Starting phenix.real_space_refine on Fri Mar 15 00:55:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pml_13538/03_2024/7pml_13538_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pml_13538/03_2024/7pml_13538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pml_13538/03_2024/7pml_13538.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pml_13538/03_2024/7pml_13538.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pml_13538/03_2024/7pml_13538_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pml_13538/03_2024/7pml_13538_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 5 5.49 5 Mg 3 5.21 5 S 63 5.16 5 C 6482 2.51 5 N 1730 2.21 5 O 1906 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 TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ASP 35": "OD1" <-> "OD2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A ASP 301": "OD1" <-> "OD2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 586": "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 PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A ASP 723": "OD1" <-> "OD2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 768": "NH1" <-> "NH2" Residue "A ARG 779": "NH1" <-> "NH2" Residue "A ARG 784": "NH1" <-> "NH2" Residue "A ARG 791": "NH1" <-> "NH2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 10189 Number of models: 1 Model: "" Number of chains: 6 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: 6105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6105 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 5 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 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: 5.95, per 1000 atoms: 0.58 Number of scatterers: 10189 At special positions: 0 Unit cell: (106.7, 126.5, 155.1, 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 5 15.00 Mg 3 11.99 O 1906 8.00 N 1730 7.00 C 6482 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: 4.13 Conformation dependent library (CDL) restraints added in 1.7 seconds 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 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: 2382 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 13 sheets defined 48.5% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 29 through 38 removed outlier: 4.220A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.665A 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: 4.119A 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 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 139 through 153 Processing helix chain 'A' and resid 169 through 183 removed outlier: 3.630A pdb=" N ALA A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.792A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 274 through 277 Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.577A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) removed outlier: 5.676A 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 315 removed outlier: 3.878A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 337 removed outlier: 3.509A pdb=" N GLY A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 3.693A 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 376 removed outlier: 3.835A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 423 Processing helix chain 'A' and resid 449 through 479 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: 3.825A 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 564 through 568 Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.913A pdb=" N SER A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 3.757A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 636 through 652 Processing helix chain 'A' and resid 675 through 684 removed outlier: 3.856A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 683 " --> pdb=" O VAL A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 704 through 714 removed outlier: 5.907A pdb=" N VAL A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) 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 55 through 60 removed outlier: 3.607A pdb=" N GLN C 59 " --> pdb=" O ASP C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 91 removed outlier: 3.659A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) 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: 3.718A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 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 183 through 196 removed outlier: 3.693A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 253 through 261 Proline residue: C 258 - end of helix removed outlier: 4.691A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.169A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.890A 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: 3.818A 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 11 through 16 removed outlier: 4.160A pdb=" N ALA A 11 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 37 through 41 Processing sheet with id= D, first strand: chain 'A' and resid 100 through 103 removed outlier: 7.754A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 340 through 342 Processing sheet with id= F, first strand: chain 'A' and resid 377 through 381 Processing sheet with id= G, first strand: chain 'A' and resid 547 through 551 Processing sheet with id= H, first strand: chain 'A' and resid 700 through 703 Processing sheet with id= I, first strand: chain 'C' and resid 8 through 11 removed outlier: 3.519A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 34 through 38 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: 6.589A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.703A 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 241 434 hydrogen bonds defined for protein. 1221 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: 2.96 Time building geometry restraints manager: 4.44 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: 1699 1.32 - 1.44: 2747 1.44 - 1.56: 5847 1.56 - 1.69: 8 1.69 - 1.81: 103 Bond restraints: 10404 Sorted by residual: bond pdb=" O3A ANP A1901 " pdb=" PB ANP A1901 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.29e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.451 0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" O5' ANP A1901 " pdb=" PA ANP A1901 " ideal model delta sigma weight residual 1.655 1.582 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.375 -0.046 1.40e-02 5.10e+03 1.08e+01 ... (remaining 10399 not shown) Histogram of bond angle deviations from ideal: 98.19 - 105.81: 246 105.81 - 113.43: 5651 113.43 - 121.05: 5417 121.05 - 128.68: 2673 128.68 - 136.30: 69 Bond angle restraints: 14056 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 121.70 111.11 10.59 1.80e+00 3.09e-01 3.46e+01 angle pdb=" PB ANP A1901 " pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 126.95 110.68 16.27 3.00e+00 1.11e-01 2.94e+01 angle pdb=" N GLY A 563 " pdb=" CA GLY A 563 " pdb=" C GLY A 563 " ideal model delta sigma weight residual 114.66 120.25 -5.59 1.24e+00 6.50e-01 2.03e+01 angle pdb=" CA TRP A 484 " pdb=" CB TRP A 484 " pdb=" CG TRP A 484 " ideal model delta sigma weight residual 113.60 121.69 -8.09 1.90e+00 2.77e-01 1.81e+01 angle pdb=" N DTH H 4 " pdb=" CA DTH H 4 " pdb=" CB DTH H 4 " ideal model delta sigma weight residual 111.50 104.41 7.09 1.70e+00 3.46e-01 1.74e+01 ... (remaining 14051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.20: 6118 32.20 - 64.40: 132 64.40 - 96.60: 39 96.60 - 128.80: 3 128.80 - 161.00: 2 Dihedral angle restraints: 6294 sinusoidal: 2601 harmonic: 3693 Sorted by residual: 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 300.00 168.16 131.84 1 2.00e+01 2.50e-03 4.00e+01 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 55.19 -115.19 1 2.00e+01 2.50e-03 3.42e+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 54.36 -114.36 1 2.00e+01 2.50e-03 3.39e+01 ... (remaining 6291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1192 0.056 - 0.112: 290 0.112 - 0.167: 48 0.167 - 0.223: 2 0.223 - 0.279: 2 Chirality restraints: 1534 Sorted by residual: chirality pdb=" C3' ANP A1901 " pdb=" C2' ANP A1901 " pdb=" C4' ANP A1901 " pdb=" O3' ANP A1901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA MET A 478 " pdb=" N MET A 478 " pdb=" C MET A 478 " pdb=" CB MET A 478 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA PHE A 564 " pdb=" N PHE A 564 " pdb=" C PHE A 564 " pdb=" CB PHE A 564 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.50e-01 ... (remaining 1531 not shown) Planarity restraints: 1793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 306 " -0.002 2.00e-02 2.50e+03 4.17e-02 3.47e+01 pdb=" CG TYR C 306 " -0.000 2.00e-02 2.50e+03 pdb=" CD1 TYR C 306 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR C 306 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 306 " 0.058 2.00e-02 2.50e+03 pdb=" CE2 TYR C 306 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 306 " 0.060 2.00e-02 2.50e+03 pdb=" OH TYR C 306 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 147 " -0.134 9.50e-02 1.11e+02 7.53e-02 2.81e+01 pdb=" NE ARG C 147 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG C 147 " -0.087 2.00e-02 2.50e+03 pdb=" NH1 ARG C 147 " 0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG C 147 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 773 " -0.112 9.50e-02 1.11e+02 6.58e-02 2.41e+01 pdb=" NE ARG A 773 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG A 773 " -0.081 2.00e-02 2.50e+03 pdb=" NH1 ARG A 773 " 0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG A 773 " 0.023 2.00e-02 2.50e+03 ... (remaining 1790 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 4 2.03 - 2.75: 1114 2.75 - 3.47: 14491 3.47 - 4.18: 23729 4.18 - 4.90: 42751 Nonbonded interactions: 82089 Sorted by model distance: nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.315 3.350 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 1.641 2.170 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.731 3.620 nonbonded pdb=" O1B ANP A1901 " pdb="MG MG A1903 " model vdw 1.814 2.170 nonbonded pdb=" O3G ANP A1901 " pdb="MG MG A1902 " model vdw 2.129 2.170 ... (remaining 82084 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 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: 0.010 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.920 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 30.070 Find NCS groups from input model: 0.300 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: 0.010 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 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 0.145 10404 Z= 0.331 Angle : 0.856 16.267 14056 Z= 0.494 Chirality : 0.049 0.279 1534 Planarity : 0.008 0.124 1793 Dihedral : 15.930 161.004 3912 Min Nonbonded Distance : 1.315 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.09 % Allowed : 0.18 % Favored : 99.72 % 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: -1.35 (0.20), residues: 1235 helix: -1.72 (0.16), residues: 604 sheet: 0.40 (0.38), residues: 152 loop : 0.15 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.005 TRP A 484 HIS 0.015 0.002 HIS A 418 PHE 0.060 0.002 PHE A 564 TYR 0.061 0.006 TYR C 306 ARG 0.088 0.012 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.8426 (m-80) cc_final: 0.8212 (m-80) REVERT: A 503 MET cc_start: 0.8521 (mmm) cc_final: 0.8311 (mmt) REVERT: C 270 GLU cc_start: 0.7295 (mt-10) cc_final: 0.7088 (mt-10) outliers start: 1 outliers final: 1 residues processed: 104 average time/residue: 0.3144 time to fit residues: 43.2048 Evaluate side-chains 60 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 147 HIS ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 398 ASN A 463 GLN A 642 ASN C 162 ASN C 280 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 10404 Z= 0.293 Angle : 0.632 7.378 14056 Z= 0.332 Chirality : 0.043 0.151 1534 Planarity : 0.004 0.038 1793 Dihedral : 11.088 174.076 1430 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.92 % Allowed : 2.30 % Favored : 96.77 % 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: 0.70 (0.23), residues: 1235 helix: 0.46 (0.20), residues: 614 sheet: 0.75 (0.39), residues: 155 loop : 0.65 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 484 HIS 0.009 0.001 HIS A 418 PHE 0.021 0.002 PHE A 564 TYR 0.018 0.001 TYR A 79 ARG 0.007 0.001 ARG A 789 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8435 (mm-40) cc_final: 0.7944 (mm-40) REVERT: B 93 PHE cc_start: 0.8394 (m-80) cc_final: 0.8174 (m-80) outliers start: 10 outliers final: 6 residues processed: 72 average time/residue: 0.2779 time to fit residues: 27.6988 Evaluate side-chains 64 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 395 HIS A 492 ASN C 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10404 Z= 0.172 Angle : 0.531 7.168 14056 Z= 0.274 Chirality : 0.040 0.182 1534 Planarity : 0.004 0.035 1793 Dihedral : 10.207 170.637 1430 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.83 % Allowed : 4.24 % Favored : 94.93 % 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: 1.40 (0.24), residues: 1235 helix: 1.25 (0.21), residues: 608 sheet: 1.06 (0.39), residues: 157 loop : 0.67 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 484 HIS 0.006 0.001 HIS A 418 PHE 0.023 0.001 PHE C 223 TYR 0.013 0.001 TYR A 456 ARG 0.009 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7915 (mm-40) outliers start: 9 outliers final: 7 residues processed: 63 average time/residue: 0.2769 time to fit residues: 24.6498 Evaluate side-chains 61 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 0.0570 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 HIS A 410 ASN A 455 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10404 Z= 0.195 Angle : 0.523 6.444 14056 Z= 0.267 Chirality : 0.040 0.186 1534 Planarity : 0.003 0.037 1793 Dihedral : 9.632 167.602 1430 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.74 % Allowed : 5.25 % Favored : 94.01 % 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: 1.51 (0.24), residues: 1235 helix: 1.41 (0.21), residues: 614 sheet: 0.84 (0.41), residues: 153 loop : 0.70 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 484 HIS 0.006 0.001 HIS A 418 PHE 0.013 0.001 PHE B 93 TYR 0.013 0.001 TYR A 456 ARG 0.009 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8409 (mm-40) cc_final: 0.7972 (mm-40) REVERT: B 62 SER cc_start: 0.8406 (m) cc_final: 0.7977 (p) REVERT: B 93 PHE cc_start: 0.8512 (m-80) cc_final: 0.8250 (m-80) outliers start: 8 outliers final: 6 residues processed: 64 average time/residue: 0.2771 time to fit residues: 24.8483 Evaluate side-chains 63 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10404 Z= 0.185 Angle : 0.531 12.136 14056 Z= 0.263 Chirality : 0.040 0.185 1534 Planarity : 0.003 0.036 1793 Dihedral : 9.322 166.245 1430 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.92 % Allowed : 6.18 % Favored : 92.90 % 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: 1.64 (0.24), residues: 1235 helix: 1.53 (0.21), residues: 615 sheet: 0.83 (0.41), residues: 153 loop : 0.77 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 484 HIS 0.005 0.001 HIS A 418 PHE 0.010 0.001 PHE A 432 TYR 0.012 0.001 TYR A 456 ARG 0.009 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8407 (mm-40) cc_final: 0.7980 (mm-40) REVERT: B 36 MET cc_start: 0.9053 (mmt) cc_final: 0.8746 (mmt) REVERT: B 62 SER cc_start: 0.8307 (m) cc_final: 0.7886 (p) REVERT: B 93 PHE cc_start: 0.8674 (m-80) cc_final: 0.8394 (m-80) REVERT: B 120 MET cc_start: 0.7579 (mpp) cc_final: 0.7089 (pmm) REVERT: A 718 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7790 (pttm) outliers start: 10 outliers final: 6 residues processed: 64 average time/residue: 0.2633 time to fit residues: 23.9181 Evaluate side-chains 62 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 0.0980 chunk 99 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10404 Z= 0.165 Angle : 0.517 11.287 14056 Z= 0.256 Chirality : 0.040 0.184 1534 Planarity : 0.003 0.036 1793 Dihedral : 9.118 165.257 1430 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.74 % Allowed : 7.10 % Favored : 92.17 % 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: 1.77 (0.24), residues: 1235 helix: 1.68 (0.22), residues: 609 sheet: 0.82 (0.41), residues: 153 loop : 0.81 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 781 HIS 0.004 0.001 HIS A 418 PHE 0.011 0.001 PHE C 223 TYR 0.011 0.001 TYR A 456 ARG 0.010 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8327 (mm-40) cc_final: 0.7889 (mm-40) REVERT: B 62 SER cc_start: 0.8301 (m) cc_final: 0.7879 (p) REVERT: B 73 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8368 (ttp) REVERT: B 93 PHE cc_start: 0.8679 (m-80) cc_final: 0.8250 (m-80) REVERT: A 718 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7755 (pttm) outliers start: 8 outliers final: 4 residues processed: 61 average time/residue: 0.2411 time to fit residues: 21.2921 Evaluate side-chains 60 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 119 optimal weight: 0.1980 chunk 74 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10404 Z= 0.162 Angle : 0.529 10.935 14056 Z= 0.260 Chirality : 0.039 0.182 1534 Planarity : 0.003 0.035 1793 Dihedral : 8.960 164.454 1430 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.55 % Allowed : 7.37 % Favored : 92.07 % 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: 1.82 (0.24), residues: 1235 helix: 1.71 (0.22), residues: 613 sheet: 0.83 (0.41), residues: 153 loop : 0.85 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 781 HIS 0.004 0.001 HIS A 418 PHE 0.010 0.001 PHE A 432 TYR 0.011 0.001 TYR A 456 ARG 0.007 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8321 (mm-40) cc_final: 0.7870 (mm-40) REVERT: B 62 SER cc_start: 0.8288 (m) cc_final: 0.7858 (p) REVERT: B 73 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8378 (ttp) REVERT: B 93 PHE cc_start: 0.8684 (m-80) cc_final: 0.8270 (m-80) REVERT: A 718 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7773 (pttm) REVERT: C 283 MET cc_start: 0.7459 (mmm) cc_final: 0.7118 (mmm) outliers start: 6 outliers final: 2 residues processed: 59 average time/residue: 0.2353 time to fit residues: 20.2065 Evaluate side-chains 58 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 740 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 0.0970 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 23 optimal weight: 4.9990 chunk 75 optimal weight: 0.3980 chunk 81 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10404 Z= 0.149 Angle : 0.535 11.049 14056 Z= 0.261 Chirality : 0.039 0.183 1534 Planarity : 0.003 0.036 1793 Dihedral : 8.813 164.010 1429 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.55 % Allowed : 7.74 % Favored : 91.71 % 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: 1.84 (0.24), residues: 1235 helix: 1.74 (0.22), residues: 609 sheet: 0.85 (0.42), residues: 153 loop : 0.85 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 781 HIS 0.008 0.001 HIS A 418 PHE 0.010 0.001 PHE A 432 TYR 0.011 0.001 TYR A 456 ARG 0.006 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8311 (mm-40) cc_final: 0.7853 (mm-40) REVERT: B 36 MET cc_start: 0.8989 (mmt) cc_final: 0.8250 (mmm) REVERT: B 62 SER cc_start: 0.8225 (m) cc_final: 0.7747 (p) REVERT: B 73 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8306 (ttp) REVERT: B 93 PHE cc_start: 0.8681 (m-80) cc_final: 0.8276 (m-80) REVERT: A 718 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7808 (pttm) REVERT: C 283 MET cc_start: 0.7447 (mmm) cc_final: 0.7143 (mmm) outliers start: 6 outliers final: 2 residues processed: 59 average time/residue: 0.2414 time to fit residues: 20.5373 Evaluate side-chains 57 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 740 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN A 481 GLN ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10404 Z= 0.217 Angle : 0.561 11.413 14056 Z= 0.276 Chirality : 0.040 0.185 1534 Planarity : 0.003 0.042 1793 Dihedral : 8.795 163.155 1429 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.74 % Allowed : 8.39 % Favored : 90.88 % 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: 1.89 (0.25), residues: 1235 helix: 1.83 (0.22), residues: 602 sheet: 0.82 (0.42), residues: 153 loop : 0.82 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 484 HIS 0.003 0.001 HIS C 87 PHE 0.010 0.001 PHE A 432 TYR 0.011 0.001 TYR A 102 ARG 0.006 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8305 (mm-40) cc_final: 0.7836 (mm-40) REVERT: B 93 PHE cc_start: 0.8702 (m-80) cc_final: 0.8287 (m-80) REVERT: A 718 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7880 (pttm) REVERT: C 283 MET cc_start: 0.7410 (mmm) cc_final: 0.7127 (mmm) outliers start: 8 outliers final: 4 residues processed: 56 average time/residue: 0.2511 time to fit residues: 20.5618 Evaluate side-chains 57 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain C residue 123 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 113 optimal weight: 0.0980 chunk 98 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10404 Z= 0.152 Angle : 0.566 17.461 14056 Z= 0.274 Chirality : 0.039 0.185 1534 Planarity : 0.003 0.035 1793 Dihedral : 8.672 163.568 1429 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.46 % Allowed : 8.39 % Favored : 91.15 % 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: 1.88 (0.25), residues: 1235 helix: 1.81 (0.22), residues: 607 sheet: 0.84 (0.42), residues: 153 loop : 0.82 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 781 HIS 0.007 0.001 HIS A 418 PHE 0.010 0.001 PHE A 432 TYR 0.012 0.001 TYR A 102 ARG 0.006 0.000 ARG A 343 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8342 (mm-40) cc_final: 0.7886 (mm-40) REVERT: B 36 MET cc_start: 0.9058 (mmt) cc_final: 0.8377 (mmm) REVERT: B 62 SER cc_start: 0.8269 (m) cc_final: 0.7804 (p) REVERT: B 73 MET cc_start: 0.8578 (ttp) cc_final: 0.8265 (ttp) REVERT: B 93 PHE cc_start: 0.8693 (m-80) cc_final: 0.8266 (m-80) REVERT: A 718 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7840 (pttm) REVERT: C 283 MET cc_start: 0.7416 (mmm) cc_final: 0.7144 (mmm) outliers start: 5 outliers final: 4 residues processed: 56 average time/residue: 0.2446 time to fit residues: 19.8560 Evaluate side-chains 58 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain C residue 123 MET 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: 0.3980 chunk 14 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 18 optimal weight: 0.0170 chunk 86 optimal weight: 0.7980 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 = 0.3329 r_free = 0.3329 target = 0.050819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.037388 restraints weight = 52389.818| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.92 r_work: 0.2699 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10404 Z= 0.140 Angle : 0.549 12.648 14056 Z= 0.263 Chirality : 0.039 0.184 1534 Planarity : 0.003 0.036 1793 Dihedral : 8.533 163.292 1429 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.37 % Allowed : 8.29 % Favored : 91.34 % 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: 1.98 (0.25), residues: 1235 helix: 1.89 (0.22), residues: 607 sheet: 1.09 (0.43), residues: 150 loop : 0.78 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 484 HIS 0.008 0.001 HIS A 418 PHE 0.010 0.001 PHE A 432 TYR 0.011 0.001 TYR A 456 ARG 0.006 0.000 ARG A 343 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2082.87 seconds wall clock time: 38 minutes 28.98 seconds (2308.98 seconds total)