Starting phenix.real_space_refine on Sat Jul 4 10:49:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t37_25650/07_2026/7t37_25650.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t37_25650/07_2026/7t37_25650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t37_25650/07_2026/7t37_25650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t37_25650/07_2026/7t37_25650.map" model { file = "/net/cci-nas-00/data/ceres_data/7t37_25650/07_2026/7t37_25650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t37_25650/07_2026/7t37_25650.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7t37_25650/07_2026/7t37_25650.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t37_25650/07_2026/7t37_25650.cif" } resolution = 3.7 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= 0.019 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 116 5.16 5 B 4 2.79 5 C 13224 2.51 5 N 3388 2.21 5 O 3444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20176 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 5004 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 594} Chain breaks: 5 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 5004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 5004 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 594} Chain breaks: 5 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 5004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 5004 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 594} Chain breaks: 5 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 5004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 5004 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 594} Chain breaks: 5 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'FZ4': 1, 'P0T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'FZ4': 1, 'P0T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'FZ4': 1, 'P0T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'FZ4': 1, 'P0T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.44, per 1000 atoms: 0.22 Number of scatterers: 20176 At special positions: 0 Unit cell: (140.17, 140.17, 112.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 O 3444 8.00 N 3388 7.00 C 13224 6.00 B 4 5.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 809.3 milliseconds 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4688 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 4 sheets defined 63.7% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.877A pdb=" N THR A 93 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 135 through 147 removed outlier: 3.624A pdb=" N GLY A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.779A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 186 removed outlier: 3.547A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.971A pdb=" N VAL A 226 " --> pdb=" O GLN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 removed outlier: 4.067A pdb=" N ASN A 247 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 256 removed outlier: 3.623A pdb=" N VAL A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.659A pdb=" N ARG A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 removed outlier: 4.153A pdb=" N ILE A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 306 removed outlier: 3.667A pdb=" N GLY A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.580A pdb=" N PHE A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 removed outlier: 3.568A pdb=" N LEU A 326 " --> pdb=" O TYR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 378 through 413 removed outlier: 3.532A pdb=" N ARG A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 467 through 470 Processing helix chain 'A' and resid 471 through 492 removed outlier: 3.520A pdb=" N LEU A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE A 476 " --> pdb=" O PHE A 472 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LEU A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR A 483 " --> pdb=" O GLN A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 3.880A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 501 " --> pdb=" O TYR A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 removed outlier: 4.078A pdb=" N GLY A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 530 removed outlier: 3.774A pdb=" N TYR A 525 " --> pdb=" O HIS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 559 removed outlier: 3.590A pdb=" N LEU A 537 " --> pdb=" O ILE A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 618 through 650 removed outlier: 3.635A pdb=" N VAL A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASN A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 672 removed outlier: 4.299A pdb=" N SER A 658 " --> pdb=" O ASP A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 719 removed outlier: 3.735A pdb=" N TRP A 715 " --> pdb=" O ASN A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.874A pdb=" N THR B 93 " --> pdb=" O GLU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 135 through 147 removed outlier: 3.618A pdb=" N GLY B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.757A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 186 removed outlier: 3.544A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.984A pdb=" N VAL B 226 " --> pdb=" O GLN B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 247 removed outlier: 4.066A pdb=" N ASN B 247 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 256 removed outlier: 3.911A pdb=" N VAL B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.678A pdb=" N ARG B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 removed outlier: 4.164A pdb=" N ILE B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 306 removed outlier: 3.683A pdb=" N GLY B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.670A pdb=" N PHE B 311 " --> pdb=" O LYS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 327 removed outlier: 3.541A pdb=" N LEU B 326 " --> pdb=" O TYR B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 378 through 413 removed outlier: 3.530A pdb=" N ARG B 388 " --> pdb=" O GLU B 384 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 467 through 470 Processing helix chain 'B' and resid 471 through 492 removed outlier: 3.522A pdb=" N LEU B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE B 476 " --> pdb=" O PHE B 472 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LEU B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR B 483 " --> pdb=" O GLN B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 3.874A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 501 " --> pdb=" O TYR B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 removed outlier: 4.075A pdb=" N GLY B 518 " --> pdb=" O TYR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 530 removed outlier: 3.788A pdb=" N TYR B 525 " --> pdb=" O HIS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 559 removed outlier: 3.590A pdb=" N LEU B 537 " --> pdb=" O ILE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 618 through 650 removed outlier: 3.636A pdb=" N VAL B 635 " --> pdb=" O LEU B 631 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 672 removed outlier: 4.306A pdb=" N SER B 658 " --> pdb=" O ASP B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 719 removed outlier: 3.741A pdb=" N TRP B 715 " --> pdb=" O ASN B 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.873A pdb=" N THR C 93 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 135 through 147 removed outlier: 3.624A pdb=" N GLY C 147 " --> pdb=" O ASP C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.756A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 186 removed outlier: 3.545A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.965A pdb=" N VAL C 226 " --> pdb=" O GLN C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 247 removed outlier: 4.078A pdb=" N ASN C 247 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 256 removed outlier: 3.534A pdb=" N LEU C 253 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.683A pdb=" N ARG C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 removed outlier: 4.161A pdb=" N ILE C 290 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 306 removed outlier: 3.666A pdb=" N GLY C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.577A pdb=" N PHE C 311 " --> pdb=" O LYS C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 327 removed outlier: 3.560A pdb=" N LEU C 326 " --> pdb=" O TYR C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 378 through 413 removed outlier: 3.530A pdb=" N ARG C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 467 through 470 Processing helix chain 'C' and resid 471 through 492 removed outlier: 3.540A pdb=" N LEU C 475 " --> pdb=" O TYR C 471 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE C 476 " --> pdb=" O PHE C 472 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR C 483 " --> pdb=" O GLN C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 3.871A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 501 " --> pdb=" O TYR C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 removed outlier: 4.076A pdb=" N GLY C 518 " --> pdb=" O TYR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 530 removed outlier: 3.787A pdb=" N TYR C 525 " --> pdb=" O HIS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 559 removed outlier: 3.586A pdb=" N LEU C 537 " --> pdb=" O ILE C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 Processing helix chain 'C' and resid 618 through 650 removed outlier: 3.637A pdb=" N VAL C 635 " --> pdb=" O LEU C 631 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASN C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 672 removed outlier: 4.306A pdb=" N SER C 658 " --> pdb=" O ASP C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 719 removed outlier: 3.742A pdb=" N TRP C 715 " --> pdb=" O ASN C 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.864A pdb=" N THR D 93 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 135 through 147 removed outlier: 3.628A pdb=" N GLY D 147 " --> pdb=" O ASP D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.757A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 186 removed outlier: 3.544A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.964A pdb=" N VAL D 226 " --> pdb=" O GLN D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 247 removed outlier: 4.067A pdb=" N ASN D 247 " --> pdb=" O SER D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 256 removed outlier: 3.913A pdb=" N VAL D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.683A pdb=" N ARG D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 removed outlier: 4.162A pdb=" N ILE D 290 " --> pdb=" O LEU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 306 removed outlier: 3.673A pdb=" N GLY D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.600A pdb=" N PHE D 311 " --> pdb=" O LYS D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 327 removed outlier: 3.556A pdb=" N LEU D 326 " --> pdb=" O TYR D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 378 through 413 removed outlier: 3.530A pdb=" N ARG D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 467 through 470 Processing helix chain 'D' and resid 471 through 492 removed outlier: 3.539A pdb=" N LEU D 475 " --> pdb=" O TYR D 471 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE D 476 " --> pdb=" O PHE D 472 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N LEU D 477 " --> pdb=" O GLU D 473 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR D 483 " --> pdb=" O GLN D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 3.872A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU D 501 " --> pdb=" O TYR D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 removed outlier: 4.055A pdb=" N GLY D 518 " --> pdb=" O TYR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 530 removed outlier: 3.786A pdb=" N TYR D 525 " --> pdb=" O HIS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 559 removed outlier: 3.589A pdb=" N LEU D 537 " --> pdb=" O ILE D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 602 Processing helix chain 'D' and resid 618 through 650 removed outlier: 3.632A pdb=" N VAL D 635 " --> pdb=" O LEU D 631 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASN D 650 " --> pdb=" O SER D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 672 removed outlier: 4.272A pdb=" N SER D 658 " --> pdb=" O ASP D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 719 removed outlier: 3.748A pdb=" N TRP D 715 " --> pdb=" O ASN D 711 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 330 through 335 removed outlier: 7.135A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 330 through 335 removed outlier: 7.135A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 330 through 335 removed outlier: 7.134A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 330 through 335 removed outlier: 7.107A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) 1059 hydrogen bonds defined for protein. 3045 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: 3.57 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6264 1.34 - 1.46: 4694 1.46 - 1.58: 9546 1.58 - 1.70: 0 1.70 - 1.81: 180 Bond restraints: 20684 Sorted by residual: bond pdb=" C12 P0T D 802 " pdb=" O02 P0T D 802 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.80e+00 bond pdb=" C12 P0T A1001 " pdb=" O02 P0T A1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.71e+00 bond pdb=" C12 P0T C1001 " pdb=" O02 P0T C1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.71e+00 bond pdb=" C12 P0T B1001 " pdb=" O02 P0T B1001 " ideal model delta sigma weight residual 1.352 1.403 -0.051 2.00e-02 2.50e+03 6.57e+00 bond pdb=" C15 P0T B1001 " pdb=" C18 P0T B1001 " ideal model delta sigma weight residual 1.503 1.554 -0.051 2.00e-02 2.50e+03 6.47e+00 ... (remaining 20679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 27185 2.19 - 4.38: 740 4.38 - 6.57: 74 6.57 - 8.76: 38 8.76 - 10.95: 7 Bond angle restraints: 28044 Sorted by residual: angle pdb=" CA VAL B 190 " pdb=" CB VAL B 190 " pdb=" CG1 VAL B 190 " ideal model delta sigma weight residual 110.40 117.27 -6.87 1.70e+00 3.46e-01 1.63e+01 angle pdb=" CA VAL A 190 " pdb=" CB VAL A 190 " pdb=" CG1 VAL A 190 " ideal model delta sigma weight residual 110.40 117.25 -6.85 1.70e+00 3.46e-01 1.62e+01 angle pdb=" CA VAL D 190 " pdb=" CB VAL D 190 " pdb=" CG1 VAL D 190 " ideal model delta sigma weight residual 110.40 117.21 -6.81 1.70e+00 3.46e-01 1.61e+01 angle pdb=" CA VAL C 190 " pdb=" CB VAL C 190 " pdb=" CG1 VAL C 190 " ideal model delta sigma weight residual 110.40 117.10 -6.70 1.70e+00 3.46e-01 1.56e+01 angle pdb=" CB MET C 404 " pdb=" CG MET C 404 " pdb=" SD MET C 404 " ideal model delta sigma weight residual 112.70 101.75 10.95 3.00e+00 1.11e-01 1.33e+01 ... (remaining 28039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.02: 11274 19.02 - 38.04: 749 38.04 - 57.05: 81 57.05 - 76.07: 16 76.07 - 95.09: 12 Dihedral angle restraints: 12132 sinusoidal: 4892 harmonic: 7240 Sorted by residual: dihedral pdb=" CA ALA C 480 " pdb=" C ALA C 480 " pdb=" N LEU C 481 " pdb=" CA LEU C 481 " ideal model delta harmonic sigma weight residual -180.00 -160.82 -19.18 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ALA D 480 " pdb=" C ALA D 480 " pdb=" N LEU D 481 " pdb=" CA LEU D 481 " ideal model delta harmonic sigma weight residual -180.00 -160.82 -19.18 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ALA B 480 " pdb=" C ALA B 480 " pdb=" N LEU B 481 " pdb=" CA LEU B 481 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 12129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2013 0.040 - 0.080: 871 0.080 - 0.120: 213 0.120 - 0.159: 39 0.159 - 0.199: 8 Chirality restraints: 3144 Sorted by residual: chirality pdb=" CB VAL B 190 " pdb=" CA VAL B 190 " pdb=" CG1 VAL B 190 " pdb=" CG2 VAL B 190 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" CB VAL D 190 " pdb=" CA VAL D 190 " pdb=" CG1 VAL D 190 " pdb=" CG2 VAL D 190 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CB VAL C 190 " pdb=" CA VAL C 190 " pdb=" CG1 VAL C 190 " pdb=" CG2 VAL C 190 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.40e-01 ... (remaining 3141 not shown) Planarity restraints: 3460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 484 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.83e+00 pdb=" C VAL D 484 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL D 484 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU D 485 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 484 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" C VAL B 484 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL B 484 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU B 485 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 484 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C VAL A 484 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL A 484 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 485 " 0.014 2.00e-02 2.50e+03 ... (remaining 3457 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4477 2.78 - 3.31: 18265 3.31 - 3.84: 31943 3.84 - 4.37: 35471 4.37 - 4.90: 63596 Nonbonded interactions: 153752 Sorted by model distance: nonbonded pdb=" OH TYR A 455 " pdb=" OE1 GLU A 473 " model vdw 2.247 3.040 nonbonded pdb=" NH2 ARG C 706 " pdb=" OE1 GLN D 40 " model vdw 2.323 3.120 nonbonded pdb=" NH2 ARG B 706 " pdb=" OE1 GLN C 40 " model vdw 2.324 3.120 nonbonded pdb=" NH2 ARG A 706 " pdb=" OE1 GLN B 40 " model vdw 2.325 3.120 nonbonded pdb=" OE1 GLN A 40 " pdb=" NH2 ARG D 706 " model vdw 2.329 3.120 ... (remaining 153747 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: 0.06 Found NCS groups: ncs_group { reference = (chain 'A' and resid 31 through 720) selection = (chain 'B' and resid 31 through 720) selection = (chain 'C' and resid 31 through 720) selection = (chain 'D' and resid 31 through 720) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 18.080 Find NCS groups from input model: 0.530 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: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 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 : 0.007 0.062 20684 Z= 0.279 Angle : 0.847 10.948 28044 Z= 0.429 Chirality : 0.046 0.199 3144 Planarity : 0.006 0.051 3460 Dihedral : 13.066 95.088 7444 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.43 (0.15), residues: 2428 helix: -0.34 (0.13), residues: 1420 sheet: -0.34 (0.66), residues: 68 loop : -1.86 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 706 TYR 0.027 0.002 TYR B 335 PHE 0.020 0.003 PHE C 394 TRP 0.019 0.002 TRP A 333 HIS 0.007 0.002 HIS D 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00651 / 0.28 (20684) covalent geometry : angle 0.84720 / 0.43 (28044) hydrogen bonds : bond 0.15885 / 10.62 ( 1059) hydrogen bonds : angle 5.21364 / 3.68 ( 3045) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.788 Fit side-chains REVERT: A 42 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6800 (mm-30) REVERT: A 529 ILE cc_start: 0.9180 (tp) cc_final: 0.8947 (tp) REVERT: B 42 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6794 (mm-30) REVERT: B 529 ILE cc_start: 0.9184 (tp) cc_final: 0.8948 (tp) REVERT: C 42 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6825 (mm-30) REVERT: C 529 ILE cc_start: 0.9196 (tp) cc_final: 0.8957 (tp) REVERT: D 42 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6839 (mm-30) REVERT: D 529 ILE cc_start: 0.9181 (tp) cc_final: 0.8949 (tp) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1284 time to fit residues: 37.0080 Evaluate side-chains 141 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.0770 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 0.9980 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 ASN A 370 HIS B 370 HIS C 370 HIS D 370 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.108459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.087289 restraints weight = 38857.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.090133 restraints weight = 22543.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.092049 restraints weight = 15835.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.093345 restraints weight = 12540.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.094212 restraints weight = 10673.227| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20684 Z= 0.129 Angle : 0.507 6.068 28044 Z= 0.256 Chirality : 0.035 0.115 3144 Planarity : 0.004 0.038 3460 Dihedral : 6.004 77.091 2740 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.74 % Allowed : 5.37 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.14 (0.17), residues: 2428 helix: 1.03 (0.14), residues: 1428 sheet: 0.04 (0.68), residues: 68 loop : -1.38 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 369 TYR 0.015 0.001 TYR A 98 PHE 0.007 0.001 PHE A 519 TRP 0.007 0.001 TRP A 333 HIS 0.005 0.001 HIS D 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (20684) covalent geometry : angle 0.50747 / 0.26 (28044) hydrogen bonds : bond 0.03719 / 2.46 ( 1059) hydrogen bonds : angle 3.37369 / 2.38 ( 3045) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.633 Fit side-chains REVERT: A 42 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6863 (mm-30) REVERT: A 529 ILE cc_start: 0.9159 (tp) cc_final: 0.8824 (tp) REVERT: B 42 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6858 (mm-30) REVERT: B 529 ILE cc_start: 0.9150 (tp) cc_final: 0.8810 (tp) REVERT: C 42 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6879 (mm-30) REVERT: C 529 ILE cc_start: 0.9129 (tp) cc_final: 0.8778 (tp) REVERT: D 42 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6882 (mm-30) REVERT: D 122 MET cc_start: 0.8779 (mtp) cc_final: 0.8567 (mtp) REVERT: D 529 ILE cc_start: 0.9155 (tp) cc_final: 0.8814 (tp) outliers start: 16 outliers final: 13 residues processed: 159 average time/residue: 0.1137 time to fit residues: 30.6792 Evaluate side-chains 163 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 648 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 0.0970 chunk 226 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 222 optimal weight: 0.0470 chunk 90 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 overall best weight: 0.9678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.109954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.088678 restraints weight = 38754.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.091633 restraints weight = 21949.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.093645 restraints weight = 15178.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.094952 restraints weight = 11874.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.095826 restraints weight = 10080.689| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20684 Z= 0.094 Angle : 0.439 6.409 28044 Z= 0.221 Chirality : 0.034 0.113 3144 Planarity : 0.003 0.035 3460 Dihedral : 5.431 75.785 2740 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.09 % Allowed : 7.96 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.84 (0.17), residues: 2428 helix: 1.70 (0.14), residues: 1432 sheet: 0.11 (0.67), residues: 68 loop : -1.27 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 369 TYR 0.019 0.001 TYR A 98 PHE 0.006 0.001 PHE D 551 TRP 0.006 0.001 TRP D 333 HIS 0.004 0.001 HIS D 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.09 (20684) covalent geometry : angle 0.43873 / 0.22 (28044) hydrogen bonds : bond 0.02990 / 1.97 ( 1059) hydrogen bonds : angle 3.03460 / 2.13 ( 3045) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.486 Fit side-chains REVERT: A 221 LYS cc_start: 0.8618 (tttt) cc_final: 0.8131 (tptt) REVERT: A 494 THR cc_start: 0.8905 (t) cc_final: 0.8667 (t) REVERT: A 529 ILE cc_start: 0.9118 (tp) cc_final: 0.8712 (tp) REVERT: A 640 MET cc_start: 0.7744 (tmm) cc_final: 0.7528 (tmm) REVERT: B 221 LYS cc_start: 0.8659 (tttt) cc_final: 0.8105 (tptt) REVERT: B 494 THR cc_start: 0.8917 (t) cc_final: 0.8667 (t) REVERT: B 529 ILE cc_start: 0.9114 (tp) cc_final: 0.8700 (tp) REVERT: B 640 MET cc_start: 0.7798 (tmm) cc_final: 0.7561 (tmm) REVERT: C 221 LYS cc_start: 0.8630 (tttt) cc_final: 0.8142 (tptt) REVERT: C 494 THR cc_start: 0.8899 (t) cc_final: 0.8660 (t) REVERT: C 529 ILE cc_start: 0.9124 (tp) cc_final: 0.8712 (tp) REVERT: D 221 LYS cc_start: 0.8652 (tttt) cc_final: 0.8160 (tptt) REVERT: D 494 THR cc_start: 0.8911 (t) cc_final: 0.8660 (t) REVERT: D 529 ILE cc_start: 0.9112 (tp) cc_final: 0.8774 (tt) REVERT: D 640 MET cc_start: 0.7792 (tmm) cc_final: 0.7551 (tmm) outliers start: 2 outliers final: 2 residues processed: 160 average time/residue: 0.1152 time to fit residues: 31.5014 Evaluate side-chains 157 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain D residue 152 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 43 optimal weight: 2.9990 chunk 234 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 205 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.108681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.087367 restraints weight = 38917.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.090280 restraints weight = 22290.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.092250 restraints weight = 15588.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.093560 restraints weight = 12299.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.094393 restraints weight = 10467.193| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20684 Z= 0.114 Angle : 0.452 6.002 28044 Z= 0.226 Chirality : 0.035 0.117 3144 Planarity : 0.003 0.034 3460 Dihedral : 5.309 76.016 2740 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.79 % Allowed : 9.63 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.12 (0.17), residues: 2428 helix: 1.94 (0.14), residues: 1432 sheet: 0.12 (0.66), residues: 68 loop : -1.17 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 369 TYR 0.017 0.001 TYR B 98 PHE 0.007 0.001 PHE D 519 TRP 0.006 0.001 TRP D 333 HIS 0.003 0.001 HIS D 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.11 (20684) covalent geometry : angle 0.45183 / 0.23 (28044) hydrogen bonds : bond 0.03073 / 2.03 ( 1059) hydrogen bonds : angle 2.98502 / 2.09 ( 3045) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.833 Fit side-chains REVERT: A 221 LYS cc_start: 0.8654 (tttt) cc_final: 0.8152 (tptt) REVERT: A 494 THR cc_start: 0.8903 (t) cc_final: 0.8648 (t) REVERT: A 503 LEU cc_start: 0.7941 (tp) cc_final: 0.7640 (tt) REVERT: A 640 MET cc_start: 0.7768 (tmm) cc_final: 0.7498 (tmm) REVERT: B 221 LYS cc_start: 0.8692 (tttt) cc_final: 0.8130 (tptt) REVERT: B 494 THR cc_start: 0.8900 (t) cc_final: 0.8650 (t) REVERT: B 503 LEU cc_start: 0.7950 (tp) cc_final: 0.7653 (tt) REVERT: B 640 MET cc_start: 0.7820 (tmm) cc_final: 0.7549 (tmm) REVERT: C 221 LYS cc_start: 0.8655 (tttt) cc_final: 0.8124 (tptt) REVERT: C 494 THR cc_start: 0.8884 (t) cc_final: 0.8643 (t) REVERT: C 503 LEU cc_start: 0.7961 (tp) cc_final: 0.7657 (tt) REVERT: D 221 LYS cc_start: 0.8684 (tttt) cc_final: 0.8154 (tptt) REVERT: D 494 THR cc_start: 0.8898 (t) cc_final: 0.8649 (t) REVERT: D 503 LEU cc_start: 0.7948 (tp) cc_final: 0.7653 (tt) REVERT: D 640 MET cc_start: 0.7821 (tmm) cc_final: 0.7551 (tmm) outliers start: 17 outliers final: 12 residues processed: 164 average time/residue: 0.1190 time to fit residues: 32.8708 Evaluate side-chains 164 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 483 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 48 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 194 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.105608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.084182 restraints weight = 39222.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.087008 restraints weight = 22605.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.088944 restraints weight = 15879.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.090226 restraints weight = 12543.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.091041 restraints weight = 10698.660| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20684 Z= 0.162 Angle : 0.513 6.673 28044 Z= 0.255 Chirality : 0.037 0.122 3144 Planarity : 0.003 0.032 3460 Dihedral : 5.411 76.782 2740 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.30 % Allowed : 10.05 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.11 (0.17), residues: 2428 helix: 1.91 (0.14), residues: 1432 sheet: 0.13 (0.66), residues: 68 loop : -1.14 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.019 0.002 TYR A 98 PHE 0.008 0.001 PHE B 519 TRP 0.007 0.001 TRP D 333 HIS 0.004 0.001 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (20684) covalent geometry : angle 0.51280 / 0.25 (28044) hydrogen bonds : bond 0.03527 / 2.33 ( 1059) hydrogen bonds : angle 3.12467 / 2.19 ( 3045) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.808 Fit side-chains REVERT: A 221 LYS cc_start: 0.8722 (tttt) cc_final: 0.8223 (tptt) REVERT: A 494 THR cc_start: 0.8900 (t) cc_final: 0.8641 (t) REVERT: A 640 MET cc_start: 0.7782 (tmm) cc_final: 0.7501 (tmm) REVERT: B 221 LYS cc_start: 0.8739 (tttt) cc_final: 0.8227 (tptt) REVERT: B 494 THR cc_start: 0.8885 (t) cc_final: 0.8637 (t) REVERT: B 640 MET cc_start: 0.7770 (tmm) cc_final: 0.7494 (tmm) REVERT: C 221 LYS cc_start: 0.8720 (tttt) cc_final: 0.8221 (tptt) REVERT: C 494 THR cc_start: 0.8898 (t) cc_final: 0.8635 (t) REVERT: D 221 LYS cc_start: 0.8742 (tttt) cc_final: 0.8242 (tptt) REVERT: D 494 THR cc_start: 0.8883 (t) cc_final: 0.8635 (t) REVERT: D 640 MET cc_start: 0.7827 (tmm) cc_final: 0.7538 (tmm) outliers start: 28 outliers final: 23 residues processed: 173 average time/residue: 0.1185 time to fit residues: 34.4922 Evaluate side-chains 170 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 648 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 29 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 166 optimal weight: 0.3980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.106941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.085680 restraints weight = 38474.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.088537 restraints weight = 21901.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.090415 restraints weight = 15301.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.091754 restraints weight = 12141.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.092533 restraints weight = 10301.235| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20684 Z= 0.116 Angle : 0.464 6.362 28044 Z= 0.230 Chirality : 0.035 0.118 3144 Planarity : 0.003 0.033 3460 Dihedral : 5.229 75.635 2740 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.11 % Allowed : 11.11 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.32 (0.18), residues: 2428 helix: 2.11 (0.14), residues: 1436 sheet: 0.10 (0.65), residues: 68 loop : -1.10 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 706 TYR 0.019 0.001 TYR A 98 PHE 0.009 0.001 PHE B 519 TRP 0.006 0.001 TRP D 333 HIS 0.003 0.001 HIS D 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (20684) covalent geometry : angle 0.46395 / 0.23 (28044) hydrogen bonds : bond 0.03098 / 2.04 ( 1059) hydrogen bonds : angle 2.98244 / 2.08 ( 3045) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.776 Fit side-chains REVERT: A 221 LYS cc_start: 0.8678 (tttt) cc_final: 0.8195 (tptt) REVERT: A 494 THR cc_start: 0.8844 (t) cc_final: 0.8585 (t) REVERT: A 640 MET cc_start: 0.7828 (tmm) cc_final: 0.7519 (tmm) REVERT: B 221 LYS cc_start: 0.8687 (tttt) cc_final: 0.8170 (tptt) REVERT: B 494 THR cc_start: 0.8863 (t) cc_final: 0.8598 (t) REVERT: B 640 MET cc_start: 0.7836 (tmm) cc_final: 0.7533 (tmm) REVERT: C 221 LYS cc_start: 0.8681 (tttt) cc_final: 0.8192 (tptt) REVERT: C 494 THR cc_start: 0.8844 (t) cc_final: 0.8583 (t) REVERT: D 221 LYS cc_start: 0.8700 (tttt) cc_final: 0.8213 (tptt) REVERT: D 494 THR cc_start: 0.8863 (t) cc_final: 0.8600 (t) REVERT: D 640 MET cc_start: 0.7838 (tmm) cc_final: 0.7533 (tmm) outliers start: 24 outliers final: 23 residues processed: 174 average time/residue: 0.1183 time to fit residues: 34.8063 Evaluate side-chains 175 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 648 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 133 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 211 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.104166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.082743 restraints weight = 39302.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.085516 restraints weight = 22728.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.087344 restraints weight = 16061.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.088599 restraints weight = 12860.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.089471 restraints weight = 10998.408| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 20684 Z= 0.206 Angle : 0.562 6.299 28044 Z= 0.277 Chirality : 0.038 0.126 3144 Planarity : 0.003 0.030 3460 Dihedral : 5.429 76.731 2740 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.76 % Allowed : 11.30 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.13 (0.17), residues: 2428 helix: 1.92 (0.14), residues: 1432 sheet: 0.08 (0.65), residues: 68 loop : -1.11 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 706 TYR 0.019 0.002 TYR A 98 PHE 0.011 0.002 PHE B 519 TRP 0.008 0.001 TRP D 333 HIS 0.005 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 (20684) covalent geometry : angle 0.56212 / 0.28 (28044) hydrogen bonds : bond 0.03728 / 2.46 ( 1059) hydrogen bonds : angle 3.21607 / 2.25 ( 3045) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 221 LYS cc_start: 0.8767 (tttt) cc_final: 0.8300 (tptt) REVERT: A 494 THR cc_start: 0.8911 (t) cc_final: 0.8642 (t) REVERT: A 640 MET cc_start: 0.7777 (tmm) cc_final: 0.7573 (tmm) REVERT: B 221 LYS cc_start: 0.8745 (tttt) cc_final: 0.8236 (tptt) REVERT: B 494 THR cc_start: 0.8915 (t) cc_final: 0.8645 (t) REVERT: B 640 MET cc_start: 0.7783 (tmm) cc_final: 0.7580 (tmm) REVERT: C 221 LYS cc_start: 0.8762 (tttt) cc_final: 0.8305 (tptt) REVERT: C 494 THR cc_start: 0.8909 (t) cc_final: 0.8639 (t) REVERT: D 221 LYS cc_start: 0.8771 (tttt) cc_final: 0.8263 (tptt) REVERT: D 494 THR cc_start: 0.8913 (t) cc_final: 0.8643 (t) outliers start: 38 outliers final: 34 residues processed: 180 average time/residue: 0.1092 time to fit residues: 33.3187 Evaluate side-chains 178 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 648 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 177 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 chunk 181 optimal weight: 0.0470 chunk 97 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 171 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 chunk 178 optimal weight: 0.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.108417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.087333 restraints weight = 38593.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.090204 restraints weight = 21975.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.092143 restraints weight = 15337.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.093435 restraints weight = 12099.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.094254 restraints weight = 10293.860| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20684 Z= 0.090 Angle : 0.444 8.028 28044 Z= 0.220 Chirality : 0.034 0.116 3144 Planarity : 0.003 0.031 3460 Dihedral : 5.062 74.284 2740 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.48 % Allowed : 12.13 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.57 (0.18), residues: 2428 helix: 2.32 (0.14), residues: 1440 sheet: 0.15 (0.63), residues: 68 loop : -1.05 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 706 TYR 0.020 0.001 TYR D 98 PHE 0.009 0.001 PHE D 519 TRP 0.005 0.001 TRP A 509 HIS 0.002 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 (20684) covalent geometry : angle 0.44420 / 0.22 (28044) hydrogen bonds : bond 0.02764 / 1.82 ( 1059) hydrogen bonds : angle 2.90941 / 2.03 ( 3045) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.847 Fit side-chains REVERT: A 221 LYS cc_start: 0.8640 (tttt) cc_final: 0.8137 (tptt) REVERT: A 494 THR cc_start: 0.8826 (t) cc_final: 0.8572 (t) REVERT: A 640 MET cc_start: 0.7821 (tmm) cc_final: 0.7492 (tmm) REVERT: B 221 LYS cc_start: 0.8635 (tttt) cc_final: 0.8136 (tptt) REVERT: B 494 THR cc_start: 0.8824 (t) cc_final: 0.8578 (t) REVERT: B 640 MET cc_start: 0.7826 (tmm) cc_final: 0.7522 (tmm) REVERT: C 221 LYS cc_start: 0.8631 (tttt) cc_final: 0.8127 (tptt) REVERT: C 494 THR cc_start: 0.8824 (t) cc_final: 0.8568 (t) REVERT: D 221 LYS cc_start: 0.8662 (tttt) cc_final: 0.8142 (tptt) REVERT: D 494 THR cc_start: 0.8824 (t) cc_final: 0.8578 (t) outliers start: 32 outliers final: 32 residues processed: 185 average time/residue: 0.1281 time to fit residues: 39.9365 Evaluate side-chains 184 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 710 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 90 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 chunk 190 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.101415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.080109 restraints weight = 39843.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.082754 restraints weight = 23307.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.084582 restraints weight = 16640.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.085756 restraints weight = 13248.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.086507 restraints weight = 11419.894| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 20684 Z= 0.326 Angle : 0.716 10.417 28044 Z= 0.346 Chirality : 0.042 0.135 3144 Planarity : 0.004 0.038 3460 Dihedral : 5.646 76.971 2740 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.76 % Allowed : 11.90 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.82 (0.17), residues: 2428 helix: 1.64 (0.14), residues: 1432 sheet: 0.12 (0.65), residues: 68 loop : -1.20 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 369 TYR 0.025 0.003 TYR C 105 PHE 0.015 0.003 PHE C 394 TRP 0.010 0.001 TRP D 333 HIS 0.007 0.002 HIS B 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00789 / 0.33 (20684) covalent geometry : angle 0.71588 / 0.35 (28044) hydrogen bonds : bond 0.04420 / 2.92 ( 1059) hydrogen bonds : angle 3.57230 / 2.50 ( 3045) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 491 PHE cc_start: 0.7337 (m-80) cc_final: 0.6905 (m-10) REVERT: A 494 THR cc_start: 0.8936 (t) cc_final: 0.8678 (t) REVERT: B 221 LYS cc_start: 0.8827 (tttt) cc_final: 0.8342 (tptt) REVERT: B 491 PHE cc_start: 0.7356 (m-80) cc_final: 0.6915 (m-10) REVERT: B 494 THR cc_start: 0.8925 (t) cc_final: 0.8679 (t) REVERT: C 491 PHE cc_start: 0.7349 (m-80) cc_final: 0.6915 (m-10) REVERT: C 494 THR cc_start: 0.8928 (t) cc_final: 0.8676 (t) REVERT: D 491 PHE cc_start: 0.7355 (m-80) cc_final: 0.6917 (m-10) REVERT: D 494 THR cc_start: 0.8917 (t) cc_final: 0.8681 (t) outliers start: 38 outliers final: 38 residues processed: 170 average time/residue: 0.1253 time to fit residues: 36.0342 Evaluate side-chains 172 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 648 THR Chi-restraints excluded: chain D residue 710 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 166 optimal weight: 0.0000 chunk 100 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 220 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 GLN B 487 GLN D 487 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.108139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.087110 restraints weight = 38629.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.089938 restraints weight = 21922.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.091886 restraints weight = 15345.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.093172 restraints weight = 12079.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.093987 restraints weight = 10253.428| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20684 Z= 0.092 Angle : 0.467 8.468 28044 Z= 0.230 Chirality : 0.034 0.120 3144 Planarity : 0.003 0.033 3460 Dihedral : 5.137 74.157 2740 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.44 % Allowed : 12.22 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.49 (0.18), residues: 2428 helix: 2.27 (0.14), residues: 1440 sheet: 0.06 (0.62), residues: 68 loop : -1.09 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 280 TYR 0.021 0.001 TYR D 98 PHE 0.008 0.001 PHE C 519 TRP 0.009 0.001 TRP A 509 HIS 0.003 0.001 HIS B 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.09 (20684) covalent geometry : angle 0.46675 / 0.23 (28044) hydrogen bonds : bond 0.02814 / 1.86 ( 1059) hydrogen bonds : angle 2.98382 / 2.08 ( 3045) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.746 Fit side-chains REVERT: A 491 PHE cc_start: 0.7321 (m-80) cc_final: 0.6885 (m-10) REVERT: A 494 THR cc_start: 0.8838 (t) cc_final: 0.8593 (t) REVERT: B 221 LYS cc_start: 0.8619 (tttt) cc_final: 0.8217 (tptt) REVERT: B 491 PHE cc_start: 0.7319 (m-80) cc_final: 0.6885 (m-10) REVERT: B 494 THR cc_start: 0.8848 (t) cc_final: 0.8595 (t) REVERT: C 277 MET cc_start: 0.8612 (mtp) cc_final: 0.8274 (tpp) REVERT: C 491 PHE cc_start: 0.7336 (m-80) cc_final: 0.6899 (m-10) REVERT: C 494 THR cc_start: 0.8837 (t) cc_final: 0.8590 (t) REVERT: D 491 PHE cc_start: 0.7315 (m-80) cc_final: 0.6879 (m-10) REVERT: D 494 THR cc_start: 0.8877 (t) cc_final: 0.8641 (t) outliers start: 31 outliers final: 31 residues processed: 175 average time/residue: 0.1274 time to fit residues: 37.7047 Evaluate side-chains 177 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 710 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 71 optimal weight: 0.2980 chunk 92 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 221 optimal weight: 0.8980 chunk 217 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 199 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.106937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.085954 restraints weight = 38718.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.088785 restraints weight = 22105.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.090691 restraints weight = 15477.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.091954 restraints weight = 12209.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.092764 restraints weight = 10415.897| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20684 Z= 0.113 Angle : 0.478 6.994 28044 Z= 0.234 Chirality : 0.035 0.121 3144 Planarity : 0.003 0.031 3460 Dihedral : 5.037 73.715 2740 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.48 % Allowed : 12.22 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.64 (0.18), residues: 2428 helix: 2.39 (0.14), residues: 1432 sheet: 0.10 (0.63), residues: 68 loop : -1.00 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 706 TYR 0.021 0.001 TYR A 98 PHE 0.011 0.001 PHE C 519 TRP 0.006 0.001 TRP D 333 HIS 0.003 0.001 HIS D 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 (20684) covalent geometry : angle 0.47799 / 0.23 (28044) hydrogen bonds : bond 0.03018 / 2.00 ( 1059) hydrogen bonds : angle 2.95250 / 2.06 ( 3045) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2547.68 seconds wall clock time: 45 minutes 16.00 seconds (2716.00 seconds total)