Starting phenix.real_space_refine on Fri Mar 15 00:06:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plx_13505/03_2024/7plx_13505_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plx_13505/03_2024/7plx_13505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plx_13505/03_2024/7plx_13505.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plx_13505/03_2024/7plx_13505.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plx_13505/03_2024/7plx_13505_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plx_13505/03_2024/7plx_13505_updated.pdb" } resolution = 3.6 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= 0.001 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 2 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 6462 2.51 5 N 1722 2.21 5 O 1889 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ASP 17": "OD1" <-> "OD2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 362": "OD1" <-> "OD2" Residue "A TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A GLU 689": "OE1" <-> "OE2" Residue "A PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 768": "NH1" <-> "NH2" Residue "A ARG 779": "NH1" <-> "NH2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 334": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10139 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6097 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 4 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.77, per 1000 atoms: 0.57 Number of scatterers: 10139 At special positions: 0 Unit cell: (102.82, 136.74, 150.52, 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 63 16.00 P 2 15.00 Mg 1 11.99 O 1889 8.00 N 1722 7.00 C 6462 6.00 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 - 3.50 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: 4.01 Conformation dependent library (CDL) restraints added in 1.7 seconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2378 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 13 sheets defined 50.0% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 29 through 38 removed outlier: 4.023A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 67 through 78 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 96 removed outlier: 4.380A pdb=" N PHE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 141 through 149 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 82 through 94 removed outlier: 3.539A pdb=" N ARG A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 139 through 152 removed outlier: 3.501A pdb=" N GLU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 169 through 184 removed outlier: 3.539A pdb=" N ALA A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.606A pdb=" N LEU A 197 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN A 200 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Proline residue: A 201 - end of helix removed outlier: 3.556A pdb=" N GLU A 204 " --> pdb=" O PRO A 201 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 206 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 272 through 277 removed outlier: 4.877A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.658A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLY A 291 " --> pdb=" O TYR A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 291' Processing helix chain 'A' and resid 301 through 314 removed outlier: 4.052A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 337 removed outlier: 3.833A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 393 through 423 Processing helix chain 'A' and resid 449 through 479 removed outlier: 3.567A pdb=" N MET A 478 " --> pdb=" O GLN A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' Processing helix chain 'A' and resid 493 through 500 Processing helix chain 'A' and resid 505 through 514 removed outlier: 3.697A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 561 through 567 removed outlier: 4.803A pdb=" N LEU A 565 " --> pdb=" O GLU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 582 removed outlier: 4.166A pdb=" N SER A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 592 Processing helix chain 'A' and resid 630 through 633 No H-bonds generated for 'chain 'A' and resid 630 through 633' Processing helix chain 'A' and resid 636 through 652 Processing helix chain 'A' and resid 675 through 685 removed outlier: 3.574A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 724 through 735 Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 755 through 791 Processing helix chain 'C' and resid 56 through 64 removed outlier: 3.751A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N GLY C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 removed outlier: 4.052A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 4.492A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.717A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.582A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 removed outlier: 3.882A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 252 through 261 removed outlier: 4.106A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 287 through 295 removed outlier: 4.753A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 318 Processing helix chain 'C' and resid 333 through 348 removed outlier: 4.553A pdb=" N LYS C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 345 " --> pdb=" O GLY C 342 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.552A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 26 through 28 Processing sheet with id= B, first strand: chain 'A' and resid 12 through 16 Processing sheet with id= C, first strand: chain 'A' and resid 100 through 102 Processing sheet with id= D, first strand: chain 'A' and resid 655 through 658 removed outlier: 3.896A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 377 through 382 Processing sheet with id= F, first strand: chain 'A' and resid 547 through 551 Processing sheet with id= G, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.580A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.324A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 8 through 12 Processing sheet with id= J, first strand: chain 'C' and resid 65 through 69 Processing sheet with id= K, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= L, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.282A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 238 through 241 441 hydrogen bonds defined for protein. 1206 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: 2.98 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1694 1.32 - 1.44: 2731 1.44 - 1.56: 5825 1.56 - 1.69: 3 1.69 - 1.81: 102 Bond restraints: 10355 Sorted by residual: bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.453 0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.374 -0.045 1.40e-02 5.10e+03 1.03e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.200 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.466 0.059 2.10e-02 2.27e+03 7.84e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.31e+00 ... (remaining 10350 not shown) Histogram of bond angle deviations from ideal: 98.67 - 106.16: 261 106.16 - 113.64: 5691 113.64 - 121.13: 5377 121.13 - 128.62: 2587 128.62 - 136.11: 69 Bond angle restraints: 13985 Sorted by residual: angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 110.99 10.71 1.80e+00 3.09e-01 3.54e+01 angle pdb=" N TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.50 102.55 7.95 1.70e+00 3.46e-01 2.18e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 101.62 8.48 1.90e+00 2.77e-01 1.99e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.86 -4.86 1.10e+00 8.26e-01 1.95e+01 angle pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " pdb=" CZ2 TRP H 1 " ideal model delta sigma weight residual 122.40 118.18 4.22 1.00e+00 1.00e+00 1.78e+01 ... (remaining 13980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.52: 6095 30.52 - 61.04: 113 61.04 - 91.56: 38 91.56 - 122.08: 1 122.08 - 152.60: 2 Dihedral angle restraints: 6249 sinusoidal: 2560 harmonic: 3689 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 92.60 -152.60 1 2.00e+01 2.50e-03 4.53e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 82.51 -142.51 1 2.00e+01 2.50e-03 4.30e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 178.43 121.57 1 2.00e+01 2.50e-03 3.66e+01 ... (remaining 6246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1030 0.042 - 0.084: 345 0.084 - 0.127: 126 0.127 - 0.169: 21 0.169 - 0.211: 6 Chirality restraints: 1528 Sorted by residual: chirality pdb=" CA GLU A 512 " pdb=" N GLU A 512 " pdb=" C GLU A 512 " pdb=" CB GLU A 512 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA CYS H 5 " pdb=" N CYS H 5 " pdb=" C CYS H 5 " pdb=" CB CYS H 5 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CA TYR A 175 " pdb=" N TYR A 175 " pdb=" C TYR A 175 " pdb=" CB TYR A 175 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.57e-01 ... (remaining 1525 not shown) Planarity restraints: 1790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 12 " -0.299 9.50e-02 1.11e+02 1.38e-01 2.42e+01 pdb=" NE ARG A 12 " -0.004 2.00e-02 2.50e+03 pdb=" CZ ARG A 12 " 0.066 2.00e-02 2.50e+03 pdb=" NH1 ARG A 12 " -0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG A 12 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 278 " -0.103 9.50e-02 1.11e+02 6.01e-02 2.00e+01 pdb=" NE ARG A 278 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 278 " -0.074 2.00e-02 2.50e+03 pdb=" NH1 ARG A 278 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG A 278 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 641 " -0.100 9.50e-02 1.11e+02 5.88e-02 1.92e+01 pdb=" NE ARG A 641 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 641 " -0.072 2.00e-02 2.50e+03 pdb=" NH1 ARG A 641 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG A 641 " 0.021 2.00e-02 2.50e+03 ... (remaining 1787 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 2 2.04 - 2.75: 1223 2.75 - 3.47: 14618 3.47 - 4.18: 23381 4.18 - 4.90: 42036 Nonbonded interactions: 81260 Sorted by model distance: nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.321 3.350 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.731 3.620 nonbonded pdb=" OE1 GLU A 144 " pdb=" OH TYR A 179 " model vdw 2.073 2.440 nonbonded pdb=" O THR C 149 " pdb=" ND2 ASN C 296 " model vdw 2.142 2.520 nonbonded pdb=" O TRP H 1 " pdb=" O1 EEP H 2 " model vdw 2.166 2.440 ... (remaining 81255 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=1.00 max=1.00 mean=1.00 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: 1.380 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: 6.950 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 30.060 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 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 : 0.005 0.119 10355 Z= 0.295 Angle : 0.825 12.478 13985 Z= 0.487 Chirality : 0.049 0.211 1528 Planarity : 0.008 0.138 1790 Dihedral : 14.947 152.600 3871 Min Nonbonded Distance : 1.321 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.08 % 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: -1.17 (0.21), residues: 1236 helix: -1.39 (0.17), residues: 587 sheet: 0.91 (0.38), residues: 155 loop : -0.28 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP C 79 HIS 0.010 0.002 HIS A 81 PHE 0.032 0.002 PHE A 564 TYR 0.038 0.006 TYR C 306 ARG 0.075 0.012 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 732 LEU cc_start: 0.9498 (tp) cc_final: 0.9279 (mt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2686 time to fit residues: 57.7482 Evaluate side-chains 84 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN A 81 HIS A 87 HIS A 149 GLN A 238 ASN A 264 GLN A 290 GLN A 410 ASN A 463 GLN A 497 ASN ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 HIS A 657 HIS A 755 GLN A 775 GLN C 128 ASN C 162 ASN C 280 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10355 Z= 0.248 Angle : 0.651 7.035 13985 Z= 0.344 Chirality : 0.043 0.168 1528 Planarity : 0.004 0.055 1790 Dihedral : 9.113 154.484 1397 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 1.20 % Allowed : 6.19 % Favored : 92.61 % 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: 0.86 (0.23), residues: 1236 helix: 0.67 (0.21), residues: 592 sheet: 1.20 (0.39), residues: 157 loop : 0.45 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 79 HIS 0.009 0.001 HIS C 275 PHE 0.026 0.002 PHE C 255 TYR 0.018 0.002 TYR C 279 ARG 0.006 0.001 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.6774 (tmm) cc_final: 0.6564 (ttp) REVERT: A 473 GLU cc_start: 0.7838 (tp30) cc_final: 0.7489 (tp30) outliers start: 13 outliers final: 6 residues processed: 100 average time/residue: 0.2023 time to fit residues: 30.2862 Evaluate side-chains 74 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 93 optimal weight: 0.0970 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 GLN C 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10355 Z= 0.175 Angle : 0.576 6.792 13985 Z= 0.299 Chirality : 0.041 0.157 1528 Planarity : 0.004 0.059 1790 Dihedral : 8.596 160.557 1397 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.29 % Allowed : 7.76 % Favored : 90.94 % 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: 1.38 (0.24), residues: 1236 helix: 1.20 (0.21), residues: 594 sheet: 1.47 (0.40), residues: 157 loop : 0.55 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 79 HIS 0.007 0.001 HIS C 275 PHE 0.021 0.001 PHE C 255 TYR 0.010 0.001 TYR C 279 ARG 0.010 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 GLU cc_start: 0.7899 (tp30) cc_final: 0.7644 (tp30) outliers start: 14 outliers final: 9 residues processed: 93 average time/residue: 0.2028 time to fit residues: 28.4361 Evaluate side-chains 84 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 75 optimal weight: 0.0000 chunk 113 optimal weight: 0.4980 chunk 119 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10355 Z= 0.165 Angle : 0.558 7.159 13985 Z= 0.285 Chirality : 0.040 0.156 1528 Planarity : 0.004 0.056 1790 Dihedral : 8.198 165.907 1397 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.20 % Allowed : 8.60 % Favored : 90.20 % 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: 1.53 (0.24), residues: 1236 helix: 1.37 (0.22), residues: 602 sheet: 1.57 (0.41), residues: 158 loop : 0.52 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 79 HIS 0.006 0.001 HIS C 275 PHE 0.018 0.001 PHE C 255 TYR 0.015 0.001 TYR A 711 ARG 0.005 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 GLU cc_start: 0.7908 (tp30) cc_final: 0.7657 (tp30) outliers start: 13 outliers final: 9 residues processed: 88 average time/residue: 0.1905 time to fit residues: 25.8364 Evaluate side-chains 81 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 61 optimal weight: 0.0770 chunk 107 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 overall best weight: 1.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10355 Z= 0.337 Angle : 0.635 8.929 13985 Z= 0.323 Chirality : 0.042 0.167 1528 Planarity : 0.004 0.052 1790 Dihedral : 8.247 172.085 1397 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.94 % Allowed : 8.96 % Favored : 89.09 % 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: 1.36 (0.24), residues: 1236 helix: 1.30 (0.21), residues: 599 sheet: 1.32 (0.39), residues: 160 loop : 0.40 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 79 HIS 0.009 0.002 HIS C 275 PHE 0.021 0.002 PHE C 255 TYR 0.016 0.002 TYR A 259 ARG 0.004 0.001 ARG B 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 72 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 GLU cc_start: 0.7975 (tp30) cc_final: 0.7607 (tp30) REVERT: C 299 MET cc_start: 0.7538 (mmm) cc_final: 0.7302 (mmm) outliers start: 21 outliers final: 14 residues processed: 85 average time/residue: 0.1945 time to fit residues: 25.2987 Evaluate side-chains 83 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 111 ASN Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 23 optimal weight: 0.0170 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 119 optimal weight: 0.0010 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 9 optimal weight: 0.0670 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10355 Z= 0.147 Angle : 0.558 8.821 13985 Z= 0.281 Chirality : 0.040 0.167 1528 Planarity : 0.004 0.052 1790 Dihedral : 7.857 175.045 1397 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.39 % Allowed : 10.54 % Favored : 88.08 % 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 (0.24), residues: 1236 helix: 1.54 (0.22), residues: 601 sheet: 1.51 (0.39), residues: 157 loop : 0.41 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 484 HIS 0.005 0.001 HIS C 275 PHE 0.016 0.001 PHE C 255 TYR 0.010 0.001 TYR A 368 ARG 0.004 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.8639 (mtt) cc_final: 0.8439 (mmt) REVERT: A 473 GLU cc_start: 0.7895 (tp30) cc_final: 0.7623 (tp30) outliers start: 15 outliers final: 9 residues processed: 92 average time/residue: 0.1883 time to fit residues: 26.6253 Evaluate side-chains 82 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 242 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 66 optimal weight: 0.2980 chunk 119 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10355 Z= 0.173 Angle : 0.544 7.965 13985 Z= 0.274 Chirality : 0.039 0.165 1528 Planarity : 0.004 0.050 1790 Dihedral : 7.175 149.447 1397 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.29 % Allowed : 10.81 % Favored : 87.89 % 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: 1.61 (0.24), residues: 1236 helix: 1.55 (0.22), residues: 602 sheet: 1.55 (0.39), residues: 157 loop : 0.41 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 484 HIS 0.005 0.001 HIS C 275 PHE 0.015 0.001 PHE C 255 TYR 0.010 0.001 TYR A 79 ARG 0.004 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.8594 (mtt) cc_final: 0.8340 (mmt) REVERT: A 473 GLU cc_start: 0.7945 (tp30) cc_final: 0.7665 (tp30) outliers start: 14 outliers final: 8 residues processed: 88 average time/residue: 0.2027 time to fit residues: 27.3736 Evaluate side-chains 81 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 0.0670 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10355 Z= 0.162 Angle : 0.570 12.526 13985 Z= 0.283 Chirality : 0.039 0.162 1528 Planarity : 0.004 0.050 1790 Dihedral : 6.441 115.531 1397 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.92 % Allowed : 11.74 % Favored : 87.34 % 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: 1.62 (0.24), residues: 1236 helix: 1.55 (0.22), residues: 603 sheet: 1.63 (0.39), residues: 157 loop : 0.39 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 484 HIS 0.005 0.001 HIS C 275 PHE 0.014 0.001 PHE C 255 TYR 0.011 0.001 TYR A 127 ARG 0.004 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 10 residues processed: 86 average time/residue: 0.2230 time to fit residues: 28.2403 Evaluate side-chains 85 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 324 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10355 Z= 0.218 Angle : 0.594 9.433 13985 Z= 0.297 Chirality : 0.040 0.157 1528 Planarity : 0.004 0.048 1790 Dihedral : 6.242 102.388 1397 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.48 % Allowed : 11.74 % Favored : 86.78 % 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: 1.60 (0.24), residues: 1236 helix: 1.55 (0.22), residues: 604 sheet: 1.66 (0.39), residues: 157 loop : 0.35 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 22 HIS 0.006 0.001 HIS C 275 PHE 0.014 0.001 PHE C 255 TYR 0.011 0.001 TYR A 127 ARG 0.003 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 47 MET cc_start: 0.7388 (ppp) cc_final: 0.7083 (ppp) outliers start: 16 outliers final: 12 residues processed: 86 average time/residue: 0.2007 time to fit residues: 26.3118 Evaluate side-chains 84 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 324 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.7980 chunk 71 optimal weight: 0.4980 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 75 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10355 Z= 0.175 Angle : 0.605 12.126 13985 Z= 0.296 Chirality : 0.040 0.165 1528 Planarity : 0.004 0.049 1790 Dihedral : 6.042 93.110 1397 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.11 % Allowed : 11.92 % Favored : 86.97 % 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: 1.60 (0.24), residues: 1236 helix: 1.53 (0.22), residues: 604 sheet: 1.64 (0.39), residues: 157 loop : 0.38 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 484 HIS 0.005 0.001 HIS C 275 PHE 0.014 0.001 PHE C 255 TYR 0.010 0.001 TYR A 127 ARG 0.003 0.000 ARG C 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 47 MET cc_start: 0.7393 (ppp) cc_final: 0.7170 (ppp) outliers start: 12 outliers final: 12 residues processed: 84 average time/residue: 0.2226 time to fit residues: 27.9419 Evaluate side-chains 88 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 324 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 41 optimal weight: 0.0020 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.056639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.042498 restraints weight = 51520.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.044011 restraints weight = 26876.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.045077 restraints weight = 17353.472| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10355 Z= 0.259 Angle : 0.645 11.520 13985 Z= 0.316 Chirality : 0.040 0.161 1528 Planarity : 0.004 0.048 1790 Dihedral : 6.068 89.798 1397 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.11 % Allowed : 12.11 % Favored : 86.78 % 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: 1.52 (0.24), residues: 1236 helix: 1.48 (0.22), residues: 604 sheet: 1.51 (0.39), residues: 157 loop : 0.35 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 22 HIS 0.006 0.001 HIS C 275 PHE 0.015 0.001 PHE C 255 TYR 0.011 0.001 TYR A 259 ARG 0.003 0.000 ARG B 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1948.57 seconds wall clock time: 36 minutes 12.98 seconds (2172.98 seconds total)