through 255 Processing helix chain 'RP' and resid 264 through 272 removed outlier: 3.682A pdb=" N SERRP 271 " --> pdb=" O ARGRP 267 " (cutoff:3.500A) Processing helix chain 'RP' and resid 277 through 290 removed outlier: 3.932A pdb=" N VALRP 281 " --> pdb=" O LEURP 278 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VALRP 282 " --> pdb=" O LEURP 279 " (cutoff:3.500A) Proline residue: RP 283 - end of helix removed outlier: 3.777A pdb=" N ILERP 286 " --> pdb=" O PRORP 283 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VALRP 287 " --> pdb=" O TRPRP 284 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYRRP 289 " --> pdb=" O ILERP 286 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEURP 290 " --> pdb=" O VALRP 287 " (cutoff:3.500A) Processing helix chain 'RP' and resid 310 through 320 removed outlier: 3.650A pdb=" N ALARP 316 " --> pdb=" O PRORP 312 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASNRP 320 " --> pdb=" O ALARP 316 " (cutoff:3.500A) Processing helix chain 'RP' and resid 324 through 335 removed outlier: 4.118A pdb=" N CYSRP 329 " --> pdb=" O VALRP 325 " (cutoff:3.500A) Processing helix chain 'RP' and resid 349 through 360 removed outlier: 4.019A pdb=" N LEURP 354 " --> pdb=" O ALARP 350 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEURP 356 " --> pdb=" O SERRP 352 " (cutoff:3.500A) Proline residue: RP 358 - end of helix Processing helix chain 'RP' and resid 362 through 366 removed outlier: 3.597A pdb=" N ILERP 366 " --> pdb=" O HISRP 363 " (cutoff:3.500A) Processing helix chain 'RP' and resid 383 through 389 removed outlier: 4.182A pdb=" N GLURP 387 " --> pdb=" O LYSRP 383 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEURP 388 " --> pdb=" O LEURP 384 " (cutoff:3.500A) Processing helix chain 'RP' and resid 394 through 400 Processing helix chain 'RP' and resid 407 through 413 removed outlier: 4.178A pdb=" N GLURP 412 " --> pdb=" O GLURP 408 " (cutoff:3.500A) Processing helix chain 'RP' and resid 418 through 421 No H-bonds generated for 'chain 'RP' and resid 418 through 421' Processing sheet with id= A, first strand: chain 'AP' and resid 359 through 363 removed outlier: 7.116A pdb=" N VALAP 287 " --> pdb=" O TYRAP 360 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N HISAP 362 " --> pdb=" O VALAP 287 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEUAP 289 " --> pdb=" O HISAP 362 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALAAP 243 " --> pdb=" O ARGAP 42 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VALAP 224 " --> pdb=" O LEUAP 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'BP' and resid 58 through 63 removed outlier: 7.014A pdb=" N ALABP 73 " --> pdb=" O TYRBP 59 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N METBP 61 " --> pdb=" O VALBP 71 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VALBP 71 " --> pdb=" O METBP 61 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TRPBP 63 " --> pdb=" O LEUBP 69 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEUBP 69 " --> pdb=" O TRPBP 63 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYSBP 78 " --> pdb=" O SERBP 74 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILEBP 93 " --> pdb=" O LEUBP 79 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASPBP 83 " --> pdb=" O LYSBP 89 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LYSBP 89 " --> pdb=" O ASPBP 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'BP' and resid 100 through 105 removed outlier: 6.848A pdb=" N GLYBP 115 " --> pdb=" O METBP 101 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N CYSBP 103 " --> pdb=" O ALABP 113 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALABP 113 " --> pdb=" O CYSBP 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N TYRBP 105 " --> pdb=" O TYRBP 111 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N TYRBP 111 " --> pdb=" O TYRBP 105 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ASNBP 125 " --> pdb=" O VALBP 135 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VALBP 135 " --> pdb=" O ASNBP 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'BP' and resid 146 through 151 removed outlier: 6.662A pdb=" N SERBP 160 " --> pdb=" O SERBP 147 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N CYSBP 149 " --> pdb=" O VALBP 158 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VALBP 158 " --> pdb=" O CYSBP 149 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILEBP 157 " --> pdb=" O TRPBP 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'BP' and resid 187 through 192 removed outlier: 6.954A pdb=" N GLYBP 202 " --> pdb=" O METBP 188 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEUBP 190 " --> pdb=" O VALBP 200 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VALBP 200 " --> pdb=" O LEUBP 190 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N LEUBP 192 " --> pdb=" O LEUBP 198 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEUBP 198 " --> pdb=" O LEUBP 192 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ASPBP 212 " --> pdb=" O CYSBP 218 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N CYSBP 218 " --> pdb=" O ASPBP 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'BP' and resid 262 through 264 removed outlier: 3.577A pdb=" N METBP 262 " --> pdb=" O LEUBP 252 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHEBP 241 " --> pdb=" O PHEBP 253 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'BP' and resid 273 through 278 removed outlier: 6.519A pdb=" N GLYBP 288 " --> pdb=" O THRBP 274 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VALBP 276 " --> pdb=" O LEUBP 286 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEUBP 286 " --> pdb=" O VALBP 276 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHEBP 278 " --> pdb=" O LEUBP 284 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEUBP 284 " --> pdb=" O PHEBP 278 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLYBP 306 " --> pdb=" O VALBP 296 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ASPBP 298 " --> pdb=" O ARGBP 304 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARGBP 304 " --> pdb=" O ASPBP 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'BP' and resid 327 through 329 Processing sheet with id= I, first strand: chain 'NP' and resid 3 through 6 Processing sheet with id= J, first strand: chain 'NP' and resid 122 through 124 removed outlier: 5.984A pdb=" N ARGNP 38 " --> pdb=" O TRPNP 47 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TRPNP 47 " --> pdb=" O ARGNP 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'NP' and resid 68 through 73 253 hydrogen bonds defined for protein. 708 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: 2.08 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1294 1.31 - 1.44: 2361 1.44 - 1.56: 4499 1.56 - 1.69: 0 1.69 - 1.81: 67 Bond restraints: 8221 Sorted by residual: bond pdb=" C06 N2VRP 501 " pdb=" N05 N2VRP 501 " ideal model delta sigma weight residual 1.337 1.449 -0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C21 N2VRP 501 " pdb=" O42 N2VRP 501 " ideal model delta sigma weight residual 1.357 1.436 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C22 N2VRP 501 " pdb=" O23 N2VRP 501 " ideal model delta sigma weight residual 1.356 1.428 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C07 N2VRP 501 " pdb=" N08 N2VRP 501 " ideal model delta sigma weight residual 1.450 1.521 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C34 N2VRP 501 " pdb="CL35 N2VRP 501 " ideal model delta sigma weight residual 1.722 1.786 -0.064 2.00e-02 2.50e+03 1.01e+01 ... (remaining 8216 not shown) Histogram of bond angle deviations from ideal: 98.86 - 105.95: 114 105.95 - 113.04: 4300 113.04 - 120.13: 3204 120.13 - 127.21: 3425 127.21 - 134.30: 92 Bond angle restraints: 11135 Sorted by residual: angle pdb=" C CYSRP 226 " pdb=" CA CYSRP 226 " pdb=" CB CYSRP 226 " ideal model delta sigma weight residual 110.88 102.92 7.96 1.57e+00 4.06e-01 2.57e+01 angle pdb=" N SERBP 161 " pdb=" CA SERBP 161 " pdb=" C SERBP 161 " ideal model delta sigma weight residual 108.34 113.62 -5.28 1.31e+00 5.83e-01 1.62e+01 angle pdb=" CA SERRP 225 " pdb=" C SERRP 225 " pdb=" O SERRP 225 " ideal model delta sigma weight residual 120.90 117.08 3.82 1.03e+00 9.43e-01 1.37e+01 angle pdb=" N ILERP 317 " pdb=" CA ILERP 317 " pdb=" C ILERP 317 " ideal model delta sigma weight residual 112.35 107.34 5.01 1.41e+00 5.03e-01 1.26e+01 angle pdb=" CA ILERP 146 " pdb=" C ILERP 146 " pdb=" O ILERP 146 " ideal model delta sigma weight residual 120.95 117.42 3.53 1.04e+00 9.25e-01 1.15e+01 ... (remaining 11130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.49: 4749 34.49 - 68.97: 110 68.97 - 103.46: 8 103.46 - 137.95: 1 137.95 - 172.43: 2 Dihedral angle restraints: 4870 sinusoidal: 1966 harmonic: 2904 Sorted by residual: dihedral pdb=" CA TRPBP 332 " pdb=" C TRPBP 332 " pdb=" N ASPBP 333 " pdb=" CA ASPBP 333 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA ASNAP 292 " pdb=" C ASNAP 292 " pdb=" N LYSAP 293 " pdb=" CA LYSAP 293 " ideal model delta harmonic sigma weight residual -180.00 -154.96 -25.04 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" C17 N2VRP 501 " pdb=" C09 N2VRP 501 " pdb=" C16 N2VRP 501 " pdb=" N08 N2VRP 501 " ideal model delta sinusoidal sigma weight residual 52.78 -134.79 -172.43 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 4867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 930 0.064 - 0.129: 247 0.129 - 0.193: 46 0.193 - 0.258: 4 0.258 - 0.322: 2 Chirality restraints: 1229 Sorted by residual: chirality pdb=" CA CYSRP 226 " pdb=" N CYSRP 226 " pdb=" C CYSRP 226 " pdb=" CB CYSRP 226 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" C09 N2VRP 501 " pdb=" C10 N2VRP 501 " pdb=" C16 N2VRP 501 " pdb=" N08 N2VRP 501 " both_signs ideal model delta sigma weight residual False 2.25 2.57 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CB THRBP 47 " pdb=" CA THRBP 47 " pdb=" OG1 THRBP 47 " pdb=" CG2 THRBP 47 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1226 not shown) Planarity restraints: 1410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEURP 224 " 0.022 2.00e-02 2.50e+03 4.45e-02 1.98e+01 pdb=" C LEURP 224 " -0.077 2.00e-02 2.50e+03 pdb=" O LEURP 224 " 0.029 2.00e-02 2.50e+03 pdb=" N SERRP 225 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRBP 59 " -0.029 2.00e-02 2.50e+03 2.55e-02 1.30e+01 pdb=" CG TYRBP 59 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TYRBP 59 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYRBP 59 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYRBP 59 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYRBP 59 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYRBP 59 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYRBP 59 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VALRP 276 " 0.043 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRORP 277 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRORP 277 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRORP 277 " 0.035 5.00e-02 4.00e+02 ... (remaining 1407 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 978 2.74 - 3.28: 7383 3.28 - 3.82: 13884 3.82 - 4.36: 17786 4.36 - 4.90: 29283 Nonbonded interactions: 69314 Sorted by model distance: nonbonded pdb=" OG SERBP 161 " pdb=" OD1 ASPBP 163 " model vdw 2.205 2.440 nonbonded pdb=" OG SERBP 245 " pdb=" OD1 ASPBP 247 " model vdw 2.214 2.440 nonbonded pdb=" OH TYRBP 145 " pdb=" OD2 ASPBP 186 " model vdw 2.245 2.440 nonbonded pdb=" O ILEBP 58 " pdb=" OG SERBP 316 " model vdw 2.272 2.440 nonbonded pdb=" OD1 ASPBP 228 " pdb=" OH TYRNP 117 " model vdw 2.282 2.440 ... (remaining 69309 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 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: 5.210 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 24.910 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 : 0.008 0.112 8221 Z= 0.559 Angle : 0.949 9.934 11135 Z= 0.557 Chirality : 0.061 0.322 1229 Planarity : 0.006 0.063 1410 Dihedral : 15.663 172.434 2983 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.47 % Allowed : 6.53 % Favored : 93.01 % 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: -4.66 (0.22), residues: 977 helix: -4.08 (0.18), residues: 361 sheet: -2.48 (0.31), residues: 218 loop : -2.16 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRPRP 243 HIS 0.021 0.002 HISAP 357 PHE 0.023 0.003 PHENP 108 TYR 0.062 0.003 TYRBP 59 ARG 0.021 0.001 ARGNP 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 173 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AP 388 LEU cc_start: 0.8281 (mt) cc_final: 0.7984 (mt) outliers start: 4 outliers final: 2 residues processed: 176 average time/residue: 1.3400 time to fit residues: 248.2946 Evaluate side-chains 137 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP residue 343 ASP Chi-restraints excluded: chain RP residue 379 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AP 29 GLN AP 35 GLN AP 41 HIS AP 227 GLN AP 267 GLN AP 278 ASN AP 292 ASN BP 32 GLN BP 88 ASN BP 132 ASN BP 176 GLN BP 340 ASN GP 59 ASN NP 35 ASN NP 82 GLN RP 240 ASN RP 320 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8221 Z= 0.185 Angle : 0.557 7.604 11135 Z= 0.293 Chirality : 0.043 0.211 1229 Planarity : 0.004 0.042 1410 Dihedral : 11.307 159.181 1145 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.38 % Allowed : 14.45 % Favored : 82.17 % 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: -3.53 (0.23), residues: 977 helix: -2.88 (0.22), residues: 363 sheet: -2.08 (0.31), residues: 213 loop : -1.67 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPBP 82 HIS 0.007 0.001 HISAP 357 PHE 0.016 0.001 PHEAP 212 TYR 0.013 0.001 TYRRP 305 ARG 0.005 0.000 ARGNP 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 153 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: BP 59 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.8146 (m-80) REVERT: BP 196 THR cc_start: 0.8296 (p) cc_final: 0.8030 (p) REVERT: BP 205 ASP cc_start: 0.8401 (p0) cc_final: 0.8184 (p0) REVERT: BP 217 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.6914 (ptt) REVERT: RP 147 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7285 (mt) outliers start: 29 outliers final: 9 residues processed: 166 average time/residue: 1.1614 time to fit residues: 204.3520 Evaluate side-chains 148 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BP residue 17 GLN Chi-restraints excluded: chain BP residue 47 THR Chi-restraints excluded: chain BP residue 59 TYR Chi-restraints excluded: chain BP residue 65 THR Chi-restraints excluded: chain BP residue 217 MET Chi-restraints excluded: chain BP residue 270 ILE Chi-restraints excluded: chain NP residue 78 THR Chi-restraints excluded: chain NP residue 89 GLU Chi-restraints excluded: chain RP residue 147 ILE Chi-restraints excluded: chain RP residue 303 MET Chi-restraints excluded: chain RP residue 305 TYR Chi-restraints excluded: chain RP residue 382 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AP 220 HIS AP 390 GLN BP 259 GLN ** BP 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GP 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RP 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8221 Z= 0.186 Angle : 0.539 7.701 11135 Z= 0.280 Chirality : 0.043 0.175 1229 Planarity : 0.004 0.036 1410 Dihedral : 10.601 151.619 1141 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.55 % Allowed : 16.90 % Favored : 78.55 % 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: -2.69 (0.25), residues: 977 helix: -2.00 (0.25), residues: 369 sheet: -1.66 (0.32), residues: 208 loop : -1.38 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPBP 82 HIS 0.006 0.001 HISAP 357 PHE 0.016 0.001 PHEAP 212 TYR 0.013 0.001 TYRNP 60 ARG 0.006 0.000 ARGNP 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 141 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: BP 59 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.8232 (m-80) REVERT: BP 196 THR cc_start: 0.8215 (p) cc_final: 0.7952 (p) REVERT: BP 205 ASP cc_start: 0.8392 (p0) cc_final: 0.8151 (p0) REVERT: BP 217 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.6796 (ptt) REVERT: NP 122 THR cc_start: 0.8334 (OUTLIER) cc_final: 0.8066 (t) REVERT: RP 147 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7245 (OUTLIER) REVERT: RP 247 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7449 (tp30) outliers start: 39 outliers final: 18 residues processed: 157 average time/residue: 1.1675 time to fit residues: 194.9335 Evaluate side-chains 155 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP residue 221 MET Chi-restraints excluded: chain BP residue 17 GLN Chi-restraints excluded: chain BP residue 33 ILE Chi-restraints excluded: chain BP residue 47 THR Chi-restraints excluded: chain BP residue 59 TYR Chi-restraints excluded: chain BP residue 65 THR Chi-restraints excluded: chain BP residue 70 LEU Chi-restraints excluded: chain BP residue 101 MET Chi-restraints excluded: chain BP residue 119 ASN Chi-restraints excluded: chain BP residue 217 MET Chi-restraints excluded: chain BP residue 268 ASN Chi-restraints excluded: chain BP residue 270 ILE Chi-restraints excluded: chain GP residue 19 LEU Chi-restraints excluded: chain GP residue 52 THR Chi-restraints excluded: chain NP residue 78 THR Chi-restraints excluded: chain NP residue 89 GLU Chi-restraints excluded: chain NP residue 91 THR Chi-restraints excluded: chain NP residue 122 THR Chi-restraints excluded: chain RP residue 147 ILE Chi-restraints excluded: chain RP residue 303 MET Chi-restraints excluded: chain RP residue 305 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 0.0770 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 83 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AP 220 HIS ** BP 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GP 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8221 Z= 0.150 Angle : 0.515 7.710 11135 Z= 0.264 Chirality : 0.042 0.205 1229 Planarity : 0.003 0.034 1410 Dihedral : 10.204 144.977 1141 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.31 % Allowed : 18.18 % Favored : 77.51 % 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: -2.07 (0.26), residues: 977 helix: -1.29 (0.27), residues: 365 sheet: -1.47 (0.32), residues: 208 loop : -1.15 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPBP 211 HIS 0.005 0.001 HISRP 171 PHE 0.015 0.001 PHEAP 212 TYR 0.011 0.001 TYRNP 60 ARG 0.006 0.000 ARGNP 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 137 time to evaluate : 0.963 Fit side-chains REVERT: BP 59 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.8319 (m-80) REVERT: BP 186 ASP cc_start: 0.8037 (p0) cc_final: 0.7698 (p0) REVERT: BP 217 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.6748 (ptt) REVERT: NP 122 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.8074 (t) REVERT: RP 247 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7415 (tp30) REVERT: RP 303 MET cc_start: 0.6381 (OUTLIER) cc_final: 0.6080 (mmm) outliers start: 37 outliers final: 16 residues processed: 151 average time/residue: 1.1862 time to fit residues: 190.4199 Evaluate side-chains 152 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP residue 221 MET Chi-restraints excluded: chain AP residue 224 VAL Chi-restraints excluded: chain BP residue 17 GLN Chi-restraints excluded: chain BP residue 33 ILE Chi-restraints excluded: chain BP residue 47 THR Chi-restraints excluded: chain BP residue 59 TYR Chi-restraints excluded: chain BP residue 65 THR Chi-restraints excluded: chain BP residue 119 ASN Chi-restraints excluded: chain BP residue 217 MET Chi-restraints excluded: chain BP residue 268 ASN Chi-restraints excluded: chain BP residue 270 ILE Chi-restraints excluded: chain BP residue 280 LYS Chi-restraints excluded: chain GP residue 19 LEU Chi-restraints excluded: chain GP residue 38 MET Chi-restraints excluded: chain GP residue 52 THR Chi-restraints excluded: chain NP residue 11 LEU Chi-restraints excluded: chain NP residue 78 THR Chi-restraints excluded: chain NP residue 91 THR Chi-restraints excluded: chain NP residue 122 THR Chi-restraints excluded: chain RP residue 303 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 chunk 1 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AP 220 HIS ** BP 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GP 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RP 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8221 Z= 0.191 Angle : 0.544 9.168 11135 Z= 0.275 Chirality : 0.043 0.245 1229 Planarity : 0.003 0.033 1410 Dihedral : 10.002 139.902 1141 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.66 % Allowed : 19.46 % Favored : 75.87 % 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: -1.79 (0.26), residues: 977 helix: -0.95 (0.28), residues: 365 sheet: -1.41 (0.32), residues: 208 loop : -1.06 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPBP 82 HIS 0.013 0.001 HISRP 171 PHE 0.015 0.001 PHEAP 212 TYR 0.012 0.001 TYRNP 60 ARG 0.005 0.000 ARGNP 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 129 time to evaluate : 1.027 Fit side-chains REVERT: BP 59 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.8367 (m-80) REVERT: BP 188 MET cc_start: 0.8413 (mmm) cc_final: 0.8130 (mmp) REVERT: BP 217 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.6864 (ptt) REVERT: NP 76 LYS cc_start: 0.8062 (mtmp) cc_final: 0.7820 (mtmt) REVERT: NP 122 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.8064 (t) REVERT: RP 247 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7555 (tp30) outliers start: 40 outliers final: 16 residues processed: 144 average time/residue: 1.1945 time to fit residues: 182.7697 Evaluate side-chains 146 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP residue 224 VAL Chi-restraints excluded: chain AP residue 266 LEU Chi-restraints excluded: chain BP residue 47 THR Chi-restraints excluded: chain BP residue 59 TYR Chi-restraints excluded: chain BP residue 65 THR Chi-restraints excluded: chain BP residue 146 LEU Chi-restraints excluded: chain BP residue 217 MET Chi-restraints excluded: chain BP residue 268 ASN Chi-restraints excluded: chain BP residue 270 ILE Chi-restraints excluded: chain GP residue 16 VAL Chi-restraints excluded: chain GP residue 19 LEU Chi-restraints excluded: chain GP residue 52 THR Chi-restraints excluded: chain NP residue 11 LEU Chi-restraints excluded: chain NP residue 65 LYS Chi-restraints excluded: chain NP residue 78 THR Chi-restraints excluded: chain NP residue 91 THR Chi-restraints excluded: chain NP residue 122 THR Chi-restraints excluded: chain RP residue 147 ILE Chi-restraints excluded: chain RP residue 279 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AP 220 HIS ** BP 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GP 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RP 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8221 Z= 0.185 Angle : 0.549 8.999 11135 Z= 0.276 Chirality : 0.043 0.252 1229 Planarity : 0.003 0.041 1410 Dihedral : 9.779 134.975 1141 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.20 % Allowed : 20.28 % Favored : 75.52 % 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: -1.59 (0.26), residues: 977 helix: -0.74 (0.28), residues: 363 sheet: -1.37 (0.32), residues: 210 loop : -0.96 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPBP 82 HIS 0.011 0.001 HISRP 171 PHE 0.015 0.001 PHEAP 212 TYR 0.012 0.001 TYRNP 60 ARG 0.006 0.000 ARGNP 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 135 time to evaluate : 0.873 Fit side-chains REVERT: AP 358 TYR cc_start: 0.8252 (m-80) cc_final: 0.7433 (m-80) REVERT: AP 378 ASP cc_start: 0.7262 (m-30) cc_final: 0.7055 (m-30) REVERT: BP 59 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.8346 (m-80) REVERT: BP 188 MET cc_start: 0.8391 (mmm) cc_final: 0.8136 (mmp) REVERT: BP 217 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7370 (ptt) REVERT: NP 76 LYS cc_start: 0.8086 (mtmp) cc_final: 0.7856 (mtmt) REVERT: NP 122 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.8039 (t) REVERT: RP 147 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.7095 (tt) REVERT: RP 247 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7566 (tp30) outliers start: 36 outliers final: 17 residues processed: 149 average time/residue: 1.1779 time to fit residues: 186.3106 Evaluate side-chains 147 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP residue 221 MET Chi-restraints excluded: chain AP residue 224 VAL Chi-restraints excluded: chain AP residue 266 LEU Chi-restraints excluded: chain BP residue 47 THR Chi-restraints excluded: chain BP residue 59 TYR Chi-restraints excluded: chain BP residue 65 THR Chi-restraints excluded: chain BP residue 146 LEU Chi-restraints excluded: chain BP residue 217 MET Chi-restraints excluded: chain BP residue 268 ASN Chi-restraints excluded: chain BP residue 270 ILE Chi-restraints excluded: chain BP residue 280 LYS Chi-restraints excluded: chain GP residue 16 VAL Chi-restraints excluded: chain GP residue 19 LEU Chi-restraints excluded: chain GP residue 52 THR Chi-restraints excluded: chain NP residue 11 LEU Chi-restraints excluded: chain NP residue 78 THR Chi-restraints excluded: chain NP residue 91 THR Chi-restraints excluded: chain NP residue 122 THR Chi-restraints excluded: chain RP residue 147 ILE Chi-restraints excluded: chain RP residue 189 LEU Chi-restraints excluded: chain RP residue 287 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 0.0060 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AP 220 HIS ** BP 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GP 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RP 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8221 Z= 0.242 Angle : 0.594 8.814 11135 Z= 0.296 Chirality : 0.044 0.267 1229 Planarity : 0.003 0.039 1410 Dihedral : 9.725 129.409 1141 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.31 % Allowed : 21.91 % Favored : 73.78 % 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: -1.48 (0.27), residues: 977 helix: -0.64 (0.28), residues: 357 sheet: -1.32 (0.32), residues: 215 loop : -0.87 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPBP 82 HIS 0.012 0.001 HISRP 171 PHE 0.016 0.001 PHEAP 212 TYR 0.013 0.001 TYRNP 60 ARG 0.007 0.000 ARGNP 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 132 time to evaluate : 0.939 Fit side-chains REVERT: BP 59 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.8354 (m-80) REVERT: BP 188 MET cc_start: 0.8410 (mmm) cc_final: 0.8182 (mmp) REVERT: NP 5 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.6743 (mt0) REVERT: NP 76 LYS cc_start: 0.8068 (mtmp) cc_final: 0.7862 (mtmt) REVERT: NP 122 THR cc_start: 0.8334 (OUTLIER) cc_final: 0.8071 (t) REVERT: RP 147 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7111 (tt) outliers start: 37 outliers final: 17 residues processed: 150 average time/residue: 1.2478 time to fit residues: 198.7597 Evaluate side-chains 147 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP residue 224 VAL Chi-restraints excluded: chain BP residue 47 THR Chi-restraints excluded: chain BP residue 59 TYR Chi-restraints excluded: chain BP residue 65 THR Chi-restraints excluded: chain BP residue 146 LEU Chi-restraints excluded: chain BP residue 268 ASN Chi-restraints excluded: chain BP residue 270 ILE Chi-restraints excluded: chain BP residue 280 LYS Chi-restraints excluded: chain GP residue 16 VAL Chi-restraints excluded: chain GP residue 19 LEU Chi-restraints excluded: chain GP residue 52 THR Chi-restraints excluded: chain NP residue 5 GLN Chi-restraints excluded: chain NP residue 11 LEU Chi-restraints excluded: chain NP residue 65 LYS Chi-restraints excluded: chain NP residue 78 THR Chi-restraints excluded: chain NP residue 91 THR Chi-restraints excluded: chain NP residue 122 THR Chi-restraints excluded: chain RP residue 147 ILE Chi-restraints excluded: chain RP residue 175 THR Chi-restraints excluded: chain RP residue 189 LEU Chi-restraints excluded: chain RP residue 287 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.0870 chunk 73 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 81 optimal weight: 0.0040 overall best weight: 0.5570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AP 220 HIS ** BP 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GP 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RP 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** RP 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8221 Z= 0.177 Angle : 0.590 9.018 11135 Z= 0.292 Chirality : 0.043 0.279 1229 Planarity : 0.004 0.061 1410 Dihedral : 9.500 122.860 1141 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.08 % Allowed : 22.26 % Favored : 73.66 % 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: -1.26 (0.27), residues: 977 helix: -0.46 (0.28), residues: 359 sheet: -1.20 (0.33), residues: 211 loop : -0.76 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPBP 82 HIS 0.012 0.001 HISRP 171 PHE 0.016 0.001 PHEAP 212 TYR 0.014 0.001 TYRNP 60 ARG 0.012 0.000 ARGBP 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 128 time to evaluate : 0.949 Fit side-chains REVERT: BP 59 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.8377 (m-80) REVERT: BP 188 MET cc_start: 0.8359 (mmm) cc_final: 0.8126 (mmp) REVERT: BP 217 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.6668 (pmm) REVERT: NP 5 GLN cc_start: 0.6983 (OUTLIER) cc_final: 0.6711 (mt0) REVERT: NP 122 THR cc_start: 0.8281 (OUTLIER) cc_final: 0.8018 (t) REVERT: RP 147 ILE cc_start: 0.7385 (OUTLIER) cc_final: 0.7062 (tt) REVERT: RP 303 MET cc_start: 0.6732 (mpp) cc_final: 0.6502 (mmp) outliers start: 35 outliers final: 17 residues processed: 145 average time/residue: 1.1115 time to fit residues: 171.7757 Evaluate side-chains 148 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP residue 224 VAL Chi-restraints excluded: chain AP residue 266 LEU Chi-restraints excluded: chain AP residue 292 ASN Chi-restraints excluded: chain BP residue 47 THR Chi-restraints excluded: chain BP residue 59 TYR Chi-restraints excluded: chain BP residue 65 THR Chi-restraints excluded: chain BP residue 146 LEU Chi-restraints excluded: chain BP residue 217 MET Chi-restraints excluded: chain BP residue 268 ASN Chi-restraints excluded: chain BP residue 270 ILE Chi-restraints excluded: chain BP residue 280 LYS Chi-restraints excluded: chain GP residue 16 VAL Chi-restraints excluded: chain GP residue 19 LEU Chi-restraints excluded: chain GP residue 52 THR Chi-restraints excluded: chain NP residue 5 GLN Chi-restraints excluded: chain NP residue 11 LEU Chi-restraints excluded: chain NP residue 78 THR Chi-restraints excluded: chain NP residue 91 THR Chi-restraints excluded: chain NP residue 122 THR Chi-restraints excluded: chain RP residue 147 ILE Chi-restraints excluded: chain RP residue 189 LEU Chi-restraints excluded: chain RP residue 287 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 37 optimal weight: 0.4980 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 86 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AP 220 HIS BP 16 ASN ** BP 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GP 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RP 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8221 Z= 0.321 Angle : 0.648 9.039 11135 Z= 0.325 Chirality : 0.046 0.288 1229 Planarity : 0.004 0.053 1410 Dihedral : 9.492 114.627 1141 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.96 % Allowed : 22.49 % Favored : 73.54 % 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: -1.50 (0.27), residues: 977 helix: -0.72 (0.28), residues: 367 sheet: -1.25 (0.33), residues: 210 loop : -0.89 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPRP 243 HIS 0.012 0.002 HISRP 171 PHE 0.019 0.001 PHENP 108 TYR 0.015 0.002 TYRRP 305 ARG 0.008 0.001 ARGBP 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 124 time to evaluate : 0.955 Fit side-chains REVERT: AP 378 ASP cc_start: 0.7396 (m-30) cc_final: 0.7189 (m-30) REVERT: BP 13 GLN cc_start: 0.7569 (pp30) cc_final: 0.7359 (pp30) REVERT: BP 59 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.8332 (m-80) REVERT: BP 61 MET cc_start: 0.7944 (ptm) cc_final: 0.7697 (ptm) REVERT: BP 188 MET cc_start: 0.8475 (mmm) cc_final: 0.8243 (mmp) REVERT: BP 217 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.6718 (pmm) REVERT: GP 46 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7732 (mmtt) REVERT: NP 5 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6668 (mt0) REVERT: NP 89 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7708 (pt0) REVERT: NP 122 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8118 (t) REVERT: RP 147 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7164 (tt) REVERT: RP 303 MET cc_start: 0.6808 (mpp) cc_final: 0.6566 (mmp) outliers start: 34 outliers final: 18 residues processed: 138 average time/residue: 1.2437 time to fit residues: 182.6982 Evaluate side-chains 145 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP residue 224 VAL Chi-restraints excluded: chain AP residue 266 LEU Chi-restraints excluded: chain BP residue 47 THR Chi-restraints excluded: chain BP residue 59 TYR Chi-restraints excluded: chain BP residue 65 THR Chi-restraints excluded: chain BP residue 119 ASN Chi-restraints excluded: chain BP residue 146 LEU Chi-restraints excluded: chain BP residue 217 MET Chi-restraints excluded: chain BP residue 268 ASN Chi-restraints excluded: chain BP residue 270 ILE Chi-restraints excluded: chain GP residue 16 VAL Chi-restraints excluded: chain GP residue 19 LEU Chi-restraints excluded: chain GP residue 47 GLU Chi-restraints excluded: chain GP residue 52 THR Chi-restraints excluded: chain NP residue 5 GLN Chi-restraints excluded: chain NP residue 11 LEU Chi-restraints excluded: chain NP residue 78 THR Chi-restraints excluded: chain NP residue 89 GLU Chi-restraints excluded: chain NP residue 122 THR Chi-restraints excluded: chain RP residue 147 ILE Chi-restraints excluded: chain RP residue 175 THR Chi-restraints excluded: chain RP residue 189 LEU Chi-restraints excluded: chain RP residue 279 LEU Chi-restraints excluded: chain RP residue 287 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 0.0670 chunk 88 optimal weight: 0.9990 chunk 76 optimal weight: 0.0870 chunk 7 optimal weight: 0.2980 chunk 59 optimal weight: 2.9990 chunk 47 optimal weight: 0.0670 chunk 61 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 overall best weight: 0.2634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AP 23 ASN AP 35 GLN AP 220 HIS ** BP 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GP 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 31 ASN NP 77 ASN ** RP 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8221 Z= 0.145 Angle : 0.583 9.919 11135 Z= 0.287 Chirality : 0.043 0.311 1229 Planarity : 0.003 0.066 1410 Dihedral : 8.466 104.039 1141 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.21 % Allowed : 24.59 % Favored : 73.19 % 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: -1.13 (0.27), residues: 977 helix: -0.35 (0.28), residues: 370 sheet: -1.00 (0.34), residues: 207 loop : -0.78 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPBP 82 HIS 0.007 0.001 HISRP 171 PHE 0.015 0.001 PHEAP 212 TYR 0.016 0.001 TYRNP 60 ARG 0.012 0.000 ARGBP 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 0.949 Fit side-chains REVERT: AP 24 LYS cc_start: 0.7819 (pmtt) cc_final: 0.7141 (pptt) REVERT: BP 217 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.6618 (pmm) REVERT: NP 122 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7983 (t) REVERT: RP 147 ILE cc_start: 0.7250 (OUTLIER) cc_final: 0.6973 (tt) REVERT: RP 188 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7154 (mp) outliers start: 19 outliers final: 5 residues processed: 142 average time/residue: 1.1381 time to fit residues: 172.0706 Evaluate side-chains 131 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP residue 224 VAL Chi-restraints excluded: chain BP residue 217 MET Chi-restraints excluded: chain BP residue 270 ILE Chi-restraints excluded: chain GP residue 52 THR Chi-restraints excluded: chain NP residue 78 THR Chi-restraints excluded: chain NP residue 122 THR Chi-restraints excluded: chain RP residue 147 ILE Chi-restraints excluded: chain RP residue 188 ILE Chi-restraints excluded: chain RP residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AP 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 220 HIS ** BP 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GP 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RP 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.158091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.131565 restraints weight = 8958.166| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.42 r_work: 0.3271 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8221 Z= 0.211 Angle : 0.616 9.789 11135 Z= 0.306 Chirality : 0.044 0.300 1229 Planarity : 0.004 0.052 1410 Dihedral : 8.155 103.971 1141 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.10 % Allowed : 25.17 % Favored : 72.73 % 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: -1.04 (0.27), residues: 977 helix: -0.17 (0.29), residues: 353 sheet: -1.21 (0.32), residues: 214 loop : -0.66 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPRP 243 HIS 0.014 0.001 HISRP 171 PHE 0.016 0.001 PHEAP 212 TYR 0.022 0.001 TYRRP 291 ARG 0.014 0.000 ARGBP 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3586.00 seconds wall clock time: 64 minutes 17.29 seconds (3857.29 seconds total)