Starting phenix.real_space_refine on Fri Mar 15 00:13:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plt_13501/03_2024/7plt_13501_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plt_13501/03_2024/7plt_13501.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/7plt_13501/03_2024/7plt_13501.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plt_13501/03_2024/7plt_13501.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plt_13501/03_2024/7plt_13501_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plt_13501/03_2024/7plt_13501_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 2 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 6467 2.51 5 N 1723 2.21 5 O 1892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 17": "OD1" <-> "OD2" Residue "A TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 343": "NH1" <-> "NH2" 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 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A GLU 539": "OE1" <-> "OE2" 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 PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10148 Number of models: 1 Model: "" Number of chains: 5 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: 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: "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: "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: 6.02, per 1000 atoms: 0.59 Number of scatterers: 10148 At special positions: 0 Unit cell: (103.88, 133.56, 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 1892 8.00 N 1723 7.00 C 6467 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 1.8 seconds 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 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: 2380 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 11 sheets defined 49.3% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... 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 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: 3.610A pdb=" N ALA A 151 " --> pdb=" O TYR A 147 " (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 Processing helix chain 'A' and resid 192 through 206 removed outlier: 3.810A 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 272 through 277 removed outlier: 4.645A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 301 through 315 removed outlier: 4.435A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 337 removed outlier: 3.571A 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 480 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 499 removed outlier: 3.577A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 499 " --> pdb=" O CYS A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 514 removed outlier: 3.822A 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 565 through 568 No H-bonds generated for 'chain 'A' and resid 565 through 568' Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.654A pdb=" N SER A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 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 653 removed outlier: 3.821A pdb=" N ALA A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 684 removed outlier: 3.776A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.666A pdb=" N ALA A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 714 removed outlier: 5.455A pdb=" N VAL A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 5.837A 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 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 removed outlier: 3.793A 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: 3.742A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.873A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (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: 3.633A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 4.371A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 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: 3.715A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 4.939A 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 290 through 295 Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 318 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.192A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 346 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 removed outlier: 3.819A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 removed outlier: 3.670A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 373 Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 29 through 38 removed outlier: 4.199A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.378A 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: 4.274A 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 sheet with id= A, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.570A pdb=" N LEU A 40 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.606A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 377 through 382 Processing sheet with id= D, first strand: chain 'A' and resid 547 through 551 Processing sheet with id= E, 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= F, first strand: chain 'A' and resid 340 through 344 removed outlier: 6.532A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.832A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 65 through 69 Processing sheet with id= I, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.371A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= K, first strand: chain 'B' and resid 26 through 28 432 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: 2.99 Time building geometry restraints manager: 4.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1699 1.31 - 1.44: 2744 1.44 - 1.56: 5816 1.56 - 1.69: 3 1.69 - 1.81: 102 Bond restraints: 10364 Sorted by residual: bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.439 0.133 2.00e-02 2.50e+03 4.43e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.190 0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " ideal model delta sigma weight residual 1.409 1.353 0.056 1.70e-02 3.46e+03 1.10e+01 bond pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 1.530 1.465 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.458 0.067 2.10e-02 2.27e+03 1.03e+01 ... (remaining 10359 not shown) Histogram of bond angle deviations from ideal: 94.00 - 102.29: 47 102.29 - 110.58: 3327 110.58 - 118.87: 5079 118.87 - 127.16: 5436 127.16 - 135.46: 108 Bond angle restraints: 13997 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 121.70 111.20 10.50 1.80e+00 3.09e-01 3.40e+01 angle pdb=" N PHE A 564 " pdb=" CA PHE A 564 " pdb=" CB PHE A 564 " ideal model delta sigma weight residual 110.16 118.59 -8.43 1.48e+00 4.57e-01 3.24e+01 angle pdb=" N ASN C 296 " pdb=" CA ASN C 296 " pdb=" C ASN C 296 " ideal model delta sigma weight residual 110.68 118.03 -7.35 1.39e+00 5.18e-01 2.79e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 100.47 9.63 1.90e+00 2.77e-01 2.57e+01 angle pdb=" C GLY A 563 " pdb=" N PHE A 564 " pdb=" CA PHE A 564 " ideal model delta sigma weight residual 120.29 113.34 6.95 1.42e+00 4.96e-01 2.40e+01 ... (remaining 13992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.12: 6105 32.12 - 64.24: 117 64.24 - 96.36: 30 96.36 - 128.48: 1 128.48 - 160.60: 2 Dihedral angle restraints: 6255 sinusoidal: 2563 harmonic: 3692 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 -60.00 100.59 -160.60 1 2.00e+01 2.50e-03 4.66e+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 300.00 164.34 135.66 1 2.00e+01 2.50e-03 4.12e+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 56.94 -116.94 1 2.00e+01 2.50e-03 3.49e+01 ... (remaining 6252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 886 0.054 - 0.108: 474 0.108 - 0.162: 141 0.162 - 0.216: 24 0.216 - 0.269: 4 Chirality restraints: 1529 Sorted by residual: 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 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ASN C 296 " pdb=" N ASN C 296 " pdb=" C ASN C 296 " pdb=" CB ASN C 296 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA TYR A 711 " pdb=" N TYR A 711 " pdb=" C TYR A 711 " pdb=" CB TYR A 711 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1526 not shown) Planarity restraints: 1792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 564 " -0.058 2.00e-02 2.50e+03 5.41e-02 5.12e+01 pdb=" CG PHE A 564 " 0.125 2.00e-02 2.50e+03 pdb=" CD1 PHE A 564 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE A 564 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 564 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 564 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 564 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 213 " -0.089 9.50e-02 1.11e+02 5.27e-02 1.57e+01 pdb=" NE ARG A 213 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A 213 " -0.065 2.00e-02 2.50e+03 pdb=" NH1 ARG A 213 " 0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG A 213 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 278 " -0.095 9.50e-02 1.11e+02 5.44e-02 1.55e+01 pdb=" NE ARG A 278 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 278 " -0.065 2.00e-02 2.50e+03 pdb=" NH1 ARG A 278 " 0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG A 278 " 0.018 2.00e-02 2.50e+03 ... (remaining 1789 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 2 2.03 - 2.75: 1536 2.75 - 3.46: 14155 3.46 - 4.18: 23511 4.18 - 4.90: 42497 Nonbonded interactions: 81701 Sorted by model distance: nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.312 3.350 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.727 3.620 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.098 2.170 nonbonded pdb=" OE1 GLU A 144 " pdb=" OH TYR A 179 " model vdw 2.142 2.440 nonbonded pdb=" OE2 GLU A 476 " pdb=" NH1 ARG A 701 " model vdw 2.160 2.520 ... (remaining 81696 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: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 6.900 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 31.390 Find NCS groups from input model: 0.260 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.133 10364 Z= 0.948 Angle : 1.146 13.135 13997 Z= 0.653 Chirality : 0.068 0.269 1529 Planarity : 0.008 0.095 1792 Dihedral : 14.643 160.598 3875 Min Nonbonded Distance : 1.312 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: -1.61 (0.21), residues: 1237 helix: -1.68 (0.17), residues: 615 sheet: 0.00 (0.36), residues: 172 loop : -0.22 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.006 TRP C 356 HIS 0.016 0.003 HIS A 418 PHE 0.125 0.004 PHE A 564 TYR 0.031 0.006 TYR A 439 ARG 0.066 0.010 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 305 MET cc_start: 0.8375 (mmm) cc_final: 0.8171 (mmt) REVERT: C 360 GLN cc_start: 0.7925 (tp40) cc_final: 0.7191 (tp40) REVERT: B 66 ASP cc_start: 0.9237 (p0) cc_final: 0.8896 (p0) REVERT: B 93 PHE cc_start: 0.9258 (m-80) cc_final: 0.8850 (m-80) REVERT: B 110 ARG cc_start: 0.9019 (mtt-85) cc_final: 0.8733 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.3189 time to fit residues: 50.9040 Evaluate side-chains 68 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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: 0.7980 chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 264 GLN A 398 ASN A 410 ASN A 458 ASN A 463 GLN A 464 GLN A 481 GLN A 497 ASN A 638 HIS ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN C 121 GLN C 162 ASN C 296 ASN ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 147 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10364 Z= 0.239 Angle : 0.619 7.265 13997 Z= 0.326 Chirality : 0.043 0.160 1529 Planarity : 0.004 0.053 1792 Dihedral : 9.049 157.012 1398 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.83 % Allowed : 4.34 % Favored : 94.83 % 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: 0.51 (0.23), residues: 1237 helix: 0.32 (0.20), residues: 613 sheet: 0.40 (0.37), residues: 163 loop : 0.65 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 523 HIS 0.007 0.001 HIS A 418 PHE 0.040 0.002 PHE A 564 TYR 0.019 0.001 TYR B 29 ARG 0.006 0.001 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.8809 (mmt) cc_final: 0.8504 (mmt) REVERT: B 66 ASP cc_start: 0.9169 (p0) cc_final: 0.8839 (p0) REVERT: B 93 PHE cc_start: 0.9253 (m-80) cc_final: 0.8812 (m-80) REVERT: B 110 ARG cc_start: 0.9041 (mtt-85) cc_final: 0.8732 (ttm-80) outliers start: 9 outliers final: 4 residues processed: 91 average time/residue: 0.2446 time to fit residues: 31.6334 Evaluate side-chains 74 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 147 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 90 optimal weight: 0.0370 overall best weight: 0.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10364 Z= 0.239 Angle : 0.559 7.130 13997 Z= 0.287 Chirality : 0.042 0.180 1529 Planarity : 0.004 0.051 1792 Dihedral : 8.568 160.532 1398 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.48 % Allowed : 4.89 % Favored : 93.63 % 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: 1.16 (0.24), residues: 1237 helix: 1.04 (0.21), residues: 614 sheet: 0.41 (0.38), residues: 166 loop : 0.80 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 79 HIS 0.007 0.001 HIS B 147 PHE 0.043 0.002 PHE B 12 TYR 0.013 0.001 TYR A 259 ARG 0.006 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7936 (tptp) cc_final: 0.7663 (tppt) REVERT: A 511 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8013 (tm-30) REVERT: A 717 GLN cc_start: 0.8465 (tp-100) cc_final: 0.8165 (tp-100) REVERT: B 36 MET cc_start: 0.8709 (mmt) cc_final: 0.8473 (mmt) REVERT: B 66 ASP cc_start: 0.9103 (p0) cc_final: 0.8743 (p0) REVERT: B 93 PHE cc_start: 0.9296 (m-80) cc_final: 0.8859 (m-80) REVERT: B 110 ARG cc_start: 0.9012 (mtt-85) cc_final: 0.8791 (ttm-80) outliers start: 16 outliers final: 8 residues processed: 88 average time/residue: 0.2261 time to fit residues: 28.9901 Evaluate side-chains 78 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 GLN C 225 ASN B 8 GLN ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10364 Z= 0.375 Angle : 0.615 9.650 13997 Z= 0.310 Chirality : 0.043 0.179 1529 Planarity : 0.004 0.047 1792 Dihedral : 8.414 161.550 1398 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.66 % Allowed : 6.00 % Favored : 92.34 % 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: 1.29 (0.24), residues: 1237 helix: 1.34 (0.22), residues: 610 sheet: 0.24 (0.39), residues: 166 loop : 0.64 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 484 HIS 0.008 0.001 HIS A 418 PHE 0.043 0.002 PHE B 12 TYR 0.016 0.001 TYR A 259 ARG 0.007 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7968 (tptp) cc_final: 0.7723 (tppt) REVERT: A 511 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7910 (tm-30) REVERT: A 717 GLN cc_start: 0.8516 (tp-100) cc_final: 0.8225 (tp-100) REVERT: C 44 MET cc_start: 0.8024 (mtp) cc_final: 0.7805 (mtm) REVERT: B 66 ASP cc_start: 0.9132 (p0) cc_final: 0.8706 (p0) REVERT: B 93 PHE cc_start: 0.9319 (m-80) cc_final: 0.8889 (m-80) REVERT: B 110 ARG cc_start: 0.8981 (mtt-85) cc_final: 0.8673 (ttm-80) outliers start: 18 outliers final: 11 residues processed: 89 average time/residue: 0.2285 time to fit residues: 29.5560 Evaluate side-chains 80 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 44 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN B 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10364 Z= 0.253 Angle : 0.551 10.242 13997 Z= 0.277 Chirality : 0.041 0.197 1529 Planarity : 0.004 0.047 1792 Dihedral : 8.328 170.005 1398 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.48 % Allowed : 6.93 % Favored : 91.60 % 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: 1.46 (0.24), residues: 1237 helix: 1.55 (0.22), residues: 608 sheet: 0.23 (0.39), residues: 166 loop : 0.66 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 484 HIS 0.006 0.001 HIS A 418 PHE 0.045 0.002 PHE B 12 TYR 0.012 0.001 TYR A 259 ARG 0.004 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7945 (tptp) cc_final: 0.7730 (tppt) REVERT: A 511 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7882 (tm-30) REVERT: A 717 GLN cc_start: 0.8527 (tp-100) cc_final: 0.8236 (tp-100) REVERT: A 788 MET cc_start: 0.9395 (mmm) cc_final: 0.9137 (tpp) REVERT: C 44 MET cc_start: 0.8027 (mtp) cc_final: 0.7806 (mtm) REVERT: C 305 MET cc_start: 0.8456 (mmt) cc_final: 0.8240 (mmt) REVERT: B 93 PHE cc_start: 0.9319 (m-80) cc_final: 0.8877 (m-80) REVERT: B 110 ARG cc_start: 0.8949 (mtt-85) cc_final: 0.8662 (ttm-80) outliers start: 16 outliers final: 11 residues processed: 82 average time/residue: 0.2289 time to fit residues: 27.3254 Evaluate side-chains 77 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN B 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10364 Z= 0.183 Angle : 0.533 11.028 13997 Z= 0.264 Chirality : 0.040 0.197 1529 Planarity : 0.003 0.048 1792 Dihedral : 8.008 171.591 1398 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.48 % Allowed : 8.31 % Favored : 90.21 % 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: 1.58 (0.25), residues: 1237 helix: 1.69 (0.22), residues: 610 sheet: 0.23 (0.39), residues: 169 loop : 0.68 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.005 0.001 HIS A 418 PHE 0.044 0.001 PHE B 12 TYR 0.010 0.001 TYR A 259 ARG 0.004 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 511 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7876 (tm-30) REVERT: A 717 GLN cc_start: 0.8520 (tp-100) cc_final: 0.8233 (tp-100) REVERT: C 305 MET cc_start: 0.8419 (mmt) cc_final: 0.8208 (mmt) REVERT: B 36 MET cc_start: 0.8752 (mmt) cc_final: 0.8552 (mmt) REVERT: B 93 PHE cc_start: 0.9315 (m-80) cc_final: 0.8869 (m-80) REVERT: B 120 MET cc_start: 0.6156 (mmt) cc_final: 0.5929 (mmt) outliers start: 16 outliers final: 9 residues processed: 85 average time/residue: 0.2071 time to fit residues: 26.3638 Evaluate side-chains 78 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain B residue 44 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 594 GLN A 743 GLN B 8 GLN B 147 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 10364 Z= 0.430 Angle : 0.634 10.332 13997 Z= 0.317 Chirality : 0.044 0.212 1529 Planarity : 0.004 0.046 1792 Dihedral : 7.496 145.893 1398 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.66 % Allowed : 8.49 % Favored : 89.84 % 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: 1.30 (0.25), residues: 1237 helix: 1.53 (0.22), residues: 611 sheet: 0.05 (0.40), residues: 167 loop : 0.45 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 79 HIS 0.007 0.001 HIS A 418 PHE 0.049 0.002 PHE B 12 TYR 0.017 0.001 TYR A 259 ARG 0.004 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8028 (tptp) cc_final: 0.7797 (tppt) REVERT: A 511 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7879 (tm-30) REVERT: A 717 GLN cc_start: 0.8623 (tp-100) cc_final: 0.8375 (tp-100) REVERT: C 305 MET cc_start: 0.8492 (mmt) cc_final: 0.8267 (mmt) REVERT: B 93 PHE cc_start: 0.9332 (m-80) cc_final: 0.8887 (m-80) REVERT: B 110 ARG cc_start: 0.9105 (ttm-80) cc_final: 0.8646 (mmt180) outliers start: 18 outliers final: 13 residues processed: 85 average time/residue: 0.2275 time to fit residues: 28.2549 Evaluate side-chains 83 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 147 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 11 optimal weight: 0.0670 chunk 93 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10364 Z= 0.198 Angle : 0.569 11.589 13997 Z= 0.283 Chirality : 0.041 0.213 1529 Planarity : 0.003 0.047 1792 Dihedral : 7.031 128.072 1398 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.29 % Allowed : 9.23 % Favored : 89.47 % 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: 1.46 (0.25), residues: 1237 helix: 1.66 (0.22), residues: 609 sheet: 0.12 (0.40), residues: 167 loop : 0.52 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 79 HIS 0.008 0.001 HIS B 147 PHE 0.051 0.001 PHE B 12 TYR 0.011 0.001 TYR A 259 ARG 0.003 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8100 (tptp) cc_final: 0.7846 (tppt) REVERT: A 511 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7852 (tm-30) REVERT: A 717 GLN cc_start: 0.8636 (tp-100) cc_final: 0.8401 (tp-100) REVERT: B 93 PHE cc_start: 0.9321 (m-80) cc_final: 0.8880 (m-80) REVERT: B 110 ARG cc_start: 0.9137 (ttm-80) cc_final: 0.8753 (mmt180) outliers start: 14 outliers final: 10 residues processed: 81 average time/residue: 0.2466 time to fit residues: 29.0127 Evaluate side-chains 81 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 0.1980 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10364 Z= 0.191 Angle : 0.583 12.600 13997 Z= 0.285 Chirality : 0.041 0.199 1529 Planarity : 0.004 0.047 1792 Dihedral : 6.596 114.336 1398 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.29 % Allowed : 9.51 % Favored : 89.20 % 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: 1.58 (0.25), residues: 1237 helix: 1.73 (0.22), residues: 615 sheet: 0.22 (0.40), residues: 165 loop : 0.60 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 79 HIS 0.016 0.001 HIS B 111 PHE 0.052 0.001 PHE B 12 TYR 0.010 0.001 TYR A 259 ARG 0.004 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 511 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7869 (tm-30) REVERT: A 717 GLN cc_start: 0.8664 (tp-100) cc_final: 0.8446 (tp-100) REVERT: A 781 TRP cc_start: 0.7834 (OUTLIER) cc_final: 0.7620 (t60) REVERT: B 93 PHE cc_start: 0.9319 (m-80) cc_final: 0.8874 (m-80) REVERT: B 110 ARG cc_start: 0.9184 (ttm-80) cc_final: 0.8818 (mmm160) outliers start: 14 outliers final: 9 residues processed: 85 average time/residue: 0.2205 time to fit residues: 27.3380 Evaluate side-chains 79 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 781 TRP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 98 optimal weight: 0.0170 chunk 10 optimal weight: 0.0970 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 overall best weight: 1.3820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10364 Z= 0.308 Angle : 0.627 12.589 13997 Z= 0.309 Chirality : 0.042 0.195 1529 Planarity : 0.004 0.046 1792 Dihedral : 6.666 117.107 1398 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.02 % Allowed : 10.34 % Favored : 88.64 % 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: 1.43 (0.25), residues: 1237 helix: 1.66 (0.22), residues: 617 sheet: -0.02 (0.40), residues: 169 loop : 0.52 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 79 HIS 0.009 0.001 HIS B 111 PHE 0.049 0.002 PHE B 12 TYR 0.014 0.001 TYR A 259 ARG 0.005 0.000 ARG A 343 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8155 (tptp) cc_final: 0.7884 (tppt) REVERT: A 511 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7868 (tm-30) REVERT: A 717 GLN cc_start: 0.8662 (tp-100) cc_final: 0.8459 (tp-100) REVERT: C 47 MET cc_start: 0.7451 (ppp) cc_final: 0.7008 (ppp) REVERT: B 93 PHE cc_start: 0.9327 (m-80) cc_final: 0.8883 (m-80) REVERT: B 110 ARG cc_start: 0.9191 (ttm-80) cc_final: 0.8769 (mmm160) outliers start: 11 outliers final: 10 residues processed: 78 average time/residue: 0.2166 time to fit residues: 24.9264 Evaluate side-chains 79 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.0570 chunk 41 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 12 optimal weight: 0.0670 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 HIS B 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.071997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.049087 restraints weight = 31818.657| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.37 r_work: 0.2664 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10364 Z= 0.161 Angle : 0.571 12.407 13997 Z= 0.282 Chirality : 0.041 0.195 1529 Planarity : 0.003 0.048 1792 Dihedral : 6.447 111.557 1398 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.02 % Allowed : 10.34 % Favored : 88.64 % 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: 1.55 (0.25), residues: 1237 helix: 1.72 (0.22), residues: 612 sheet: 0.19 (0.40), residues: 165 loop : 0.58 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.005 0.001 HIS B 111 PHE 0.051 0.001 PHE B 12 TYR 0.008 0.001 TYR A 259 ARG 0.004 0.000 ARG A 343 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2107.45 seconds wall clock time: 38 minutes 52.49 seconds (2332.49 seconds total)