Starting phenix.real_space_refine on Thu Mar 5 09:06:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q4d_13803/03_2026/7q4d_13803_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q4d_13803/03_2026/7q4d_13803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q4d_13803/03_2026/7q4d_13803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q4d_13803/03_2026/7q4d_13803.map" model { file = "/net/cci-nas-00/data/ceres_data/7q4d_13803/03_2026/7q4d_13803_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q4d_13803/03_2026/7q4d_13803_trim.cif" } resolution = 3.78 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= 0.001 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 38 5.16 5 C 6772 2.51 5 N 1736 2.21 5 O 2088 1.98 5 H 9462 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20098 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 9690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 9690 Classifications: {'peptide': 608} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 569} Chain: "B" Number of atoms: 9690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 9690 Classifications: {'peptide': 608} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 569} Chain: "C" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 85 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 85 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "N" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.68, per 1000 atoms: 0.18 Number of scatterers: 20098 At special positions: 0 Unit cell: (101.76, 156.88, 93.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 38 16.00 O 2088 8.00 N 1736 7.00 C 6772 6.00 H 9462 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 528 " distance=2.02 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 330 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 516 " - pdb=" SG CYS B 528 " distance=2.02 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 ALPHA1-3 " BMA C 3 " - " MAN C 6 " " BMA E 3 " - " MAN E 4 " " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 6 " ALPHA1-6 " BMA C 3 " - " MAN C 4 " " BMA F 3 " - " MAN F 4 " " BMA L 3 " - " MAN L 4 " " BMA M 3 " - " MAN M 4 " BETA1-2 " MAN C 4 " - " NAG C 5 " " MAN F 4 " - " NAG F 5 " " MAN L 4 " - " NAG L 5 " " MAN M 4 " - " NAG M 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " BETA1-6 " NAG C 1 " - " FUC C 7 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG M 1 " - " FUC M 7 " NAG-ASN " NAG A1302 " - " ASN A 416 " " NAG B1302 " - " ASN B 416 " " NAG C 1 " - " ASN A 289 " " NAG D 1 " - " ASN A 117 " " NAG E 1 " - " ASN A 45 " " NAG F 1 " - " ASN A 25 " " NAG G 1 " - " ASN A 480 " " NAG H 1 " - " ASN A 9 " " NAG I 1 " - " ASN A 82 " " NAG J 1 " - " ASN B 480 " " NAG K 1 " - " ASN B 45 " " NAG L 1 " - " ASN B 25 " " NAG M 1 " - " ASN B 289 " " NAG N 1 " - " ASN B 117 " " NAG O 1 " - " ASN B 82 " " NAG P 1 " - " ASN B 9 " Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 670.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" NE2 HIS A 365 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" NE2 HIS B 365 " 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2300 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 4 sheets defined 71.1% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 13 through 45 removed outlier: 3.506A pdb=" N LEU A 19 " --> pdb=" O ALA A 15 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN A 34 " --> pdb=" O GLN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 77 removed outlier: 3.891A pdb=" N LYS A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 104 through 124 Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 152 through 169 Processing helix chain 'A' and resid 170 through 190 removed outlier: 4.651A pdb=" N LEU A 174 " --> pdb=" O PRO A 170 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.761A pdb=" N TRP A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 238 removed outlier: 3.552A pdb=" N GLU A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Proline residue: A 220 - end of helix removed outlier: 3.541A pdb=" N GLY A 238 " --> pdb=" O HIS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 254 removed outlier: 3.951A pdb=" N GLY A 254 " --> pdb=" O HIS A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 254' Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 289 through 304 removed outlier: 3.622A pdb=" N PHE A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 317 removed outlier: 3.744A pdb=" N TRP A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 373 removed outlier: 3.595A pdb=" N HIS A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 380 Processing helix chain 'A' and resid 386 through 401 removed outlier: 4.273A pdb=" N LEU A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 408 Processing helix chain 'A' and resid 417 through 433 Processing helix chain 'A' and resid 434 through 451 removed outlier: 4.021A pdb=" N PHE A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP A 443 " --> pdb=" O GLY A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 484 through 489 removed outlier: 3.604A pdb=" N LYS A 489 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 519 removed outlier: 3.660A pdb=" N PHE A 502 " --> pdb=" O TYR A 498 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE A 509 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 Processing helix chain 'A' and resid 533 through 547 removed outlier: 3.592A pdb=" N LYS A 539 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 561 Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'A' and resid 574 through 589 Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 13 through 45 removed outlier: 3.631A pdb=" N LEU B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN B 30 " --> pdb=" O SER B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 77 removed outlier: 3.680A pdb=" N LYS B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 85 through 96 Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'B' and resid 104 through 124 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'B' and resid 152 through 169 Processing helix chain 'B' and resid 170 through 190 removed outlier: 4.579A pdb=" N LEU B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.724A pdb=" N TRP B 201 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 238 Proline residue: B 220 - end of helix Processing helix chain 'B' and resid 261 through 263 No H-bonds generated for 'chain 'B' and resid 261 through 263' Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 279 through 286 Processing helix chain 'B' and resid 289 through 304 removed outlier: 3.649A pdb=" N PHE B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 317 removed outlier: 3.807A pdb=" N TRP B 314 " --> pdb=" O PRO B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 373 Processing helix chain 'B' and resid 376 through 380 Processing helix chain 'B' and resid 386 through 401 removed outlier: 4.098A pdb=" N LEU B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 398 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 408 removed outlier: 3.632A pdb=" N LYS B 407 " --> pdb=" O GLU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 433 Processing helix chain 'B' and resid 434 through 451 removed outlier: 4.035A pdb=" N PHE B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP B 443 " --> pdb=" O GLY B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 458 through 471 Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'B' and resid 498 through 519 removed outlier: 3.649A pdb=" N PHE B 502 " --> pdb=" O TYR B 498 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE B 509 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 514 " --> pdb=" O GLN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 528 Processing helix chain 'B' and resid 533 through 545 removed outlier: 3.521A pdb=" N LYS B 539 " --> pdb=" O LYS B 535 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 542 " --> pdb=" O ALA B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 574 Processing helix chain 'B' and resid 574 through 589 Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249 removed outlier: 5.990A pdb=" N ILE A 248 " --> pdb=" O CYS A 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 333 through 336 Processing sheet with id=AA3, first strand: chain 'B' and resid 248 through 249 removed outlier: 6.040A pdb=" N ILE B 248 " --> pdb=" O CYS B 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 333 through 336 574 hydrogen bonds defined for protein. 1635 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: 5.04 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9460 1.03 - 1.23: 76 1.23 - 1.42: 4775 1.42 - 1.62: 6037 1.62 - 1.82: 62 Bond restraints: 20410 Sorted by residual: bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.80e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.60e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.43e+00 bond pdb=" C1 MAN C 6 " pdb=" C2 MAN C 6 " ideal model delta sigma weight residual 1.526 1.573 -0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.360 0.046 2.00e-02 2.50e+03 5.36e+00 ... (remaining 20405 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 36036 2.99 - 5.97: 345 5.97 - 8.96: 34 8.96 - 11.95: 0 11.95 - 14.93: 1 Bond angle restraints: 36416 Sorted by residual: angle pdb=" C3 MAN M 4 " pdb=" C2 MAN M 4 " pdb=" O2 MAN M 4 " ideal model delta sigma weight residual 111.77 96.84 14.93 3.00e+00 1.11e-01 2.48e+01 angle pdb=" CA TYR A 372 " pdb=" CB TYR A 372 " pdb=" CG TYR A 372 " ideal model delta sigma weight residual 113.90 120.36 -6.46 1.80e+00 3.09e-01 1.29e+01 angle pdb=" CA GLU A 389 " pdb=" CB GLU A 389 " pdb=" CG GLU A 389 " ideal model delta sigma weight residual 114.10 106.95 7.15 2.00e+00 2.50e-01 1.28e+01 angle pdb=" N LYS B 341 " pdb=" CA LYS B 341 " pdb=" C LYS B 341 " ideal model delta sigma weight residual 111.69 116.08 -4.39 1.23e+00 6.61e-01 1.28e+01 angle pdb=" CA ARG B 380 " pdb=" CB ARG B 380 " pdb=" CG ARG B 380 " ideal model delta sigma weight residual 114.10 106.98 7.12 2.00e+00 2.50e-01 1.27e+01 ... (remaining 36411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.29: 9613 21.29 - 42.58: 541 42.58 - 63.88: 218 63.88 - 85.17: 95 85.17 - 106.46: 60 Dihedral angle restraints: 10527 sinusoidal: 6057 harmonic: 4470 Sorted by residual: dihedral pdb=" CA TRP B 594 " pdb=" C TRP B 594 " pdb=" N PRO B 595 " pdb=" CA PRO B 595 " ideal model delta harmonic sigma weight residual 180.00 154.17 25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA PRO A 604 " pdb=" C PRO A 604 " pdb=" N ASP A 605 " pdb=" CA ASP A 605 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA ALA A 383 " pdb=" C ALA A 383 " pdb=" N ASN A 384 " pdb=" CA ASN A 384 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 10524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1585 0.094 - 0.189: 113 0.189 - 0.283: 7 0.283 - 0.377: 9 0.377 - 0.472: 2 Chirality restraints: 1716 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 82 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B 82 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 1713 not shown) Planarity restraints: 3008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 96 " -0.564 9.50e-02 1.11e+02 1.90e-01 5.27e+01 pdb=" NE ARG A 96 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG A 96 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG A 96 " -0.046 2.00e-02 2.50e+03 pdb=" NH2 ARG A 96 " 0.035 2.00e-02 2.50e+03 pdb="HH11 ARG A 96 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 96 " 0.042 2.00e-02 2.50e+03 pdb="HH21 ARG A 96 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 96 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 467 " -0.560 9.50e-02 1.11e+02 1.88e-01 4.60e+01 pdb=" NE ARG A 467 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG A 467 " -0.036 2.00e-02 2.50e+03 pdb=" NH1 ARG A 467 " 0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG A 467 " -0.011 2.00e-02 2.50e+03 pdb="HH11 ARG A 467 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 467 " -0.008 2.00e-02 2.50e+03 pdb="HH21 ARG A 467 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 467 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 413 " 0.223 9.50e-02 1.11e+02 8.53e-02 4.46e+01 pdb=" NE ARG B 413 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG B 413 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG B 413 " -0.087 2.00e-02 2.50e+03 pdb=" NH2 ARG B 413 " 0.011 2.00e-02 2.50e+03 pdb="HH11 ARG B 413 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG B 413 " 0.081 2.00e-02 2.50e+03 pdb="HH21 ARG B 413 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 413 " -0.011 2.00e-02 2.50e+03 ... (remaining 3005 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 954 2.19 - 2.79: 39398 2.79 - 3.39: 56661 3.39 - 4.00: 72443 4.00 - 4.60: 114237 Nonbonded interactions: 283693 Sorted by model distance: nonbonded pdb=" HE1 TRP B 464 " pdb=" OD2 ASP B 485 " model vdw 1.581 2.450 nonbonded pdb=" OD2 ASP B 443 " pdb=" H ILE B 499 " model vdw 1.593 2.450 nonbonded pdb=" HE1 TRP A 464 " pdb=" OD2 ASP A 485 " model vdw 1.596 2.450 nonbonded pdb=" HG1 THR B 291 " pdb=" OE2 GLU B 320 " model vdw 1.632 2.450 nonbonded pdb=" OD2 ASP A 443 " pdb=" H ILE A 499 " model vdw 1.638 2.450 ... (remaining 283688 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 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.590 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: 0.090 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 26.570 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 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:1.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 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 0.056 11012 Z= 0.358 Angle : 1.082 14.932 15100 Z= 0.516 Chirality : 0.056 0.472 1716 Planarity : 0.014 0.255 1854 Dihedral : 19.012 106.459 4824 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.89 (0.21), residues: 1212 helix: -1.26 (0.16), residues: 688 sheet: 0.48 (1.06), residues: 20 loop : -1.09 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.004 ARG A 467 TYR 0.030 0.006 TYR A 369 PHE 0.022 0.003 PHE A 387 TRP 0.025 0.004 TRP A 68 HIS 0.012 0.003 HIS B 526 Details of bonding type rmsd covalent geometry : bond 0.00763 (10948) covalent geometry : angle 1.00795 (14920) SS BOND : bond 0.00453 ( 6) SS BOND : angle 1.76878 ( 12) hydrogen bonds : bond 0.22651 ( 574) hydrogen bonds : angle 8.70944 ( 1635) metal coordination : bond 0.04023 ( 2) link_ALPHA1-3 : bond 0.00884 ( 4) link_ALPHA1-3 : angle 2.33202 ( 12) link_ALPHA1-6 : bond 0.00560 ( 4) link_ALPHA1-6 : angle 1.72507 ( 12) link_BETA1-2 : bond 0.01098 ( 4) link_BETA1-2 : angle 2.57510 ( 12) link_BETA1-4 : bond 0.00766 ( 26) link_BETA1-4 : angle 3.67593 ( 78) link_BETA1-6 : bond 0.00460 ( 2) link_BETA1-6 : angle 4.25555 ( 6) link_NAG-ASN : bond 0.00938 ( 16) link_NAG-ASN : angle 4.87156 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 MET cc_start: 0.8891 (ttt) cc_final: 0.8555 (ttt) REVERT: A 590 GLU cc_start: 0.7432 (tp30) cc_final: 0.6752 (tp30) REVERT: B 155 MET cc_start: 0.8621 (tpt) cc_final: 0.8330 (mmp) REVERT: B 431 GLU cc_start: 0.8374 (tt0) cc_final: 0.8169 (tt0) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.3467 time to fit residues: 60.5699 Evaluate side-chains 75 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A 494 ASN ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 GLN A 588 ASN A 598 GLN B 112 ASN B 216 GLN B 292 HIS B 483 HIS B 494 ASN B 545 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.089361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.075618 restraints weight = 77872.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.078642 restraints weight = 33366.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.080677 restraints weight = 18869.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.082030 restraints weight = 12569.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.082929 restraints weight = 9390.501| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11012 Z= 0.184 Angle : 0.812 9.237 15100 Z= 0.396 Chirality : 0.044 0.305 1716 Planarity : 0.006 0.054 1854 Dihedral : 14.273 81.960 2466 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.57 % Allowed : 5.16 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.21 (0.22), residues: 1212 helix: 0.26 (0.18), residues: 728 sheet: 1.16 (1.12), residues: 20 loop : -0.69 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 467 TYR 0.025 0.002 TYR A 372 PHE 0.019 0.002 PHE A 178 TRP 0.021 0.002 TRP A 163 HIS 0.011 0.002 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00383 (10948) covalent geometry : angle 0.77778 (14920) SS BOND : bond 0.00280 ( 6) SS BOND : angle 1.10111 ( 12) hydrogen bonds : bond 0.06729 ( 574) hydrogen bonds : angle 5.59675 ( 1635) metal coordination : bond 0.00255 ( 2) link_ALPHA1-3 : bond 0.00948 ( 4) link_ALPHA1-3 : angle 2.48700 ( 12) link_ALPHA1-6 : bond 0.00766 ( 4) link_ALPHA1-6 : angle 1.73216 ( 12) link_BETA1-2 : bond 0.00419 ( 4) link_BETA1-2 : angle 1.32134 ( 12) link_BETA1-4 : bond 0.00514 ( 26) link_BETA1-4 : angle 2.54985 ( 78) link_BETA1-6 : bond 0.00312 ( 2) link_BETA1-6 : angle 2.18831 ( 6) link_NAG-ASN : bond 0.00402 ( 16) link_NAG-ASN : angle 2.27224 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 ARG cc_start: 0.8788 (mtm-85) cc_final: 0.7875 (mtm-85) REVERT: B 155 MET cc_start: 0.8326 (tpt) cc_final: 0.8032 (mmp) outliers start: 6 outliers final: 4 residues processed: 96 average time/residue: 0.2556 time to fit residues: 33.1156 Evaluate side-chains 79 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 588 ASN Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 555 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 68 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 588 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.088854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.074743 restraints weight = 79550.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.077786 restraints weight = 34532.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.079806 restraints weight = 19755.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.081200 restraints weight = 13329.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.082020 restraints weight = 9952.947| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11012 Z= 0.222 Angle : 0.738 7.136 15100 Z= 0.360 Chirality : 0.042 0.303 1716 Planarity : 0.005 0.043 1854 Dihedral : 11.826 73.507 2466 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.67 % Allowed : 6.41 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.08 (0.23), residues: 1212 helix: 0.37 (0.18), residues: 734 sheet: 1.13 (1.13), residues: 20 loop : -0.65 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 231 TYR 0.022 0.002 TYR A 372 PHE 0.014 0.002 PHE B 300 TRP 0.016 0.002 TRP B 288 HIS 0.011 0.002 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00481 (10948) covalent geometry : angle 0.70987 (14920) SS BOND : bond 0.00244 ( 6) SS BOND : angle 0.76549 ( 12) hydrogen bonds : bond 0.06148 ( 574) hydrogen bonds : angle 5.40402 ( 1635) metal coordination : bond 0.00809 ( 2) link_ALPHA1-3 : bond 0.01159 ( 4) link_ALPHA1-3 : angle 1.81700 ( 12) link_ALPHA1-6 : bond 0.00897 ( 4) link_ALPHA1-6 : angle 1.69932 ( 12) link_BETA1-2 : bond 0.00474 ( 4) link_BETA1-2 : angle 1.20941 ( 12) link_BETA1-4 : bond 0.00409 ( 26) link_BETA1-4 : angle 2.33666 ( 78) link_BETA1-6 : bond 0.00250 ( 2) link_BETA1-6 : angle 2.03568 ( 6) link_NAG-ASN : bond 0.00419 ( 16) link_NAG-ASN : angle 1.82686 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 155 MET cc_start: 0.8331 (tpt) cc_final: 0.7843 (mmp) outliers start: 7 outliers final: 6 residues processed: 83 average time/residue: 0.2306 time to fit residues: 26.4117 Evaluate side-chains 78 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 588 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 119 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 GLN A 579 GLN B 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.088045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.073908 restraints weight = 79800.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.076919 restraints weight = 35048.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.078937 restraints weight = 20095.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.080177 restraints weight = 13611.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.081173 restraints weight = 10417.109| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11012 Z= 0.248 Angle : 0.730 7.433 15100 Z= 0.359 Chirality : 0.042 0.275 1716 Planarity : 0.005 0.075 1854 Dihedral : 10.314 61.114 2466 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.15 % Allowed : 7.46 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.13 (0.23), residues: 1212 helix: 0.30 (0.18), residues: 738 sheet: 1.35 (1.14), residues: 20 loop : -0.65 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 340 TYR 0.023 0.002 TYR A 372 PHE 0.015 0.002 PHE B 300 TRP 0.013 0.001 TRP A 163 HIS 0.011 0.002 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00537 (10948) covalent geometry : angle 0.70148 (14920) SS BOND : bond 0.00299 ( 6) SS BOND : angle 0.93134 ( 12) hydrogen bonds : bond 0.05603 ( 574) hydrogen bonds : angle 5.28821 ( 1635) metal coordination : bond 0.00975 ( 2) link_ALPHA1-3 : bond 0.01107 ( 4) link_ALPHA1-3 : angle 1.98492 ( 12) link_ALPHA1-6 : bond 0.01076 ( 4) link_ALPHA1-6 : angle 1.48382 ( 12) link_BETA1-2 : bond 0.00442 ( 4) link_BETA1-2 : angle 1.17240 ( 12) link_BETA1-4 : bond 0.00436 ( 26) link_BETA1-4 : angle 2.29700 ( 78) link_BETA1-6 : bond 0.00299 ( 2) link_BETA1-6 : angle 2.02960 ( 6) link_NAG-ASN : bond 0.00487 ( 16) link_NAG-ASN : angle 1.81038 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 363 MET cc_start: 0.8352 (ttm) cc_final: 0.8080 (tmm) outliers start: 12 outliers final: 11 residues processed: 84 average time/residue: 0.2139 time to fit residues: 25.2874 Evaluate side-chains 79 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 579 GLN Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 555 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.089966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.075818 restraints weight = 79033.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.078853 restraints weight = 34149.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.080891 restraints weight = 19499.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.082297 restraints weight = 13129.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.083246 restraints weight = 9782.135| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11012 Z= 0.151 Angle : 0.646 8.102 15100 Z= 0.315 Chirality : 0.038 0.262 1716 Planarity : 0.005 0.045 1854 Dihedral : 9.030 59.662 2466 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.05 % Allowed : 8.22 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.28 (0.24), residues: 1212 helix: 0.64 (0.19), residues: 738 sheet: 1.55 (1.20), residues: 20 loop : -0.49 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 340 TYR 0.020 0.002 TYR A 372 PHE 0.013 0.001 PHE A 178 TRP 0.015 0.001 TRP A 163 HIS 0.009 0.001 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00319 (10948) covalent geometry : angle 0.62305 (14920) SS BOND : bond 0.00166 ( 6) SS BOND : angle 0.74556 ( 12) hydrogen bonds : bond 0.05243 ( 574) hydrogen bonds : angle 4.95864 ( 1635) metal coordination : bond 0.00491 ( 2) link_ALPHA1-3 : bond 0.01152 ( 4) link_ALPHA1-3 : angle 1.87022 ( 12) link_ALPHA1-6 : bond 0.01272 ( 4) link_ALPHA1-6 : angle 1.62116 ( 12) link_BETA1-2 : bond 0.00361 ( 4) link_BETA1-2 : angle 1.08049 ( 12) link_BETA1-4 : bond 0.00364 ( 26) link_BETA1-4 : angle 1.92584 ( 78) link_BETA1-6 : bond 0.00113 ( 2) link_BETA1-6 : angle 1.78352 ( 6) link_NAG-ASN : bond 0.00252 ( 16) link_NAG-ASN : angle 1.54190 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 363 MET cc_start: 0.8252 (ttm) cc_final: 0.8027 (tmm) outliers start: 11 outliers final: 11 residues processed: 84 average time/residue: 0.2204 time to fit residues: 26.2661 Evaluate side-chains 79 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 588 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 112 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 103 optimal weight: 0.3980 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.088813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.074660 restraints weight = 79194.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.077688 restraints weight = 34431.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.079754 restraints weight = 19780.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.081101 restraints weight = 13326.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.082024 restraints weight = 10011.787| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11012 Z= 0.197 Angle : 0.655 7.742 15100 Z= 0.323 Chirality : 0.038 0.254 1716 Planarity : 0.005 0.044 1854 Dihedral : 8.149 52.222 2466 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.63 % Allowed : 8.32 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.30 (0.24), residues: 1212 helix: 0.69 (0.19), residues: 738 sheet: 1.64 (1.25), residues: 20 loop : -0.56 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 340 TYR 0.020 0.002 TYR A 372 PHE 0.043 0.002 PHE B 83 TRP 0.013 0.001 TRP A 163 HIS 0.011 0.002 HIS A 512 Details of bonding type rmsd covalent geometry : bond 0.00428 (10948) covalent geometry : angle 0.63215 (14920) SS BOND : bond 0.00264 ( 6) SS BOND : angle 0.72525 ( 12) hydrogen bonds : bond 0.04999 ( 574) hydrogen bonds : angle 4.91711 ( 1635) metal coordination : bond 0.00725 ( 2) link_ALPHA1-3 : bond 0.01042 ( 4) link_ALPHA1-3 : angle 1.76801 ( 12) link_ALPHA1-6 : bond 0.01433 ( 4) link_ALPHA1-6 : angle 2.27784 ( 12) link_BETA1-2 : bond 0.00379 ( 4) link_BETA1-2 : angle 1.07825 ( 12) link_BETA1-4 : bond 0.00361 ( 26) link_BETA1-4 : angle 1.84875 ( 78) link_BETA1-6 : bond 0.00164 ( 2) link_BETA1-6 : angle 1.86877 ( 6) link_NAG-ASN : bond 0.00386 ( 16) link_NAG-ASN : angle 1.56800 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 14 residues processed: 85 average time/residue: 0.2168 time to fit residues: 26.2647 Evaluate side-chains 84 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 555 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 70 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS A 292 HIS B 588 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.089018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.074811 restraints weight = 79829.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.077864 restraints weight = 34651.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.079940 restraints weight = 19813.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.081269 restraints weight = 13300.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.082214 restraints weight = 10044.174| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11012 Z= 0.176 Angle : 0.625 7.287 15100 Z= 0.308 Chirality : 0.037 0.262 1716 Planarity : 0.004 0.040 1854 Dihedral : 7.743 55.430 2466 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.34 % Allowed : 8.80 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.44 (0.24), residues: 1212 helix: 0.83 (0.19), residues: 734 sheet: 1.42 (1.22), residues: 20 loop : -0.54 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 340 TYR 0.019 0.002 TYR A 372 PHE 0.022 0.002 PHE B 83 TRP 0.013 0.001 TRP A 163 HIS 0.008 0.001 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00380 (10948) covalent geometry : angle 0.60403 (14920) SS BOND : bond 0.00239 ( 6) SS BOND : angle 0.66000 ( 12) hydrogen bonds : bond 0.04824 ( 574) hydrogen bonds : angle 4.81048 ( 1635) metal coordination : bond 0.00711 ( 2) link_ALPHA1-3 : bond 0.00976 ( 4) link_ALPHA1-3 : angle 1.64239 ( 12) link_ALPHA1-6 : bond 0.01367 ( 4) link_ALPHA1-6 : angle 1.96802 ( 12) link_BETA1-2 : bond 0.00355 ( 4) link_BETA1-2 : angle 1.06363 ( 12) link_BETA1-4 : bond 0.00344 ( 26) link_BETA1-4 : angle 1.72970 ( 78) link_BETA1-6 : bond 0.00122 ( 2) link_BETA1-6 : angle 1.75258 ( 6) link_NAG-ASN : bond 0.00363 ( 16) link_NAG-ASN : angle 1.50902 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.6281 (t80) REVERT: B 363 MET cc_start: 0.8363 (ttm) cc_final: 0.8137 (tmm) outliers start: 14 outliers final: 13 residues processed: 82 average time/residue: 0.2181 time to fit residues: 25.2611 Evaluate side-chains 84 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 588 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.089399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.075159 restraints weight = 79256.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.078215 restraints weight = 34411.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.080283 restraints weight = 19694.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.081689 restraints weight = 13267.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.082588 restraints weight = 9883.144| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11012 Z= 0.157 Angle : 0.610 7.319 15100 Z= 0.301 Chirality : 0.036 0.252 1716 Planarity : 0.004 0.038 1854 Dihedral : 7.498 59.697 2466 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.43 % Allowed : 8.99 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.55 (0.24), residues: 1212 helix: 0.94 (0.19), residues: 734 sheet: 1.31 (1.20), residues: 20 loop : -0.53 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 340 TYR 0.019 0.002 TYR A 372 PHE 0.024 0.001 PHE B 83 TRP 0.012 0.001 TRP A 163 HIS 0.008 0.001 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00336 (10948) covalent geometry : angle 0.58915 (14920) SS BOND : bond 0.00153 ( 6) SS BOND : angle 0.63547 ( 12) hydrogen bonds : bond 0.04732 ( 574) hydrogen bonds : angle 4.73793 ( 1635) metal coordination : bond 0.00554 ( 2) link_ALPHA1-3 : bond 0.00950 ( 4) link_ALPHA1-3 : angle 1.57827 ( 12) link_ALPHA1-6 : bond 0.01409 ( 4) link_ALPHA1-6 : angle 1.98528 ( 12) link_BETA1-2 : bond 0.00365 ( 4) link_BETA1-2 : angle 1.04750 ( 12) link_BETA1-4 : bond 0.00333 ( 26) link_BETA1-4 : angle 1.68903 ( 78) link_BETA1-6 : bond 0.00099 ( 2) link_BETA1-6 : angle 1.71916 ( 6) link_NAG-ASN : bond 0.00353 ( 16) link_NAG-ASN : angle 1.46349 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 LEU cc_start: 0.9089 (mt) cc_final: 0.8704 (mt) REVERT: B 363 MET cc_start: 0.8298 (ttm) cc_final: 0.8034 (tmm) outliers start: 15 outliers final: 13 residues processed: 82 average time/residue: 0.2123 time to fit residues: 24.9959 Evaluate side-chains 84 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 555 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 113 optimal weight: 2.9990 chunk 101 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 107 optimal weight: 0.0050 chunk 80 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 HIS B 588 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.090603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.076337 restraints weight = 78707.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.079455 restraints weight = 34093.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.081556 restraints weight = 19413.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.082952 restraints weight = 13026.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.083888 restraints weight = 9697.827| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11012 Z= 0.124 Angle : 0.574 7.129 15100 Z= 0.281 Chirality : 0.035 0.243 1716 Planarity : 0.004 0.034 1854 Dihedral : 6.872 55.812 2466 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.43 % Allowed : 9.18 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.76 (0.24), residues: 1212 helix: 1.08 (0.19), residues: 750 sheet: 1.03 (1.20), residues: 20 loop : -0.41 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 236 TYR 0.017 0.001 TYR A 372 PHE 0.015 0.001 PHE B 83 TRP 0.013 0.001 TRP A 163 HIS 0.009 0.001 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00262 (10948) covalent geometry : angle 0.55502 (14920) SS BOND : bond 0.00122 ( 6) SS BOND : angle 0.58501 ( 12) hydrogen bonds : bond 0.04497 ( 574) hydrogen bonds : angle 4.58710 ( 1635) metal coordination : bond 0.00354 ( 2) link_ALPHA1-3 : bond 0.00926 ( 4) link_ALPHA1-3 : angle 1.43749 ( 12) link_ALPHA1-6 : bond 0.01370 ( 4) link_ALPHA1-6 : angle 2.02672 ( 12) link_BETA1-2 : bond 0.00343 ( 4) link_BETA1-2 : angle 1.00074 ( 12) link_BETA1-4 : bond 0.00329 ( 26) link_BETA1-4 : angle 1.57715 ( 78) link_BETA1-6 : bond 0.00076 ( 2) link_BETA1-6 : angle 1.57178 ( 6) link_NAG-ASN : bond 0.00253 ( 16) link_NAG-ASN : angle 1.30760 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 LEU cc_start: 0.9092 (mt) cc_final: 0.8725 (mt) REVERT: A 267 MET cc_start: 0.8187 (ttm) cc_final: 0.7986 (ttm) REVERT: B 363 MET cc_start: 0.8220 (ttm) cc_final: 0.7996 (tmm) REVERT: B 606 ASN cc_start: 0.7610 (m-40) cc_final: 0.6950 (t0) outliers start: 15 outliers final: 15 residues processed: 85 average time/residue: 0.2031 time to fit residues: 25.0471 Evaluate side-chains 85 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 555 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 21 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.090493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.076280 restraints weight = 79298.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.079384 restraints weight = 34147.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.081461 restraints weight = 19408.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.082826 restraints weight = 13071.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.083709 restraints weight = 9793.382| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11012 Z= 0.132 Angle : 0.577 7.031 15100 Z= 0.284 Chirality : 0.035 0.237 1716 Planarity : 0.004 0.032 1854 Dihedral : 6.730 52.586 2466 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.43 % Allowed : 9.46 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.80 (0.24), residues: 1212 helix: 1.12 (0.19), residues: 752 sheet: 0.98 (1.23), residues: 20 loop : -0.42 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 340 TYR 0.017 0.001 TYR A 372 PHE 0.014 0.001 PHE B 83 TRP 0.012 0.001 TRP A 163 HIS 0.012 0.001 HIS A 331 Details of bonding type rmsd covalent geometry : bond 0.00280 (10948) covalent geometry : angle 0.55735 (14920) SS BOND : bond 0.00349 ( 6) SS BOND : angle 0.90270 ( 12) hydrogen bonds : bond 0.04447 ( 574) hydrogen bonds : angle 4.56485 ( 1635) metal coordination : bond 0.00407 ( 2) link_ALPHA1-3 : bond 0.00863 ( 4) link_ALPHA1-3 : angle 1.41818 ( 12) link_ALPHA1-6 : bond 0.01338 ( 4) link_ALPHA1-6 : angle 2.04369 ( 12) link_BETA1-2 : bond 0.00334 ( 4) link_BETA1-2 : angle 1.01018 ( 12) link_BETA1-4 : bond 0.00328 ( 26) link_BETA1-4 : angle 1.57205 ( 78) link_BETA1-6 : bond 0.00064 ( 2) link_BETA1-6 : angle 1.58261 ( 6) link_NAG-ASN : bond 0.00270 ( 16) link_NAG-ASN : angle 1.30391 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 LEU cc_start: 0.9101 (mt) cc_final: 0.8724 (mt) REVERT: B 164 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.7051 (m90) REVERT: B 363 MET cc_start: 0.8248 (ttm) cc_final: 0.8010 (tmm) REVERT: B 606 ASN cc_start: 0.7607 (m-40) cc_final: 0.6951 (t0) outliers start: 15 outliers final: 13 residues processed: 80 average time/residue: 0.2084 time to fit residues: 23.9438 Evaluate side-chains 83 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 555 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 114 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 97 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.0000 chunk 116 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.091014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.076730 restraints weight = 79207.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.079848 restraints weight = 34220.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.081949 restraints weight = 19371.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.083351 restraints weight = 13010.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.084259 restraints weight = 9685.153| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11012 Z= 0.122 Angle : 0.561 6.908 15100 Z= 0.276 Chirality : 0.035 0.229 1716 Planarity : 0.004 0.032 1854 Dihedral : 6.369 48.222 2466 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.43 % Allowed : 9.46 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.94 (0.24), residues: 1212 helix: 1.25 (0.19), residues: 750 sheet: 0.89 (1.25), residues: 20 loop : -0.39 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 236 TYR 0.016 0.001 TYR A 372 PHE 0.012 0.001 PHE B 83 TRP 0.013 0.001 TRP A 163 HIS 0.009 0.001 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00257 (10948) covalent geometry : angle 0.54262 (14920) SS BOND : bond 0.00127 ( 6) SS BOND : angle 0.68025 ( 12) hydrogen bonds : bond 0.04339 ( 574) hydrogen bonds : angle 4.49866 ( 1635) metal coordination : bond 0.00348 ( 2) link_ALPHA1-3 : bond 0.00817 ( 4) link_ALPHA1-3 : angle 1.35124 ( 12) link_ALPHA1-6 : bond 0.01325 ( 4) link_ALPHA1-6 : angle 2.08333 ( 12) link_BETA1-2 : bond 0.00326 ( 4) link_BETA1-2 : angle 0.99123 ( 12) link_BETA1-4 : bond 0.00320 ( 26) link_BETA1-4 : angle 1.51701 ( 78) link_BETA1-6 : bond 0.00045 ( 2) link_BETA1-6 : angle 1.53401 ( 6) link_NAG-ASN : bond 0.00247 ( 16) link_NAG-ASN : angle 1.24260 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2721.73 seconds wall clock time: 47 minutes 19.38 seconds (2839.38 seconds total)