Starting phenix.real_space_refine on Sat Sep 12 18:33:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ezn_4161/09_2026/6ezn_4161.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ezn_4161/09_2026/6ezn_4161.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 { model { file = "/net/cci-nas-00/data/ceres_data/6ezn_4161/09_2026/6ezn_4161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ezn_4161/09_2026/6ezn_4161.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ezn_4161/09_2026/6ezn_4161.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ezn_4161/09_2026/6ezn_4161.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ezn_4161/09_2026/6ezn_4161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ezn_4161/09_2026/6ezn_4161.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 52 5.16 5 C 11176 2.51 5 N 2670 2.21 5 O 3105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17008 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3534 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 413} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 879 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 106} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 973 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain breaks: 1 Chain: "D" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "E" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 666 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "F" Number of atoms: 5186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5186 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 1, 'PTRANS': 23, 'TRANS': 625} Chain breaks: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 3179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3179 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 377} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1880 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 15, 'TRANS': 243} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'HIS:plan': 2, 'PHE:plan': 2, 'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 83 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 94 Unusual residues: {'CPL': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.36, per 1000 atoms: 0.20 Number of scatterers: 17008 At special positions: 0 Unit cell: (123.54, 117.15, 159.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 5 15.00 O 3105 8.00 N 2670 7.00 C 11176 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN K 4 " - " MAN K 5 " " MAN K 5 " - " MAN K 6 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " MAN K 7 " - " MAN K 8 " ALPHA1-6 " BMA K 3 " - " MAN K 7 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG G 503 " - " ASN G 332 " " NAG I 1 " - " ASN A 336 " " NAG J 1 " - " ASN A 400 " " NAG K 1 " - " ASN F 539 " " NAG L 1 " - " ASN G 60 " Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 588.1 milliseconds 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3968 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 0 sheets defined 37.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 72 through 75 No H-bonds generated for 'chain 'A' and resid 72 through 75' Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 443 through 446 No H-bonds generated for 'chain 'A' and resid 443 through 446' Processing helix chain 'A' and resid 448 through 466 Processing helix chain 'B' and resid 24 through 40 removed outlier: 3.624A pdb=" N LYS B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 67 removed outlier: 3.835A pdb=" N LEU B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 99 removed outlier: 3.966A pdb=" N CYS B 84 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 128 removed outlier: 3.809A pdb=" N GLU B 113 " --> pdb=" O ARG B 109 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 232 Processing helix chain 'C' and resid 235 through 240 Processing helix chain 'C' and resid 269 through 289 Processing helix chain 'C' and resid 291 through 297 removed outlier: 4.273A pdb=" N SER C 296 " --> pdb=" O GLN C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 334 removed outlier: 4.177A pdb=" N VAL C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 31 Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 25 through 41 Processing helix chain 'E' and resid 54 through 82 removed outlier: 3.830A pdb=" N PHE E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 30 Processing helix chain 'F' and resid 48 through 60 Processing helix chain 'F' and resid 63 through 67 Processing helix chain 'F' and resid 90 through 103 Processing helix chain 'F' and resid 111 through 116 Processing helix chain 'F' and resid 119 through 137 removed outlier: 4.109A pdb=" N GLY F 124 " --> pdb=" O PRO F 120 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL F 125 " --> pdb=" O LEU F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 152 removed outlier: 3.794A pdb=" N LEU F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 157 No H-bonds generated for 'chain 'F' and resid 154 through 157' Processing helix chain 'F' and resid 172 through 188 removed outlier: 4.180A pdb=" N VAL F 177 " --> pdb=" O THR F 173 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR F 188 " --> pdb=" O LYS F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 205 removed outlier: 3.611A pdb=" N ALA F 198 " --> pdb=" O ALA F 194 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE F 200 " --> pdb=" O CYS F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 216 No H-bonds generated for 'chain 'F' and resid 214 through 216' Processing helix chain 'F' and resid 218 through 227 Processing helix chain 'F' and resid 233 through 249 removed outlier: 4.865A pdb=" N THR F 241 " --> pdb=" O SER F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 267 through 286 removed outlier: 4.122A pdb=" N GLN F 277 " --> pdb=" O PHE F 273 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE F 278 " --> pdb=" O GLY F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 294 No H-bonds generated for 'chain 'F' and resid 291 through 294' Processing helix chain 'F' and resid 356 through 362 Processing helix chain 'F' and resid 366 through 378 Proline residue: F 371 - end of helix removed outlier: 3.566A pdb=" N VAL F 374 " --> pdb=" O PHE F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 401 removed outlier: 3.595A pdb=" N CYS F 395 " --> pdb=" O TYR F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 428 removed outlier: 3.549A pdb=" N LEU F 407 " --> pdb=" O ARG F 404 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR F 408 " --> pdb=" O LEU F 405 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR F 410 " --> pdb=" O LEU F 407 " (cutoff:3.500A) Proline residue: F 411 - end of helix removed outlier: 3.775A pdb=" N SER F 416 " --> pdb=" O ILE F 413 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA F 417 " --> pdb=" O CYS F 414 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA F 420 " --> pdb=" O ALA F 417 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU F 421 " --> pdb=" O ALA F 418 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER F 422 " --> pdb=" O VAL F 419 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE F 424 " --> pdb=" O LEU F 421 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE F 425 " --> pdb=" O SER F 422 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR F 428 " --> pdb=" O PHE F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 473 removed outlier: 4.221A pdb=" N SER F 454 " --> pdb=" O ILE F 450 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE F 455 " --> pdb=" O VAL F 451 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL F 463 " --> pdb=" O LEU F 459 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE F 464 " --> pdb=" O TYR F 460 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR F 470 " --> pdb=" O SER F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 505 Processing helix chain 'F' and resid 517 through 526 removed outlier: 5.501A pdb=" N TYR F 521 " --> pdb=" O ASP F 518 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN F 522 " --> pdb=" O TYR F 519 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE F 523 " --> pdb=" O GLY F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 550 removed outlier: 3.914A pdb=" N VAL F 546 " --> pdb=" O HIS F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 563 removed outlier: 3.692A pdb=" N GLU F 559 " --> pdb=" O GLU F 555 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE F 560 " --> pdb=" O LYS F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 595 removed outlier: 3.872A pdb=" N ILE F 593 " --> pdb=" O TRP F 589 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER F 594 " --> pdb=" O MET F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 622 through 625 No H-bonds generated for 'chain 'F' and resid 622 through 625' Processing helix chain 'F' and resid 628 through 633 Processing helix chain 'F' and resid 692 through 698 Processing helix chain 'G' and resid 38 through 49 removed outlier: 6.436A pdb=" N VAL G 42 " --> pdb=" O GLU G 39 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU G 44 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS G 45 " --> pdb=" O VAL G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 93 Processing helix chain 'G' and resid 96 through 105 removed outlier: 4.066A pdb=" N ASN G 105 " --> pdb=" O LYS G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 129 Processing helix chain 'G' and resid 155 through 157 No H-bonds generated for 'chain 'G' and resid 155 through 157' Processing helix chain 'G' and resid 248 through 257 Processing helix chain 'G' and resid 393 through 415 Processing helix chain 'H' and resid 122 through 128 Processing helix chain 'H' and resid 193 through 215 Processing helix chain 'H' and resid 231 through 252 removed outlier: 3.676A pdb=" N GLU H 245 " --> pdb=" O ILE H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 274 Proline residue: H 270 - end of helix removed outlier: 4.309A pdb=" N LEU H 273 " --> pdb=" O ALA H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 277 through 281 494 hydrogen bonds defined for protein. 1422 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: 2.28 Time building geometry restraints manager: 1.81 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: 2626 1.31 - 1.43: 5025 1.43 - 1.56: 9695 1.56 - 1.69: 12 1.69 - 1.81: 87 Bond restraints: 17445 Sorted by residual: bond pdb=" C8 PTY F 810 " pdb=" O7 PTY F 810 " ideal model delta sigma weight residual 1.331 1.457 -0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" C30 PTY F 810 " pdb=" O4 PTY F 810 " ideal model delta sigma weight residual 1.331 1.449 -0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" C11 CPL E 101 " pdb=" O3 CPL E 101 " ideal model delta sigma weight residual 1.327 1.421 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C31 CPL E 101 " pdb=" O2 CPL E 101 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C31 CPL F 809 " pdb=" O2 CPL F 809 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.00e+01 ... (remaining 17440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.80: 23285 3.80 - 7.61: 309 7.61 - 11.41: 63 11.41 - 15.22: 11 15.22 - 19.02: 6 Bond angle restraints: 23674 Sorted by residual: angle pdb=" N PRO H 45 " pdb=" CA PRO H 45 " pdb=" CB PRO H 45 " ideal model delta sigma weight residual 103.25 111.56 -8.31 1.05e+00 9.07e-01 6.26e+01 angle pdb=" N PRO H 54 " pdb=" CA PRO H 54 " pdb=" CB PRO H 54 " ideal model delta sigma weight residual 103.25 111.14 -7.89 1.05e+00 9.07e-01 5.65e+01 angle pdb=" N PRO H 29 " pdb=" CA PRO H 29 " pdb=" CB PRO H 29 " ideal model delta sigma weight residual 103.25 110.87 -7.62 1.05e+00 9.07e-01 5.27e+01 angle pdb=" N PRO H 62 " pdb=" CA PRO H 62 " pdb=" CB PRO H 62 " ideal model delta sigma weight residual 103.25 110.70 -7.45 1.05e+00 9.07e-01 5.04e+01 angle pdb=" CA LEU A 310 " pdb=" CB LEU A 310 " pdb=" CG LEU A 310 " ideal model delta sigma weight residual 116.30 135.32 -19.02 3.50e+00 8.16e-02 2.95e+01 ... (remaining 23669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.26: 9911 33.26 - 66.52: 136 66.52 - 99.78: 10 99.78 - 133.04: 1 133.04 - 166.30: 3 Dihedral angle restraints: 10061 sinusoidal: 3922 harmonic: 6139 Sorted by residual: dihedral pdb=" CA GLN A 280 " pdb=" C GLN A 280 " pdb=" N ASN A 281 " pdb=" CA ASN A 281 " ideal model delta harmonic sigma weight residual 180.00 136.48 43.52 0 5.00e+00 4.00e-02 7.58e+01 dihedral pdb=" CA ARG F 605 " pdb=" C ARG F 605 " pdb=" N ASP F 606 " pdb=" CA ASP F 606 " ideal model delta harmonic sigma weight residual 180.00 142.05 37.95 0 5.00e+00 4.00e-02 5.76e+01 dihedral pdb=" CA TYR A 144 " pdb=" C TYR A 144 " pdb=" N PRO A 145 " pdb=" CA PRO A 145 " ideal model delta harmonic sigma weight residual 180.00 148.47 31.53 0 5.00e+00 4.00e-02 3.98e+01 ... (remaining 10058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2283 0.086 - 0.172: 367 0.172 - 0.259: 36 0.259 - 0.345: 10 0.345 - 0.431: 2 Chirality restraints: 2698 Sorted by residual: chirality pdb=" CB ILE G 232 " pdb=" CA ILE G 232 " pdb=" CG1 ILE G 232 " pdb=" CG2 ILE G 232 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 336 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CG LEU C 342 " pdb=" CB LEU C 342 " pdb=" CD1 LEU C 342 " pdb=" CD2 LEU C 342 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 2695 not shown) Planarity restraints: 2929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 318 " -0.015 2.00e-02 2.50e+03 3.10e-02 9.63e+00 pdb=" C ARG A 318 " 0.054 2.00e-02 2.50e+03 pdb=" O ARG A 318 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP A 319 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 318 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.48e+00 pdb=" C GLN G 318 " -0.053 2.00e-02 2.50e+03 pdb=" O GLN G 318 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL G 319 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 153 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO F 154 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO F 154 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 154 " 0.039 5.00e-02 4.00e+02 ... (remaining 2926 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4870 2.81 - 3.33: 15120 3.33 - 3.86: 27640 3.86 - 4.38: 32360 4.38 - 4.90: 56065 Nonbonded interactions: 136055 Sorted by model distance: nonbonded pdb=" OH TYR F 630 " pdb=" OD2 ASP F 659 " model vdw 2.291 3.040 nonbonded pdb=" OG SER G 386 " pdb=" OH TYR H 252 " model vdw 2.295 3.040 nonbonded pdb=" OD2 ASP D 29 " pdb=" OG SER F 141 " model vdw 2.321 3.040 nonbonded pdb=" O GLU B 25 " pdb=" OG1 THR B 29 " model vdw 2.334 3.040 nonbonded pdb=" NH2 ARG G 385 " pdb=" O TYR H 252 " model vdw 2.339 3.120 ... (remaining 136050 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'J' selection = chain 'L' } 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: 1.790 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 14.800 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.126 17461 Z= 0.351 Angle : 1.214 19.020 23722 Z= 0.598 Chirality : 0.065 0.431 2698 Planarity : 0.007 0.072 2924 Dihedral : 12.502 166.296 6093 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.54 % Favored : 91.08 % Rotamer: Outliers : 0.51 % Allowed : 3.75 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.12 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.93 (0.13), residues: 2062 helix: -3.24 (0.11), residues: 839 sheet: -2.43 (0.23), residues: 376 loop : -3.55 (0.16), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 326 TYR 0.046 0.003 TYR F 391 PHE 0.037 0.003 PHE B 50 TRP 0.035 0.004 TRP F 208 HIS 0.018 0.003 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00786 / 0.35 (17445) covalent geometry : angle 1.20811 / 0.60 (23674) hydrogen bonds : bond 0.10215 / 6.10 ( 494) hydrogen bonds : angle 8.63235 / 5.86 ( 1422) link_ALPHA1-2 : bond 0.00604 / 0.30 ( 2) link_ALPHA1-2 : angle 2.80629 / 1.68 ( 6) link_ALPHA1-3 : bond 0.00730 / 0.37 ( 2) link_ALPHA1-3 : angle 3.84306 / 2.13 ( 6) link_ALPHA1-6 : bond 0.00136 / 0.07 ( 1) link_ALPHA1-6 : angle 1.38919 / 0.79 ( 3) link_BETA1-4 : bond 0.00741 / 0.37 ( 6) link_BETA1-4 : angle 2.53554 / 1.51 ( 18) link_NAG-ASN : bond 0.00667 / 0.34 ( 5) link_NAG-ASN : angle 3.01471 / 1.66 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 384 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 PRO cc_start: 0.6948 (Cg_endo) cc_final: 0.6719 (Cg_exo) REVERT: A 185 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7461 (mt-10) REVERT: A 201 ASN cc_start: 0.7587 (m110) cc_final: 0.6652 (t0) REVERT: A 324 ARG cc_start: 0.7935 (mtp85) cc_final: 0.7733 (mtt90) REVERT: A 378 GLU cc_start: 0.7430 (pt0) cc_final: 0.6884 (pm20) REVERT: A 462 MET cc_start: 0.7417 (mmm) cc_final: 0.7014 (mmt) REVERT: B 44 LEU cc_start: 0.7881 (mp) cc_final: 0.7660 (mt) REVERT: B 100 ASN cc_start: 0.7217 (m-40) cc_final: 0.6770 (p0) REVERT: C 264 HIS cc_start: 0.7896 (m-70) cc_final: 0.7671 (m-70) REVERT: C 338 TYR cc_start: 0.8445 (t80) cc_final: 0.8127 (t80) REVERT: E 5 GLN cc_start: 0.8393 (mt0) cc_final: 0.8110 (mm-40) REVERT: F 445 LEU cc_start: 0.8733 (tm) cc_final: 0.8493 (tp) REVERT: F 476 SER cc_start: 0.7996 (t) cc_final: 0.7758 (m) REVERT: F 510 ASP cc_start: 0.6959 (p0) cc_final: 0.6668 (m-30) REVERT: F 528 ASP cc_start: 0.7675 (t70) cc_final: 0.7426 (t0) REVERT: F 550 MET cc_start: 0.8371 (mmt) cc_final: 0.8126 (mmt) REVERT: F 609 THR cc_start: 0.8426 (p) cc_final: 0.7698 (p) REVERT: F 626 ASN cc_start: 0.8110 (m-40) cc_final: 0.7852 (m-40) REVERT: F 632 MET cc_start: 0.8882 (mtp) cc_final: 0.8624 (mtm) REVERT: G 32 GLN cc_start: 0.7141 (mm110) cc_final: 0.6909 (mm110) REVERT: G 161 LYS cc_start: 0.6562 (mtpt) cc_final: 0.6258 (ttpt) REVERT: G 234 SER cc_start: 0.7226 (t) cc_final: 0.6878 (t) REVERT: H 115 LEU cc_start: 0.6140 (mp) cc_final: 0.5842 (tt) REVERT: H 201 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6692 (mp) REVERT: H 225 ILE cc_start: 0.6639 (mp) cc_final: 0.6292 (pt) outliers start: 9 outliers final: 5 residues processed: 391 average time/residue: 0.1364 time to fit residues: 80.3456 Evaluate side-chains 224 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 218 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 716 LEU Chi-restraints excluded: chain H residue 201 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.0270 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN A 95 GLN A 121 ASN A 201 ASN A 217 ASN A 334 ASN B 127 HIS E 80 ASN F 68 ASN F 221 HIS ** F 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 ASN F 688 GLN G 214 GLN G 222 GLN G 243 GLN G 247 GLN G 271 HIS G 337 GLN ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.164385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.132251 restraints weight = 21454.642| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.59 r_work: 0.3229 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17461 Z= 0.134 Angle : 0.654 9.026 23722 Z= 0.329 Chirality : 0.044 0.214 2698 Planarity : 0.005 0.064 2924 Dihedral : 11.402 179.654 2412 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.55 % Favored : 93.31 % Rotamer: Outliers : 2.27 % Allowed : 8.97 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.16), residues: 2062 helix: -1.18 (0.16), residues: 834 sheet: -2.02 (0.25), residues: 380 loop : -3.10 (0.18), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 651 TYR 0.021 0.001 TYR F 203 PHE 0.022 0.001 PHE G 409 TRP 0.017 0.002 TRP F 208 HIS 0.004 0.001 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (17445) covalent geometry : angle 0.64969 / 0.33 (23674) hydrogen bonds : bond 0.04348 / 2.73 ( 494) hydrogen bonds : angle 4.71608 / 3.19 ( 1422) link_ALPHA1-2 : bond 0.00049 / 0.03 ( 2) link_ALPHA1-2 : angle 1.99813 / 1.21 ( 6) link_ALPHA1-3 : bond 0.00436 / 0.22 ( 2) link_ALPHA1-3 : angle 2.26900 / 1.31 ( 6) link_ALPHA1-6 : bond 0.00031 / 0.02 ( 1) link_ALPHA1-6 : angle 1.50360 / 0.84 ( 3) link_BETA1-4 : bond 0.00361 / 0.18 ( 6) link_BETA1-4 : angle 1.65546 / 0.95 ( 18) link_NAG-ASN : bond 0.00492 / 0.25 ( 5) link_NAG-ASN : angle 1.62987 / 0.94 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 248 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 282 MET cc_start: 0.3475 (tpt) cc_final: 0.2652 (tpp) REVERT: A 425 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7866 (m-40) REVERT: B 71 ASN cc_start: 0.6925 (p0) cc_final: 0.6723 (p0) REVERT: B 100 ASN cc_start: 0.7806 (m-40) cc_final: 0.7282 (p0) REVERT: C 333 ILE cc_start: 0.8313 (tt) cc_final: 0.8027 (tt) REVERT: D 29 ASP cc_start: 0.8285 (t0) cc_final: 0.8004 (t0) REVERT: F 74 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8915 (p) REVERT: F 451 VAL cc_start: 0.8243 (p) cc_final: 0.8021 (p) REVERT: F 528 ASP cc_start: 0.8839 (t70) cc_final: 0.8618 (t0) REVERT: F 609 THR cc_start: 0.7977 (p) cc_final: 0.7701 (p) REVERT: F 654 MET cc_start: 0.8497 (mtp) cc_final: 0.8281 (mtt) REVERT: G 199 PHE cc_start: 0.8804 (p90) cc_final: 0.8489 (p90) REVERT: G 228 ARG cc_start: 0.8819 (mtt180) cc_final: 0.8547 (mtt180) REVERT: H 115 LEU cc_start: 0.8808 (mp) cc_final: 0.8249 (tt) REVERT: H 139 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7563 (pp) REVERT: H 201 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7408 (mt) REVERT: H 225 ILE cc_start: 0.6928 (mp) cc_final: 0.6483 (pt) outliers start: 40 outliers final: 22 residues processed: 269 average time/residue: 0.1383 time to fit residues: 56.7102 Evaluate side-chains 231 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 370 LYS Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 253 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 146 optimal weight: 2.9990 chunk 195 optimal weight: 20.0000 chunk 179 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 97 optimal weight: 0.0370 chunk 189 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 overall best weight: 1.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 GLN B 87 GLN B 97 GLN E 5 GLN F 44 HIS ** F 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 626 ASN G 242 ASN G 247 GLN G 391 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.159647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.126991 restraints weight = 21522.412| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.69 r_work: 0.3126 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17461 Z= 0.182 Angle : 0.657 8.100 23722 Z= 0.333 Chirality : 0.045 0.187 2698 Planarity : 0.004 0.054 2924 Dihedral : 10.673 179.822 2404 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.27 % Favored : 92.58 % Rotamer: Outliers : 3.07 % Allowed : 10.28 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.17), residues: 2062 helix: -0.35 (0.17), residues: 840 sheet: -1.84 (0.25), residues: 401 loop : -2.99 (0.18), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 651 TYR 0.026 0.002 TYR F 203 PHE 0.026 0.002 PHE B 128 TRP 0.019 0.002 TRP A 241 HIS 0.009 0.001 HIS F 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.18 (17445) covalent geometry : angle 0.65235 / 0.33 (23674) hydrogen bonds : bond 0.04743 / 3.01 ( 494) hydrogen bonds : angle 4.28763 / 2.90 ( 1422) link_ALPHA1-2 : bond 0.00225 / 0.12 ( 2) link_ALPHA1-2 : angle 1.99039 / 1.19 ( 6) link_ALPHA1-3 : bond 0.00590 / 0.30 ( 2) link_ALPHA1-3 : angle 2.49790 / 1.40 ( 6) link_ALPHA1-6 : bond 0.00420 / 0.22 ( 1) link_ALPHA1-6 : angle 1.37359 / 0.76 ( 3) link_BETA1-4 : bond 0.00453 / 0.22 ( 6) link_BETA1-4 : angle 1.74236 / 1.03 ( 18) link_NAG-ASN : bond 0.00351 / 0.17 ( 5) link_NAG-ASN : angle 1.75824 / 1.03 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 213 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7536 (mt) REVERT: A 84 TYR cc_start: 0.7420 (m-10) cc_final: 0.6997 (m-10) REVERT: A 278 GLN cc_start: 0.7136 (mt0) cc_final: 0.6832 (tp40) REVERT: A 282 MET cc_start: 0.3635 (tpt) cc_final: 0.3231 (tpt) REVERT: A 293 MET cc_start: 0.9147 (mmm) cc_final: 0.8124 (mmm) REVERT: B 27 PHE cc_start: 0.7588 (t80) cc_final: 0.7228 (m-80) REVERT: B 100 ASN cc_start: 0.8036 (m-40) cc_final: 0.7306 (p0) REVERT: B 130 ASN cc_start: 0.7871 (t0) cc_final: 0.7307 (t0) REVERT: C 333 ILE cc_start: 0.8356 (tt) cc_final: 0.8064 (tt) REVERT: D 29 ASP cc_start: 0.8389 (t0) cc_final: 0.8083 (t0) REVERT: F 609 THR cc_start: 0.8109 (p) cc_final: 0.7810 (p) REVERT: F 654 MET cc_start: 0.8511 (mtp) cc_final: 0.8309 (mtt) REVERT: G 32 GLN cc_start: 0.7506 (mm110) cc_final: 0.7200 (mm110) REVERT: G 88 LYS cc_start: 0.8567 (tptp) cc_final: 0.8222 (tptp) REVERT: G 93 GLN cc_start: 0.8401 (mm-40) cc_final: 0.8146 (mm-40) REVERT: G 247 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7976 (tm-30) REVERT: H 115 LEU cc_start: 0.8827 (mp) cc_final: 0.8264 (tt) REVERT: H 139 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7707 (pp) REVERT: H 225 ILE cc_start: 0.7362 (mp) cc_final: 0.6880 (pt) REVERT: H 250 ARG cc_start: 0.7991 (mtp85) cc_final: 0.7744 (mtm180) outliers start: 54 outliers final: 34 residues processed: 247 average time/residue: 0.1355 time to fit residues: 51.6273 Evaluate side-chains 233 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 593 ILE Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 611 GLU Chi-restraints excluded: chain F residue 714 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 247 GLN Chi-restraints excluded: chain G residue 370 LYS Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 209 SER Chi-restraints excluded: chain H residue 253 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 15 optimal weight: 10.0000 chunk 193 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 204 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 GLN A 201 ASN C 264 HIS E 11 HIS ** F 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.154940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.121962 restraints weight = 21669.231| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.72 r_work: 0.3057 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 17461 Z= 0.281 Angle : 0.720 10.456 23722 Z= 0.364 Chirality : 0.048 0.176 2698 Planarity : 0.005 0.058 2924 Dihedral : 10.574 179.194 2402 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.05 % Favored : 91.80 % Rotamer: Outliers : 3.29 % Allowed : 12.32 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.17), residues: 2062 helix: -0.06 (0.18), residues: 833 sheet: -1.93 (0.25), residues: 399 loop : -2.92 (0.18), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 270 TYR 0.026 0.002 TYR F 203 PHE 0.031 0.002 PHE B 128 TRP 0.017 0.002 TRP G 299 HIS 0.009 0.002 HIS F 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.28 (17445) covalent geometry : angle 0.71541 / 0.36 (23674) hydrogen bonds : bond 0.05254 / 3.36 ( 494) hydrogen bonds : angle 4.28359 / 2.90 ( 1422) link_ALPHA1-2 : bond 0.00356 / 0.19 ( 2) link_ALPHA1-2 : angle 1.94174 / 1.18 ( 6) link_ALPHA1-3 : bond 0.00398 / 0.20 ( 2) link_ALPHA1-3 : angle 2.36700 / 1.34 ( 6) link_ALPHA1-6 : bond 0.00251 / 0.13 ( 1) link_ALPHA1-6 : angle 1.69715 / 0.93 ( 3) link_BETA1-4 : bond 0.00488 / 0.24 ( 6) link_BETA1-4 : angle 1.89531 / 1.13 ( 18) link_NAG-ASN : bond 0.00414 / 0.20 ( 5) link_NAG-ASN : angle 1.71810 / 1.02 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 201 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7644 (mt) REVERT: A 84 TYR cc_start: 0.7677 (m-10) cc_final: 0.7375 (m-10) REVERT: A 278 GLN cc_start: 0.7045 (mt0) cc_final: 0.6782 (tp40) REVERT: B 100 ASN cc_start: 0.8085 (m-40) cc_final: 0.7390 (p0) REVERT: B 130 ASN cc_start: 0.8071 (t0) cc_final: 0.7528 (t0) REVERT: C 333 ILE cc_start: 0.8452 (tt) cc_final: 0.8159 (tt) REVERT: D 29 ASP cc_start: 0.8528 (t0) cc_final: 0.8202 (t0) REVERT: F 235 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8979 (tt) REVERT: F 609 THR cc_start: 0.8182 (p) cc_final: 0.7869 (p) REVERT: F 654 MET cc_start: 0.8503 (mtp) cc_final: 0.8301 (mtt) REVERT: G 247 GLN cc_start: 0.8518 (tm-30) cc_final: 0.7716 (tm-30) REVERT: H 115 LEU cc_start: 0.8867 (mp) cc_final: 0.8338 (tt) REVERT: H 139 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7561 (pp) REVERT: H 225 ILE cc_start: 0.7598 (mp) cc_final: 0.7140 (pt) REVERT: H 284 GLN cc_start: 0.6360 (mt0) cc_final: 0.5909 (tp40) outliers start: 58 outliers final: 45 residues processed: 242 average time/residue: 0.1361 time to fit residues: 50.6154 Evaluate side-chains 234 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 593 ILE Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 611 GLU Chi-restraints excluded: chain F residue 655 ILE Chi-restraints excluded: chain F residue 714 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 370 LYS Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 209 SER Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 253 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 100 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 143 optimal weight: 0.0770 chunk 6 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.162073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130211 restraints weight = 21235.787| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.68 r_work: 0.3203 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17461 Z= 0.128 Angle : 0.591 8.061 23722 Z= 0.297 Chirality : 0.043 0.166 2698 Planarity : 0.004 0.048 2924 Dihedral : 10.034 178.141 2402 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.89 % Favored : 92.97 % Rotamer: Outliers : 3.29 % Allowed : 13.17 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.18), residues: 2062 helix: 0.51 (0.18), residues: 821 sheet: -1.73 (0.25), residues: 404 loop : -2.73 (0.18), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 424 TYR 0.016 0.001 TYR F 203 PHE 0.024 0.001 PHE C 307 TRP 0.014 0.001 TRP G 299 HIS 0.006 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (17445) covalent geometry : angle 0.58640 / 0.30 (23674) hydrogen bonds : bond 0.04122 / 2.57 ( 494) hydrogen bonds : angle 3.88084 / 2.62 ( 1422) link_ALPHA1-2 : bond 0.00207 / 0.11 ( 2) link_ALPHA1-2 : angle 1.79125 / 1.10 ( 6) link_ALPHA1-3 : bond 0.00579 / 0.29 ( 2) link_ALPHA1-3 : angle 2.38904 / 1.34 ( 6) link_ALPHA1-6 : bond 0.00418 / 0.22 ( 1) link_ALPHA1-6 : angle 1.36268 / 0.76 ( 3) link_BETA1-4 : bond 0.00436 / 0.21 ( 6) link_BETA1-4 : angle 1.63147 / 0.95 ( 18) link_NAG-ASN : bond 0.00436 / 0.22 ( 5) link_NAG-ASN : angle 1.69327 / 0.98 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 204 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7617 (mt) REVERT: A 278 GLN cc_start: 0.7008 (mt0) cc_final: 0.6773 (tp40) REVERT: B 71 ASN cc_start: 0.7106 (p0) cc_final: 0.6560 (p0) REVERT: B 100 ASN cc_start: 0.7815 (m-40) cc_final: 0.7197 (p0) REVERT: C 333 ILE cc_start: 0.8439 (tt) cc_final: 0.8180 (tt) REVERT: D 29 ASP cc_start: 0.8443 (t0) cc_final: 0.8125 (t0) REVERT: F 168 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6125 (mp0) REVERT: F 446 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8020 (tt) REVERT: F 451 VAL cc_start: 0.8013 (p) cc_final: 0.7811 (p) REVERT: F 609 THR cc_start: 0.7965 (p) cc_final: 0.7704 (p) REVERT: G 32 GLN cc_start: 0.7594 (mm110) cc_final: 0.7329 (mm110) REVERT: G 88 LYS cc_start: 0.8524 (tptp) cc_final: 0.8287 (tptp) REVERT: G 232 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8600 (mt) REVERT: H 115 LEU cc_start: 0.8725 (mp) cc_final: 0.8150 (tt) REVERT: H 139 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7464 (pp) REVERT: H 225 ILE cc_start: 0.7671 (mp) cc_final: 0.7213 (pt) REVERT: H 284 GLN cc_start: 0.6162 (mt0) cc_final: 0.5767 (tp40) outliers start: 58 outliers final: 35 residues processed: 241 average time/residue: 0.1279 time to fit residues: 48.0555 Evaluate side-chains 233 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 611 GLU Chi-restraints excluded: chain F residue 655 ILE Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 714 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 328 SER Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 253 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 69 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 129 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 177 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.161993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130755 restraints weight = 21304.038| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.83 r_work: 0.3161 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17461 Z= 0.134 Angle : 0.584 7.928 23722 Z= 0.293 Chirality : 0.043 0.166 2698 Planarity : 0.004 0.048 2924 Dihedral : 9.688 176.471 2402 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.13 % Favored : 92.73 % Rotamer: Outliers : 3.24 % Allowed : 13.46 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.18), residues: 2062 helix: 0.73 (0.18), residues: 823 sheet: -1.64 (0.25), residues: 401 loop : -2.63 (0.19), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 424 TYR 0.015 0.001 TYR F 203 PHE 0.017 0.001 PHE H 70 TRP 0.013 0.001 TRP G 299 HIS 0.005 0.001 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (17445) covalent geometry : angle 0.57885 / 0.29 (23674) hydrogen bonds : bond 0.04087 / 2.55 ( 494) hydrogen bonds : angle 3.77431 / 2.54 ( 1422) link_ALPHA1-2 : bond 0.00171 / 0.09 ( 2) link_ALPHA1-2 : angle 1.79378 / 1.10 ( 6) link_ALPHA1-3 : bond 0.00560 / 0.28 ( 2) link_ALPHA1-3 : angle 2.36201 / 1.33 ( 6) link_ALPHA1-6 : bond 0.00404 / 0.21 ( 1) link_ALPHA1-6 : angle 1.34127 / 0.75 ( 3) link_BETA1-4 : bond 0.00427 / 0.21 ( 6) link_BETA1-4 : angle 1.63981 / 0.96 ( 18) link_NAG-ASN : bond 0.00391 / 0.20 ( 5) link_NAG-ASN : angle 1.63927 / 0.96 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 201 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7629 (mt) REVERT: A 214 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.7154 (m-80) REVERT: A 282 MET cc_start: 0.3278 (tpt) cc_final: 0.2517 (tpp) REVERT: B 31 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.7209 (tptp) REVERT: B 71 ASN cc_start: 0.7134 (p0) cc_final: 0.6542 (p0) REVERT: B 100 ASN cc_start: 0.7896 (m-40) cc_final: 0.7339 (p0) REVERT: C 333 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8182 (tt) REVERT: D 29 ASP cc_start: 0.8474 (t0) cc_final: 0.8153 (t0) REVERT: F 168 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6121 (mp0) REVERT: F 235 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8893 (tt) REVERT: F 446 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8061 (tt) REVERT: F 609 THR cc_start: 0.7990 (p) cc_final: 0.7748 (p) REVERT: G 88 LYS cc_start: 0.8554 (tptp) cc_final: 0.8318 (tptp) REVERT: H 115 LEU cc_start: 0.8685 (mp) cc_final: 0.8134 (tt) REVERT: H 139 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7502 (pp) REVERT: H 225 ILE cc_start: 0.7710 (mp) cc_final: 0.7210 (pt) REVERT: H 284 GLN cc_start: 0.6243 (mt0) cc_final: 0.5784 (tp40) outliers start: 57 outliers final: 44 residues processed: 237 average time/residue: 0.1308 time to fit residues: 48.1691 Evaluate side-chains 245 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 193 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 570 LEU Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 611 GLU Chi-restraints excluded: chain F residue 655 ILE Chi-restraints excluded: chain F residue 714 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 328 SER Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 209 SER Chi-restraints excluded: chain H residue 253 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 194 optimal weight: 9.9990 chunk 195 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 429 GLN ** F 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN ** G 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.160479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.128341 restraints weight = 21244.028| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.84 r_work: 0.3148 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17461 Z= 0.164 Angle : 0.603 8.155 23722 Z= 0.303 Chirality : 0.044 0.166 2698 Planarity : 0.004 0.044 2924 Dihedral : 9.544 174.389 2402 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.52 % Favored : 92.34 % Rotamer: Outliers : 3.86 % Allowed : 13.57 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.18), residues: 2062 helix: 0.73 (0.18), residues: 837 sheet: -1.55 (0.26), residues: 398 loop : -2.52 (0.19), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 424 TYR 0.017 0.001 TYR F 203 PHE 0.017 0.001 PHE B 128 TRP 0.014 0.001 TRP G 299 HIS 0.005 0.001 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.16 (17445) covalent geometry : angle 0.59840 / 0.30 (23674) hydrogen bonds : bond 0.04310 / 2.72 ( 494) hydrogen bonds : angle 3.78773 / 2.56 ( 1422) link_ALPHA1-2 : bond 0.00217 / 0.11 ( 2) link_ALPHA1-2 : angle 1.81556 / 1.11 ( 6) link_ALPHA1-3 : bond 0.00498 / 0.25 ( 2) link_ALPHA1-3 : angle 2.35218 / 1.32 ( 6) link_ALPHA1-6 : bond 0.00312 / 0.16 ( 1) link_ALPHA1-6 : angle 1.37079 / 0.76 ( 3) link_BETA1-4 : bond 0.00420 / 0.21 ( 6) link_BETA1-4 : angle 1.68068 / 0.98 ( 18) link_NAG-ASN : bond 0.00382 / 0.19 ( 5) link_NAG-ASN : angle 1.66602 / 0.98 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 189 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7621 (mt) REVERT: A 456 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.7131 (t80) REVERT: B 100 ASN cc_start: 0.7908 (m-40) cc_final: 0.7308 (p0) REVERT: C 333 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8201 (tt) REVERT: D 29 ASP cc_start: 0.8437 (t0) cc_final: 0.8114 (t0) REVERT: E 25 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8177 (mt0) REVERT: F 168 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6181 (mp0) REVERT: F 235 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8912 (tt) REVERT: F 446 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8073 (tt) REVERT: F 609 THR cc_start: 0.8058 (p) cc_final: 0.7832 (p) REVERT: G 88 LYS cc_start: 0.8597 (tptp) cc_final: 0.8338 (tptp) REVERT: G 167 ARG cc_start: 0.7986 (mtm-85) cc_final: 0.7554 (mtm-85) REVERT: H 115 LEU cc_start: 0.8669 (mp) cc_final: 0.8085 (tt) REVERT: H 139 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7461 (pp) REVERT: H 225 ILE cc_start: 0.7877 (mp) cc_final: 0.7368 (pt) REVERT: H 284 GLN cc_start: 0.6422 (mt0) cc_final: 0.6011 (tp40) outliers start: 68 outliers final: 48 residues processed: 238 average time/residue: 0.1299 time to fit residues: 47.7651 Evaluate side-chains 241 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 185 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 25 GLN Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 570 LEU Chi-restraints excluded: chain F residue 593 ILE Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 611 GLU Chi-restraints excluded: chain F residue 655 ILE Chi-restraints excluded: chain F residue 714 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 328 SER Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 209 SER Chi-restraints excluded: chain H residue 253 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 20 optimal weight: 0.5980 chunk 152 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 171 optimal weight: 0.0050 chunk 173 optimal weight: 0.5980 chunk 186 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 chunk 180 optimal weight: 0.2980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 429 GLN ** F 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.164399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131465 restraints weight = 21356.801| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.77 r_work: 0.3208 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 17461 Z= 0.106 Angle : 0.555 7.807 23722 Z= 0.278 Chirality : 0.042 0.165 2698 Planarity : 0.003 0.040 2924 Dihedral : 9.148 172.002 2402 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.50 % Favored : 93.36 % Rotamer: Outliers : 3.41 % Allowed : 14.54 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.18), residues: 2062 helix: 0.96 (0.18), residues: 840 sheet: -1.45 (0.26), residues: 396 loop : -2.46 (0.19), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 32 TYR 0.012 0.001 TYR F 203 PHE 0.021 0.001 PHE H 70 TRP 0.014 0.001 TRP F 538 HIS 0.004 0.001 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (17445) covalent geometry : angle 0.54984 / 0.28 (23674) hydrogen bonds : bond 0.03763 / 2.32 ( 494) hydrogen bonds : angle 3.58785 / 2.41 ( 1422) link_ALPHA1-2 : bond 0.00097 / 0.05 ( 2) link_ALPHA1-2 : angle 1.72304 / 1.06 ( 6) link_ALPHA1-3 : bond 0.00508 / 0.25 ( 2) link_ALPHA1-3 : angle 2.39577 / 1.34 ( 6) link_ALPHA1-6 : bond 0.00283 / 0.15 ( 1) link_ALPHA1-6 : angle 1.18659 / 0.67 ( 3) link_BETA1-4 : bond 0.00424 / 0.21 ( 6) link_BETA1-4 : angle 1.55402 / 0.89 ( 18) link_NAG-ASN : bond 0.00417 / 0.21 ( 5) link_NAG-ASN : angle 1.64419 / 0.97 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 199 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7568 (mt) REVERT: A 282 MET cc_start: 0.3370 (tpt) cc_final: 0.2620 (tpp) REVERT: B 93 SER cc_start: 0.8985 (t) cc_final: 0.7963 (m) REVERT: B 100 ASN cc_start: 0.7835 (m-40) cc_final: 0.7185 (p0) REVERT: C 333 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8141 (tt) REVERT: D 29 ASP cc_start: 0.8438 (t0) cc_final: 0.8139 (t0) REVERT: F 168 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6043 (mp0) REVERT: F 446 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8053 (tt) REVERT: F 451 VAL cc_start: 0.7892 (p) cc_final: 0.7689 (p) REVERT: F 609 THR cc_start: 0.8025 (p) cc_final: 0.7814 (p) REVERT: G 167 ARG cc_start: 0.7972 (mtm-85) cc_final: 0.7524 (mtm-85) REVERT: G 377 HIS cc_start: 0.8461 (OUTLIER) cc_final: 0.7083 (t-90) REVERT: H 108 MET cc_start: 0.7430 (pmm) cc_final: 0.7022 (pmm) REVERT: H 139 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7458 (pp) REVERT: H 225 ILE cc_start: 0.7811 (mp) cc_final: 0.7313 (pt) REVERT: H 284 GLN cc_start: 0.6299 (mt0) cc_final: 0.5963 (tp40) outliers start: 60 outliers final: 39 residues processed: 239 average time/residue: 0.1301 time to fit residues: 48.3287 Evaluate side-chains 232 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 570 LEU Chi-restraints excluded: chain F residue 611 GLU Chi-restraints excluded: chain F residue 655 ILE Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 714 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 328 SER Chi-restraints excluded: chain G residue 346 LEU Chi-restraints excluded: chain G residue 364 LEU Chi-restraints excluded: chain G residue 377 HIS Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 209 SER Chi-restraints excluded: chain H residue 253 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 52 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 168 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 37 GLN ** F 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.160103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.129446 restraints weight = 21446.313| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.78 r_work: 0.3188 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17461 Z= 0.135 Angle : 0.578 7.935 23722 Z= 0.289 Chirality : 0.043 0.303 2698 Planarity : 0.004 0.041 2924 Dihedral : 9.101 171.647 2402 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.23 % Favored : 92.63 % Rotamer: Outliers : 3.01 % Allowed : 14.71 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.18), residues: 2062 helix: 0.97 (0.18), residues: 844 sheet: -1.41 (0.26), residues: 404 loop : -2.48 (0.19), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 92 TYR 0.014 0.001 TYR F 203 PHE 0.023 0.001 PHE C 307 TRP 0.012 0.001 TRP G 299 HIS 0.007 0.001 HIS F 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (17445) covalent geometry : angle 0.57295 / 0.29 (23674) hydrogen bonds : bond 0.03960 / 2.47 ( 494) hydrogen bonds : angle 3.60760 / 2.43 ( 1422) link_ALPHA1-2 : bond 0.00111 / 0.06 ( 2) link_ALPHA1-2 : angle 1.76151 / 1.08 ( 6) link_ALPHA1-3 : bond 0.00545 / 0.27 ( 2) link_ALPHA1-3 : angle 2.34667 / 1.32 ( 6) link_ALPHA1-6 : bond 0.00347 / 0.18 ( 1) link_ALPHA1-6 : angle 1.27676 / 0.72 ( 3) link_BETA1-4 : bond 0.00429 / 0.21 ( 6) link_BETA1-4 : angle 1.60948 / 0.94 ( 18) link_NAG-ASN : bond 0.00378 / 0.19 ( 5) link_NAG-ASN : angle 1.63451 / 0.97 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 188 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7634 (pt) REVERT: A 282 MET cc_start: 0.3429 (tpt) cc_final: 0.2627 (tpp) REVERT: A 429 GLN cc_start: 0.8361 (tt0) cc_final: 0.8087 (pt0) REVERT: A 472 MET cc_start: 0.7314 (mtm) cc_final: 0.6965 (mtt) REVERT: B 93 SER cc_start: 0.8998 (t) cc_final: 0.7965 (m) REVERT: B 100 ASN cc_start: 0.7902 (m-40) cc_final: 0.7233 (p0) REVERT: C 333 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8162 (tt) REVERT: D 29 ASP cc_start: 0.8442 (t0) cc_final: 0.8134 (t0) REVERT: F 168 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6117 (mp0) REVERT: G 32 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7259 (mm110) REVERT: G 92 ARG cc_start: 0.8268 (ttp-110) cc_final: 0.7895 (ttm110) REVERT: G 167 ARG cc_start: 0.7914 (mtm-85) cc_final: 0.7471 (mtm-85) REVERT: H 139 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7481 (pp) REVERT: H 225 ILE cc_start: 0.7842 (mp) cc_final: 0.7345 (pt) REVERT: H 284 GLN cc_start: 0.6292 (mt0) cc_final: 0.5981 (tp40) outliers start: 53 outliers final: 45 residues processed: 225 average time/residue: 0.1270 time to fit residues: 44.6706 Evaluate side-chains 234 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 570 LEU Chi-restraints excluded: chain F residue 611 GLU Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 655 ILE Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 714 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 328 SER Chi-restraints excluded: chain G residue 346 LEU Chi-restraints excluded: chain G residue 364 LEU Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 209 SER Chi-restraints excluded: chain H residue 253 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 30.0000 chunk 151 optimal weight: 0.4980 chunk 154 optimal weight: 0.0060 chunk 96 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 9 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.164238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131480 restraints weight = 21116.454| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.78 r_work: 0.3213 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17461 Z= 0.111 Angle : 0.560 7.652 23722 Z= 0.280 Chirality : 0.042 0.301 2698 Planarity : 0.004 0.042 2924 Dihedral : 8.889 170.490 2402 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.74 % Favored : 93.11 % Rotamer: Outliers : 2.73 % Allowed : 15.05 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.19), residues: 2062 helix: 1.11 (0.18), residues: 841 sheet: -1.36 (0.26), residues: 405 loop : -2.41 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 92 TYR 0.013 0.001 TYR F 203 PHE 0.025 0.001 PHE C 307 TRP 0.013 0.001 TRP G 299 HIS 0.006 0.001 HIS F 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (17445) covalent geometry : angle 0.55586 / 0.28 (23674) hydrogen bonds : bond 0.03716 / 2.29 ( 494) hydrogen bonds : angle 3.51818 / 2.37 ( 1422) link_ALPHA1-2 : bond 0.00045 / 0.02 ( 2) link_ALPHA1-2 : angle 1.72150 / 1.06 ( 6) link_ALPHA1-3 : bond 0.00596 / 0.30 ( 2) link_ALPHA1-3 : angle 2.36128 / 1.32 ( 6) link_ALPHA1-6 : bond 0.00343 / 0.18 ( 1) link_ALPHA1-6 : angle 1.21977 / 0.69 ( 3) link_BETA1-4 : bond 0.00419 / 0.21 ( 6) link_BETA1-4 : angle 1.53407 / 0.89 ( 18) link_NAG-ASN : bond 0.00402 / 0.20 ( 5) link_NAG-ASN : angle 1.62274 / 0.96 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 190 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7586 (mt) REVERT: A 294 LEU cc_start: 0.8494 (tp) cc_final: 0.8134 (mp) REVERT: A 429 GLN cc_start: 0.8358 (tt0) cc_final: 0.8051 (pt0) REVERT: A 472 MET cc_start: 0.7152 (mtm) cc_final: 0.6861 (mtm) REVERT: B 93 SER cc_start: 0.8973 (t) cc_final: 0.7925 (m) REVERT: B 100 ASN cc_start: 0.7841 (m-40) cc_final: 0.7104 (p0) REVERT: C 333 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8150 (tt) REVERT: D 29 ASP cc_start: 0.8473 (t0) cc_final: 0.8185 (t0) REVERT: F 168 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6058 (mp0) REVERT: F 451 VAL cc_start: 0.7813 (p) cc_final: 0.7601 (p) REVERT: G 32 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7167 (mm110) REVERT: G 92 ARG cc_start: 0.8279 (ttp-110) cc_final: 0.7995 (ttm110) REVERT: G 167 ARG cc_start: 0.7957 (mtm-85) cc_final: 0.7506 (mtm-85) REVERT: G 377 HIS cc_start: 0.8446 (OUTLIER) cc_final: 0.7031 (t-90) REVERT: H 139 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7462 (pp) REVERT: H 225 ILE cc_start: 0.7785 (mp) cc_final: 0.7283 (pt) outliers start: 48 outliers final: 40 residues processed: 224 average time/residue: 0.1290 time to fit residues: 45.0324 Evaluate side-chains 231 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 570 LEU Chi-restraints excluded: chain F residue 611 GLU Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 655 ILE Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 714 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 346 LEU Chi-restraints excluded: chain G residue 364 LEU Chi-restraints excluded: chain G residue 377 HIS Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 209 SER Chi-restraints excluded: chain H residue 253 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 39 optimal weight: 0.0870 chunk 166 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 8 optimal weight: 0.0670 chunk 162 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.164315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.132455 restraints weight = 21298.160| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.75 r_work: 0.3217 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17461 Z= 0.113 Angle : 0.560 7.805 23722 Z= 0.279 Chirality : 0.043 0.297 2698 Planarity : 0.004 0.041 2924 Dihedral : 8.807 169.713 2402 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.69 % Favored : 93.16 % Rotamer: Outliers : 2.67 % Allowed : 15.05 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.19), residues: 2062 helix: 1.17 (0.18), residues: 841 sheet: -1.34 (0.26), residues: 405 loop : -2.38 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 92 TYR 0.013 0.001 TYR F 203 PHE 0.012 0.001 PHE F 496 TRP 0.012 0.001 TRP G 299 HIS 0.008 0.001 HIS G 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (17445) covalent geometry : angle 0.55585 / 0.28 (23674) hydrogen bonds : bond 0.03734 / 2.30 ( 494) hydrogen bonds : angle 3.50207 / 2.36 ( 1422) link_ALPHA1-2 : bond 0.00072 / 0.04 ( 2) link_ALPHA1-2 : angle 1.72087 / 1.06 ( 6) link_ALPHA1-3 : bond 0.00561 / 0.28 ( 2) link_ALPHA1-3 : angle 2.34230 / 1.31 ( 6) link_ALPHA1-6 : bond 0.00351 / 0.18 ( 1) link_ALPHA1-6 : angle 1.21241 / 0.68 ( 3) link_BETA1-4 : bond 0.00417 / 0.20 ( 6) link_BETA1-4 : angle 1.54089 / 0.89 ( 18) link_NAG-ASN : bond 0.00380 / 0.19 ( 5) link_NAG-ASN : angle 1.59289 / 0.94 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3994.29 seconds wall clock time: 69 minutes 20.76 seconds (4160.76 seconds total)