Starting phenix.real_space_refine on Thu Mar 5 07:20:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t37_25650/03_2026/7t37_25650.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t37_25650/03_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_25650/03_2026/7t37_25650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t37_25650/03_2026/7t37_25650.map" model { file = "/net/cci-nas-00/data/ceres_data/7t37_25650/03_2026/7t37_25650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t37_25650/03_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-5986/lib/python3.9/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: 4.21, per 1000 atoms: 0.21 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: 1.34 Conformation dependent library (CDL) restraints added in 929.7 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: 0.46 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: 3.07 Time building geometry restraints manager: 1.83 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: 11310 19.02 - 38.04: 769 38.04 - 57.05: 97 57.05 - 76.07: 16 76.07 - 95.09: 12 Dihedral angle restraints: 12204 sinusoidal: 4964 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 12201 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: 0.03 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: 1.120 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.050 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 13.204 95.088 7516 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 covalent geometry : bond 0.00651 (20684) covalent geometry : angle 0.84720 (28044) hydrogen bonds : bond 0.15885 ( 1059) hydrogen bonds : angle 5.21364 ( 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 : 0.790 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: 0.1179 time to fit residues: 34.2110 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 : 0.707 ------------------------------------------------------------------------------- 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: 0.0030 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: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3469 r_free = 0.3469 target = 0.108543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.087391 restraints weight = 38852.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.090233 restraints weight = 22465.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.092146 restraints weight = 15793.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.093255 restraints weight = 12510.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.094225 restraints weight = 10760.163| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20684 Z= 0.129 Angle : 0.506 6.073 28044 Z= 0.256 Chirality : 0.035 0.114 3144 Planarity : 0.004 0.037 3460 Dihedral : 6.381 76.609 2812 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.74 % Allowed : 5.09 % Favored : 94.17 % 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: 0.17 (0.17), residues: 2428 helix: 1.06 (0.14), residues: 1428 sheet: 0.06 (0.68), residues: 68 loop : -1.37 (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 covalent geometry : bond 0.00308 (20684) covalent geometry : angle 0.50567 (28044) hydrogen bonds : bond 0.03687 ( 1059) hydrogen bonds : angle 3.35171 ( 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 : 0.734 Fit side-chains REVERT: A 42 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6861 (mm-30) REVERT: A 529 ILE cc_start: 0.9168 (tp) cc_final: 0.8834 (tp) REVERT: B 42 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6856 (mm-30) REVERT: B 529 ILE cc_start: 0.9159 (tp) cc_final: 0.8818 (tp) REVERT: C 42 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6850 (mm-30) REVERT: C 529 ILE cc_start: 0.9142 (tp) cc_final: 0.8791 (tp) REVERT: D 42 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6852 (mm-30) REVERT: D 529 ILE cc_start: 0.9164 (tp) cc_final: 0.8823 (tp) outliers start: 16 outliers final: 13 residues processed: 159 average time/residue: 0.1095 time to fit residues: 29.6170 Evaluate side-chains 162 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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: 3.9990 chunk 226 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 222 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.106868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.085547 restraints weight = 39208.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.088425 restraints weight = 22320.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.090370 restraints weight = 15553.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.091679 restraints weight = 12243.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.092556 restraints weight = 10401.440| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20684 Z= 0.140 Angle : 0.493 5.969 28044 Z= 0.247 Chirality : 0.036 0.119 3144 Planarity : 0.003 0.034 3460 Dihedral : 5.927 76.628 2812 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.60 % Allowed : 7.92 % Favored : 91.48 % 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: 0.68 (0.17), residues: 2428 helix: 1.55 (0.14), residues: 1432 sheet: 0.10 (0.68), residues: 68 loop : -1.29 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 369 TYR 0.018 0.001 TYR A 98 PHE 0.007 0.001 PHE C 519 TRP 0.008 0.001 TRP D 333 HIS 0.004 0.001 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00338 (20684) covalent geometry : angle 0.49283 (28044) hydrogen bonds : bond 0.03479 ( 1059) hydrogen bonds : angle 3.15407 ( 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 164 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.574 Fit side-chains REVERT: A 494 THR cc_start: 0.8928 (t) cc_final: 0.8683 (t) REVERT: A 503 LEU cc_start: 0.8052 (tp) cc_final: 0.7754 (tt) REVERT: A 640 MET cc_start: 0.7758 (tmm) cc_final: 0.7540 (tmm) REVERT: B 221 LYS cc_start: 0.8688 (tttt) cc_final: 0.8149 (tptt) REVERT: B 494 THR cc_start: 0.8907 (t) cc_final: 0.8666 (t) REVERT: B 503 LEU cc_start: 0.7992 (tp) cc_final: 0.7694 (tt) REVERT: C 494 THR cc_start: 0.8870 (t) cc_final: 0.8617 (t) REVERT: C 503 LEU cc_start: 0.8032 (tp) cc_final: 0.7733 (tt) REVERT: D 494 THR cc_start: 0.8908 (t) cc_final: 0.8664 (t) REVERT: D 503 LEU cc_start: 0.8018 (tp) cc_final: 0.7724 (tt) REVERT: D 640 MET cc_start: 0.7746 (tmm) cc_final: 0.7525 (tmm) outliers start: 13 outliers final: 12 residues processed: 159 average time/residue: 0.1226 time to fit residues: 33.4130 Evaluate side-chains 158 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 43 optimal weight: 8.9990 chunk 234 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 78 optimal weight: 0.0270 chunk 123 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.104650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.083358 restraints weight = 39327.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.086156 restraints weight = 22580.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.088041 restraints weight = 15862.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.089294 restraints weight = 12571.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.090120 restraints weight = 10753.579| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1488 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= 0.185 Angle : 0.544 6.094 28044 Z= 0.270 Chirality : 0.037 0.124 3144 Planarity : 0.003 0.031 3460 Dihedral : 6.069 77.750 2812 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.25 % Allowed : 9.54 % Favored : 89.21 % 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: 0.75 (0.17), residues: 2428 helix: 1.59 (0.14), residues: 1432 sheet: -0.83 (0.57), residues: 88 loop : -1.15 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 369 TYR 0.018 0.002 TYR A 98 PHE 0.009 0.002 PHE C 612 TRP 0.008 0.001 TRP D 333 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00447 (20684) covalent geometry : angle 0.54367 (28044) hydrogen bonds : bond 0.03747 ( 1059) hydrogen bonds : angle 3.25001 ( 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 173 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.7771 (m-80) cc_final: 0.7526 (m-80) REVERT: A 494 THR cc_start: 0.8903 (t) cc_final: 0.8650 (t) REVERT: A 640 MET cc_start: 0.7781 (tmm) cc_final: 0.7534 (tmm) REVERT: B 221 LYS cc_start: 0.8756 (tttt) cc_final: 0.8183 (tptt) REVERT: B 494 THR cc_start: 0.8908 (t) cc_final: 0.8649 (t) REVERT: C 494 THR cc_start: 0.8900 (t) cc_final: 0.8642 (t) REVERT: D 494 THR cc_start: 0.8902 (t) cc_final: 0.8650 (t) REVERT: D 640 MET cc_start: 0.7762 (tmm) cc_final: 0.7519 (tmm) outliers start: 27 outliers final: 16 residues processed: 166 average time/residue: 0.1081 time to fit residues: 30.6419 Evaluate side-chains 161 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 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 483 THR 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 648 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 Chi-restraints excluded: chain D residue 648 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 48 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 17 optimal weight: 0.0970 chunk 231 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 105 optimal weight: 0.0270 chunk 82 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.107577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.086366 restraints weight = 38783.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.089237 restraints weight = 22197.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.091164 restraints weight = 15524.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.092486 restraints weight = 12267.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.093301 restraints weight = 10433.243| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1629 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= 0.104 Angle : 0.455 6.063 28044 Z= 0.226 Chirality : 0.035 0.117 3144 Planarity : 0.003 0.032 3460 Dihedral : 5.739 76.103 2812 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.79 % Allowed : 11.53 % Favored : 87.69 % 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: 1.17 (0.18), residues: 2428 helix: 1.98 (0.14), residues: 1432 sheet: 0.07 (0.65), residues: 68 loop : -1.14 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 369 TYR 0.019 0.001 TYR B 98 PHE 0.008 0.001 PHE D 519 TRP 0.005 0.001 TRP D 333 HIS 0.002 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00246 (20684) covalent geometry : angle 0.45511 (28044) hydrogen bonds : bond 0.03009 ( 1059) hydrogen bonds : angle 3.00023 ( 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 171 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.722 Fit side-chains REVERT: A 221 LYS cc_start: 0.8691 (tttt) cc_final: 0.8198 (tptt) REVERT: A 494 THR cc_start: 0.8841 (t) cc_final: 0.8584 (t) REVERT: A 640 MET cc_start: 0.7835 (tmm) cc_final: 0.7532 (tmm) REVERT: B 221 LYS cc_start: 0.8679 (tttt) cc_final: 0.8169 (tptt) REVERT: B 494 THR cc_start: 0.8845 (t) cc_final: 0.8587 (t) REVERT: C 494 THR cc_start: 0.8844 (t) cc_final: 0.8587 (t) REVERT: D 221 LYS cc_start: 0.8740 (tttt) cc_final: 0.8269 (tptt) REVERT: D 494 THR cc_start: 0.8846 (t) cc_final: 0.8589 (t) REVERT: D 640 MET cc_start: 0.7848 (tmm) cc_final: 0.7549 (tmm) outliers start: 17 outliers final: 16 residues processed: 167 average time/residue: 0.1169 time to fit residues: 33.0997 Evaluate side-chains 168 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 29 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 223 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 0.0470 chunk 120 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.106697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.085415 restraints weight = 38644.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.088286 restraints weight = 22018.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.090234 restraints weight = 15407.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.091553 restraints weight = 12155.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.092361 restraints weight = 10336.102| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20684 Z= 0.128 Angle : 0.474 6.259 28044 Z= 0.236 Chirality : 0.036 0.119 3144 Planarity : 0.003 0.032 3460 Dihedral : 5.715 76.022 2812 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.11 % Allowed : 12.55 % 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: 1.33 (0.18), residues: 2428 helix: 2.11 (0.14), residues: 1432 sheet: 0.05 (0.65), residues: 68 loop : -1.07 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 706 TYR 0.019 0.001 TYR B 98 PHE 0.009 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 covalent geometry : bond 0.00308 (20684) covalent geometry : angle 0.47372 (28044) hydrogen bonds : bond 0.03180 ( 1059) hydrogen bonds : angle 3.00463 ( 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 175 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.577 Fit side-chains REVERT: A 221 LYS cc_start: 0.8705 (tttt) cc_final: 0.8237 (tptt) REVERT: A 494 THR cc_start: 0.8841 (t) cc_final: 0.8582 (t) REVERT: A 640 MET cc_start: 0.7802 (tmm) cc_final: 0.7493 (tmm) REVERT: B 221 LYS cc_start: 0.8698 (tttt) cc_final: 0.8204 (tptt) REVERT: B 494 THR cc_start: 0.8862 (t) cc_final: 0.8596 (t) REVERT: C 494 THR cc_start: 0.8853 (t) cc_final: 0.8589 (t) REVERT: D 221 LYS cc_start: 0.8740 (tttt) cc_final: 0.8243 (tptt) REVERT: D 494 THR cc_start: 0.8858 (t) cc_final: 0.8586 (t) REVERT: D 640 MET cc_start: 0.7869 (tmm) cc_final: 0.7559 (tmm) outliers start: 24 outliers final: 24 residues processed: 171 average time/residue: 0.1117 time to fit residues: 32.0944 Evaluate side-chains 173 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 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 533 ILE 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 533 ILE 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 533 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 133 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 211 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 140 optimal weight: 0.0020 overall best weight: 2.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.104583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.083321 restraints weight = 39000.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.086128 restraints weight = 22394.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.088017 restraints weight = 15716.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.089239 restraints weight = 12454.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.090104 restraints weight = 10669.551| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20684 Z= 0.172 Angle : 0.529 7.668 28044 Z= 0.261 Chirality : 0.037 0.123 3144 Planarity : 0.003 0.030 3460 Dihedral : 5.868 76.150 2812 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.94 % Allowed : 12.18 % Favored : 85.88 % 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: 1.22 (0.17), residues: 2428 helix: 2.01 (0.14), residues: 1432 sheet: 0.03 (0.65), residues: 68 loop : -1.10 (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 B 98 PHE 0.009 0.001 PHE D 519 TRP 0.007 0.001 TRP D 333 HIS 0.004 0.001 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00416 (20684) covalent geometry : angle 0.52865 (28044) hydrogen bonds : bond 0.03557 ( 1059) hydrogen bonds : angle 3.14757 ( 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 190 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 494 THR cc_start: 0.8904 (t) cc_final: 0.8638 (t) REVERT: A 640 MET cc_start: 0.7806 (tmm) cc_final: 0.7498 (tmm) REVERT: B 221 LYS cc_start: 0.8746 (tttt) cc_final: 0.8233 (tptt) REVERT: B 494 THR cc_start: 0.8915 (t) cc_final: 0.8643 (t) REVERT: C 494 THR cc_start: 0.8903 (t) cc_final: 0.8636 (t) REVERT: D 494 THR cc_start: 0.8903 (t) cc_final: 0.8639 (t) REVERT: D 640 MET cc_start: 0.7836 (tmm) cc_final: 0.7512 (tmm) outliers start: 42 outliers final: 37 residues processed: 186 average time/residue: 0.1240 time to fit residues: 39.3870 Evaluate side-chains 182 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 177 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 200 optimal weight: 0.0870 chunk 181 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.108512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.087455 restraints weight = 38647.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.090344 restraints weight = 21984.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.092277 restraints weight = 15356.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.093571 restraints weight = 12113.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.094406 restraints weight = 10303.749| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20684 Z= 0.093 Angle : 0.448 8.066 28044 Z= 0.221 Chirality : 0.034 0.115 3144 Planarity : 0.003 0.032 3460 Dihedral : 5.487 73.794 2812 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.57 % Allowed : 12.50 % Favored : 85.93 % 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: 0.11 (0.63), residues: 68 loop : -1.03 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 706 TYR 0.021 0.001 TYR D 98 PHE 0.009 0.001 PHE B 519 TRP 0.006 0.001 TRP C 509 HIS 0.002 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00219 (20684) covalent geometry : angle 0.44837 (28044) hydrogen bonds : bond 0.02781 ( 1059) hydrogen bonds : angle 2.91240 ( 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: 34 poor density : 155 time to evaluate : 0.829 Fit side-chains REVERT: A 221 LYS cc_start: 0.8647 (tttt) cc_final: 0.8151 (tptt) REVERT: A 494 THR cc_start: 0.8820 (t) cc_final: 0.8576 (t) REVERT: A 640 MET cc_start: 0.7852 (tmm) cc_final: 0.7527 (tmm) REVERT: B 221 LYS cc_start: 0.8646 (tttt) cc_final: 0.8151 (tptt) REVERT: B 494 THR cc_start: 0.8826 (t) cc_final: 0.8571 (t) REVERT: B 528 MET cc_start: 0.7373 (ttm) cc_final: 0.7157 (mtt) REVERT: C 494 THR cc_start: 0.8820 (t) cc_final: 0.8577 (t) REVERT: C 528 MET cc_start: 0.7355 (ttm) cc_final: 0.7152 (mtt) REVERT: D 221 LYS cc_start: 0.8682 (tttt) cc_final: 0.8182 (tptt) REVERT: D 494 THR cc_start: 0.8831 (t) cc_final: 0.8580 (t) REVERT: D 640 MET cc_start: 0.7860 (tmm) cc_final: 0.7545 (tmm) outliers start: 34 outliers final: 33 residues processed: 185 average time/residue: 0.1167 time to fit residues: 36.7207 Evaluate side-chains 184 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 118 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.101114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.079754 restraints weight = 39985.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.082382 restraints weight = 23493.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.084159 restraints weight = 16835.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.085255 restraints weight = 13475.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.086130 restraints weight = 11662.231| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.061 20684 Z= 0.353 Angle : 0.751 10.629 28044 Z= 0.361 Chirality : 0.043 0.140 3144 Planarity : 0.004 0.040 3460 Dihedral : 6.337 77.952 2812 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.71 % Allowed : 12.92 % Favored : 85.37 % 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: 0.71 (0.17), residues: 2428 helix: 1.55 (0.14), residues: 1432 sheet: 0.02 (0.65), residues: 68 loop : -1.23 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 369 TYR 0.031 0.003 TYR C 105 PHE 0.018 0.003 PHE A 394 TRP 0.011 0.002 TRP D 333 HIS 0.008 0.002 HIS A 683 Details of bonding type rmsd covalent geometry : bond 0.00855 (20684) covalent geometry : angle 0.75105 (28044) hydrogen bonds : bond 0.04575 ( 1059) hydrogen bonds : angle 3.67639 ( 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 176 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 491 PHE cc_start: 0.7341 (m-80) cc_final: 0.6869 (m-10) REVERT: A 494 THR cc_start: 0.8950 (t) cc_final: 0.8687 (t) REVERT: A 640 MET cc_start: 0.7839 (tmm) cc_final: 0.7634 (tmm) REVERT: B 491 PHE cc_start: 0.7346 (m-80) cc_final: 0.6872 (m-10) REVERT: B 494 THR cc_start: 0.8945 (t) cc_final: 0.8694 (t) REVERT: C 491 PHE cc_start: 0.7349 (m-80) cc_final: 0.6874 (m-10) REVERT: C 494 THR cc_start: 0.8949 (t) cc_final: 0.8688 (t) REVERT: D 491 PHE cc_start: 0.7346 (m-80) cc_final: 0.6874 (m-10) REVERT: D 494 THR cc_start: 0.8945 (t) cc_final: 0.8695 (t) REVERT: D 640 MET cc_start: 0.7835 (tmm) cc_final: 0.7633 (tmm) outliers start: 37 outliers final: 36 residues processed: 172 average time/residue: 0.1139 time to fit residues: 34.0462 Evaluate side-chains 171 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 100 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 220 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.106966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.085614 restraints weight = 38549.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.088579 restraints weight = 21124.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.090586 restraints weight = 14453.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.091889 restraints weight = 11266.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.092780 restraints weight = 9528.532| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20684 Z= 0.099 Angle : 0.475 8.914 28044 Z= 0.236 Chirality : 0.035 0.113 3144 Planarity : 0.003 0.030 3460 Dihedral : 5.674 74.546 2812 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.48 % Allowed : 13.24 % Favored : 85.28 % 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 (0.18), residues: 2428 helix: 2.24 (0.14), residues: 1436 sheet: -0.12 (0.62), residues: 68 loop : -1.13 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 706 TYR 0.021 0.001 TYR C 98 PHE 0.009 0.001 PHE B 519 TRP 0.009 0.001 TRP B 509 HIS 0.003 0.001 HIS B 370 Details of bonding type rmsd covalent geometry : bond 0.00230 (20684) covalent geometry : angle 0.47478 (28044) hydrogen bonds : bond 0.02953 ( 1059) hydrogen bonds : angle 3.05277 ( 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 178 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.692 Fit side-chains REVERT: A 491 PHE cc_start: 0.7341 (m-80) cc_final: 0.6861 (m-10) REVERT: A 494 THR cc_start: 0.8900 (t) cc_final: 0.8660 (t) REVERT: A 640 MET cc_start: 0.7860 (tmm) cc_final: 0.7512 (tmm) REVERT: B 491 PHE cc_start: 0.7340 (m-80) cc_final: 0.6860 (m-10) REVERT: B 494 THR cc_start: 0.8907 (t) cc_final: 0.8667 (t) REVERT: C 491 PHE cc_start: 0.7341 (m-80) cc_final: 0.6862 (m-10) REVERT: C 494 THR cc_start: 0.8902 (t) cc_final: 0.8660 (t) REVERT: D 491 PHE cc_start: 0.7343 (m-80) cc_final: 0.6860 (m-10) REVERT: D 494 THR cc_start: 0.8898 (t) cc_final: 0.8658 (t) REVERT: D 640 MET cc_start: 0.7845 (tmm) cc_final: 0.7508 (tmm) outliers start: 32 outliers final: 32 residues processed: 174 average time/residue: 0.1167 time to fit residues: 35.0946 Evaluate side-chains 176 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 488 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 71 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 221 optimal weight: 0.7980 chunk 217 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 230 optimal weight: 2.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.105477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.084135 restraints weight = 38906.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.086968 restraints weight = 22300.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.088892 restraints weight = 15622.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.090145 restraints weight = 12310.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.090975 restraints weight = 10534.142| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20684 Z= 0.147 Angle : 0.513 7.950 28044 Z= 0.252 Chirality : 0.036 0.121 3144 Planarity : 0.003 0.030 3460 Dihedral : 5.705 75.155 2812 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.53 % Allowed : 13.10 % Favored : 85.37 % 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: 1.46 (0.18), residues: 2428 helix: 2.23 (0.14), residues: 1432 sheet: -0.12 (0.61), residues: 68 loop : -1.03 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 706 TYR 0.021 0.001 TYR C 98 PHE 0.013 0.001 PHE A 519 TRP 0.007 0.001 TRP D 333 HIS 0.003 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00357 (20684) covalent geometry : angle 0.51314 (28044) hydrogen bonds : bond 0.03307 ( 1059) hydrogen bonds : angle 3.08949 ( 3045) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2506.29 seconds wall clock time: 44 minutes 28.41 seconds (2668.41 seconds total)