Starting phenix.real_space_refine on Fri Mar 6 21:36:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rlf_24528/03_2026/7rlf_24528.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rlf_24528/03_2026/7rlf_24528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rlf_24528/03_2026/7rlf_24528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rlf_24528/03_2026/7rlf_24528.map" model { file = "/net/cci-nas-00/data/ceres_data/7rlf_24528/03_2026/7rlf_24528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rlf_24528/03_2026/7rlf_24528.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 192 5.16 5 C 21630 2.51 5 N 6090 2.21 5 O 6618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s 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: 34578 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5699 Classifications: {'peptide': 728} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} Chain breaks: 1 Chain: "B" Number of atoms: 5699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5699 Classifications: {'peptide': 728} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} Chain breaks: 1 Chain: "C" Number of atoms: 5699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5699 Classifications: {'peptide': 728} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} Chain breaks: 1 Chain: "D" Number of atoms: 5699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5699 Classifications: {'peptide': 728} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} Chain breaks: 1 Chain: "E" Number of atoms: 5699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5699 Classifications: {'peptide': 728} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} Chain breaks: 1 Chain: "F" Number of atoms: 5699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5699 Classifications: {'peptide': 728} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.43, per 1000 atoms: 0.21 Number of scatterers: 34578 At special positions: 0 Unit cell: (169.113, 175.338, 98.5625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 192 16.00 P 36 15.00 Mg 12 11.99 O 6618 8.00 N 6090 7.00 C 21630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.4 seconds 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8148 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 24 sheets defined 48.6% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 removed outlier: 3.825A pdb=" N MET A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 90 removed outlier: 4.058A pdb=" N ASN A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.855A pdb=" N LEU A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 210 through 226 removed outlier: 4.993A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 234 Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 305 through 310 removed outlier: 4.137A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 334 removed outlier: 3.608A pdb=" N ARG A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 339 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.694A pdb=" N ARG A 359 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 386 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.582A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.029A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.794A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.823A pdb=" N ARG A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 584 removed outlier: 3.982A pdb=" N ILE A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 610 removed outlier: 3.929A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 707 Processing helix chain 'A' and resid 732 through 742 removed outlier: 3.603A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 761 Processing helix chain 'B' and resid 42 through 49 removed outlier: 3.824A pdb=" N MET B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 90 removed outlier: 4.057A pdb=" N ASN B 90 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 135 through 140 removed outlier: 3.854A pdb=" N LEU B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 210 through 226 removed outlier: 4.992A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 234 Processing helix chain 'B' and resid 250 through 261 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 281 through 296 Processing helix chain 'B' and resid 305 through 310 removed outlier: 4.137A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 334 removed outlier: 3.606A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 339 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.695A pdb=" N ARG B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.582A pdb=" N MET B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 removed outlier: 4.028A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.793A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 536 Processing helix chain 'B' and resid 544 through 552 Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.824A pdb=" N ARG B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 584 removed outlier: 3.982A pdb=" N ILE B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 610 removed outlier: 3.928A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 707 Processing helix chain 'B' and resid 732 through 742 removed outlier: 3.603A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 761 Processing helix chain 'C' and resid 42 through 49 removed outlier: 3.824A pdb=" N MET C 46 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP C 47 " --> pdb=" O GLN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 removed outlier: 4.058A pdb=" N ASN C 90 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 135 through 140 removed outlier: 3.854A pdb=" N LEU C 140 " --> pdb=" O LYS C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 210 through 226 removed outlier: 4.993A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 234 Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 305 through 310 removed outlier: 4.137A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 334 removed outlier: 3.607A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 339 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.693A pdb=" N ARG C 359 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 386 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 407 through 425 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.581A pdb=" N MET C 442 " --> pdb=" O ASP C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 removed outlier: 4.029A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.795A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 536 Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.823A pdb=" N ARG C 560 " --> pdb=" O GLU C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 584 removed outlier: 3.982A pdb=" N ILE C 582 " --> pdb=" O GLU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 610 removed outlier: 3.929A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 707 Processing helix chain 'C' and resid 732 through 742 removed outlier: 3.603A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 761 Processing helix chain 'D' and resid 42 through 49 removed outlier: 3.824A pdb=" N MET D 46 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP D 47 " --> pdb=" O GLN D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 90 removed outlier: 4.058A pdb=" N ASN D 90 " --> pdb=" O ARG D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 135 Processing helix chain 'D' and resid 135 through 140 removed outlier: 3.854A pdb=" N LEU D 140 " --> pdb=" O LYS D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 210 through 226 removed outlier: 4.993A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 234 Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 281 through 296 Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.138A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 334 removed outlier: 3.607A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 339 Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.693A pdb=" N ARG D 359 " --> pdb=" O ALA D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 386 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 407 through 425 Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.583A pdb=" N MET D 442 " --> pdb=" O ASP D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 499 removed outlier: 4.028A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.794A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 536 Processing helix chain 'D' and resid 544 through 552 Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.823A pdb=" N ARG D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 584 removed outlier: 3.982A pdb=" N ILE D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 610 removed outlier: 3.929A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 707 Processing helix chain 'D' and resid 732 through 742 removed outlier: 3.603A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 761 Processing helix chain 'E' and resid 42 through 49 removed outlier: 3.824A pdb=" N MET E 46 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 90 removed outlier: 4.058A pdb=" N ASN E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 135 through 140 removed outlier: 3.854A pdb=" N LEU E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 210 through 226 removed outlier: 4.993A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 234 Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 281 through 296 Processing helix chain 'E' and resid 305 through 310 removed outlier: 4.136A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 334 removed outlier: 3.606A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 339 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.694A pdb=" N ARG E 359 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 386 Processing helix chain 'E' and resid 395 through 403 Processing helix chain 'E' and resid 407 through 425 Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.582A pdb=" N MET E 442 " --> pdb=" O ASP E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 458 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 499 removed outlier: 4.029A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 507 removed outlier: 3.794A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 536 Processing helix chain 'E' and resid 544 through 552 Processing helix chain 'E' and resid 556 through 569 removed outlier: 3.824A pdb=" N ARG E 560 " --> pdb=" O GLU E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 584 removed outlier: 3.982A pdb=" N ILE E 582 " --> pdb=" O GLU E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 610 removed outlier: 3.929A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 Processing helix chain 'E' and resid 649 through 661 Processing helix chain 'E' and resid 671 through 679 Processing helix chain 'E' and resid 683 through 707 Processing helix chain 'E' and resid 732 through 742 removed outlier: 3.602A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 761 Processing helix chain 'F' and resid 42 through 49 removed outlier: 3.824A pdb=" N MET F 46 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 90 removed outlier: 4.058A pdb=" N ASN F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 135 Processing helix chain 'F' and resid 135 through 140 removed outlier: 3.854A pdb=" N LEU F 140 " --> pdb=" O LYS F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 210 through 226 removed outlier: 4.993A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 234 Processing helix chain 'F' and resid 250 through 261 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 281 through 296 Processing helix chain 'F' and resid 305 through 310 removed outlier: 4.137A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 334 removed outlier: 3.607A pdb=" N ARG F 322 " --> pdb=" O GLY F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 339 Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 354 through 359 removed outlier: 3.694A pdb=" N ARG F 359 " --> pdb=" O ALA F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 386 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 407 through 425 Processing helix chain 'F' and resid 438 through 443 removed outlier: 3.582A pdb=" N MET F 442 " --> pdb=" O ASP F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 removed outlier: 4.030A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 507 removed outlier: 3.794A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 536 Processing helix chain 'F' and resid 544 through 552 Processing helix chain 'F' and resid 556 through 569 removed outlier: 3.823A pdb=" N ARG F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 584 removed outlier: 3.982A pdb=" N ILE F 582 " --> pdb=" O GLU F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 610 removed outlier: 3.928A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 Processing helix chain 'F' and resid 649 through 661 Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 707 Processing helix chain 'F' and resid 732 through 742 removed outlier: 3.603A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 118 removed outlier: 6.838A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.294A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 543 removed outlier: 6.558A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 27 Processing sheet with id=AA6, first strand: chain 'B' and resid 114 through 118 removed outlier: 6.837A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.294A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 538 through 543 removed outlier: 6.558A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 25 through 27 Processing sheet with id=AB1, first strand: chain 'C' and resid 114 through 118 removed outlier: 6.837A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.294A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 538 through 543 removed outlier: 6.558A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 25 through 27 Processing sheet with id=AB5, first strand: chain 'D' and resid 114 through 118 removed outlier: 6.838A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.293A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 538 through 543 removed outlier: 6.558A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 25 through 27 Processing sheet with id=AB9, first strand: chain 'E' and resid 114 through 118 removed outlier: 6.838A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.294A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 538 through 543 removed outlier: 6.558A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 25 through 27 Processing sheet with id=AC4, first strand: chain 'F' and resid 114 through 118 removed outlier: 6.838A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.293A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 538 through 543 removed outlier: 6.559A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) 1464 hydrogen bonds defined for protein. 4176 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: 7.01 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 11947 1.37 - 1.51: 9625 1.51 - 1.66: 13276 1.66 - 1.80: 211 1.80 - 1.95: 89 Bond restraints: 35148 Sorted by residual: bond pdb=" CD ARG A 225 " pdb=" NE ARG A 225 " ideal model delta sigma weight residual 1.458 1.481 -0.023 1.40e-02 5.10e+03 2.62e+00 bond pdb=" CD ARG D 113 " pdb=" NE ARG D 113 " ideal model delta sigma weight residual 1.458 1.481 -0.023 1.40e-02 5.10e+03 2.60e+00 bond pdb=" CD ARG E 225 " pdb=" NE ARG E 225 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.58e+00 bond pdb=" CD ARG C 225 " pdb=" NE ARG C 225 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.55e+00 bond pdb=" CD ARG F 113 " pdb=" NE ARG F 113 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.50e+00 ... (remaining 35143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 46288 1.50 - 3.01: 1014 3.01 - 4.51: 187 4.51 - 6.01: 49 6.01 - 7.52: 12 Bond angle restraints: 47550 Sorted by residual: angle pdb=" N ASP D 121 " pdb=" CA ASP D 121 " pdb=" C ASP D 121 " ideal model delta sigma weight residual 114.56 108.72 5.84 1.27e+00 6.20e-01 2.12e+01 angle pdb=" N ASP A 121 " pdb=" CA ASP A 121 " pdb=" C ASP A 121 " ideal model delta sigma weight residual 114.56 108.72 5.84 1.27e+00 6.20e-01 2.12e+01 angle pdb=" N ASP E 121 " pdb=" CA ASP E 121 " pdb=" C ASP E 121 " ideal model delta sigma weight residual 114.56 108.72 5.84 1.27e+00 6.20e-01 2.11e+01 angle pdb=" N ASP B 121 " pdb=" CA ASP B 121 " pdb=" C ASP B 121 " ideal model delta sigma weight residual 114.56 108.75 5.81 1.27e+00 6.20e-01 2.10e+01 angle pdb=" N ASP F 121 " pdb=" CA ASP F 121 " pdb=" C ASP F 121 " ideal model delta sigma weight residual 114.56 108.75 5.81 1.27e+00 6.20e-01 2.10e+01 ... (remaining 47545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.22: 19289 16.22 - 32.45: 1751 32.45 - 48.67: 530 48.67 - 64.89: 198 64.89 - 81.12: 60 Dihedral angle restraints: 21828 sinusoidal: 9258 harmonic: 12570 Sorted by residual: dihedral pdb=" CA ALA E 297 " pdb=" C ALA E 297 " pdb=" N PRO E 298 " pdb=" CA PRO E 298 " ideal model delta harmonic sigma weight residual 180.00 162.11 17.89 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ALA D 297 " pdb=" C ALA D 297 " pdb=" N PRO D 298 " pdb=" CA PRO D 298 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ALA B 297 " pdb=" C ALA B 297 " pdb=" N PRO B 298 " pdb=" CA PRO B 298 " ideal model delta harmonic sigma weight residual 180.00 162.13 17.87 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 21825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2908 0.026 - 0.052: 1408 0.052 - 0.078: 556 0.078 - 0.104: 341 0.104 - 0.130: 151 Chirality restraints: 5364 Sorted by residual: chirality pdb=" CA ILE A 371 " pdb=" N ILE A 371 " pdb=" C ILE A 371 " pdb=" CB ILE A 371 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE C 371 " pdb=" N ILE C 371 " pdb=" C ILE C 371 " pdb=" CB ILE C 371 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ILE B 371 " pdb=" N ILE B 371 " pdb=" C ILE B 371 " pdb=" CB ILE B 371 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 5361 not shown) Planarity restraints: 6234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 297 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO A 298 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 298 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 298 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 297 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO B 298 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 298 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 298 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 297 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO D 298 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 298 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 298 " -0.030 5.00e-02 4.00e+02 ... (remaining 6231 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 445 2.61 - 3.18: 30553 3.18 - 3.76: 55294 3.76 - 4.33: 75297 4.33 - 4.90: 122098 Nonbonded interactions: 283687 Sorted by model distance: nonbonded pdb=" OG1 THR A 525 " pdb="MG MG A 904 " model vdw 2.042 2.170 nonbonded pdb=" OG1 THR C 525 " pdb="MG MG C 904 " model vdw 2.042 2.170 nonbonded pdb=" OG1 THR B 525 " pdb="MG MG B 904 " model vdw 2.043 2.170 nonbonded pdb=" OG1 THR F 525 " pdb="MG MG F 904 " model vdw 2.043 2.170 nonbonded pdb=" OG1 THR E 525 " pdb="MG MG E 904 " model vdw 2.043 2.170 ... (remaining 283682 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 30.700 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.090 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 : 0.011 0.890 35154 Z= 1.042 Angle : 0.577 7.519 47550 Z= 0.322 Chirality : 0.043 0.130 5364 Planarity : 0.004 0.055 6234 Dihedral : 15.176 81.118 13680 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.87 % Favored : 95.86 % Rotamer: Outliers : 0.19 % Allowed : 14.11 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.50 (0.14), residues: 4344 helix: 1.20 (0.13), residues: 1854 sheet: 0.28 (0.21), residues: 636 loop : -0.48 (0.16), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 766 TYR 0.012 0.001 TYR E 138 PHE 0.009 0.001 PHE F 736 TRP 0.008 0.001 TRP E 551 HIS 0.005 0.001 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00355 (35148) covalent geometry : angle 0.57728 (47550) hydrogen bonds : bond 0.18224 ( 1464) hydrogen bonds : angle 5.89656 ( 4176) Misc. bond : bond 0.78784 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 229 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.6033 (tpt) cc_final: 0.5826 (tpt) REVERT: A 230 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8534 (t80) REVERT: A 236 LYS cc_start: 0.8824 (mmmt) cc_final: 0.8604 (mmtm) REVERT: B 84 MET cc_start: 0.5722 (tpt) cc_final: 0.5401 (tpt) REVERT: B 344 MET cc_start: 0.8851 (mtp) cc_final: 0.8548 (ttm) REVERT: B 420 LEU cc_start: 0.8813 (mt) cc_final: 0.8570 (mt) REVERT: B 449 MET cc_start: 0.8843 (tpt) cc_final: 0.7984 (tpp) REVERT: C 84 MET cc_start: 0.5027 (tpt) cc_final: 0.4813 (tpt) REVERT: C 158 MET cc_start: 0.9254 (ttm) cc_final: 0.9030 (ttp) REVERT: D 84 MET cc_start: 0.6025 (tpt) cc_final: 0.5780 (tpt) REVERT: D 230 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8527 (t80) REVERT: E 84 MET cc_start: 0.6091 (tpt) cc_final: 0.5777 (tpt) REVERT: F 608 MET cc_start: 0.9050 (mtm) cc_final: 0.8778 (mtp) outliers start: 7 outliers final: 4 residues processed: 236 average time/residue: 0.2135 time to fit residues: 83.0277 Evaluate side-chains 174 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 168 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain E residue 230 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 0.0570 chunk 424 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 overall best weight: 2.8106 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.114099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.069304 restraints weight = 69015.544| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.16 r_work: 0.2691 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 35154 Z= 0.236 Angle : 0.624 8.054 47550 Z= 0.319 Chirality : 0.046 0.150 5364 Planarity : 0.005 0.065 6234 Dihedral : 8.518 59.832 4992 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.45 % Favored : 96.27 % Rotamer: Outliers : 1.70 % Allowed : 13.00 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.41 (0.14), residues: 4344 helix: 1.13 (0.13), residues: 1836 sheet: -0.22 (0.19), residues: 684 loop : -0.30 (0.17), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 83 TYR 0.011 0.002 TYR D 138 PHE 0.014 0.002 PHE D 506 TRP 0.011 0.002 TRP A 551 HIS 0.005 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00567 (35148) covalent geometry : angle 0.62366 (47550) hydrogen bonds : bond 0.04530 ( 1464) hydrogen bonds : angle 4.70175 ( 4176) Misc. bond : bond 0.00360 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 179 time to evaluate : 1.339 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.6794 (tpt) cc_final: 0.6216 (tpt) REVERT: A 230 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8433 (t80) REVERT: B 84 MET cc_start: 0.6713 (tpt) cc_final: 0.6369 (tpt) REVERT: B 161 VAL cc_start: 0.7599 (m) cc_final: 0.7315 (m) REVERT: D 84 MET cc_start: 0.6763 (tpt) cc_final: 0.6280 (tpt) REVERT: D 146 ILE cc_start: 0.8325 (mp) cc_final: 0.7974 (mp) REVERT: D 230 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8456 (t80) REVERT: E 84 MET cc_start: 0.6818 (tpt) cc_final: 0.6439 (tpt) REVERT: E 152 PHE cc_start: 0.8479 (p90) cc_final: 0.7845 (p90) outliers start: 63 outliers final: 18 residues processed: 233 average time/residue: 0.1916 time to fit residues: 78.0985 Evaluate side-chains 181 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 230 PHE Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 20 optimal weight: 3.9990 chunk 399 optimal weight: 0.9990 chunk 331 optimal weight: 0.9990 chunk 268 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 378 optimal weight: 0.5980 chunk 27 optimal weight: 0.0870 chunk 263 optimal weight: 0.6980 chunk 415 optimal weight: 0.7980 chunk 327 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.116342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.071848 restraints weight = 69084.052| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.22 r_work: 0.2749 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35154 Z= 0.109 Angle : 0.523 8.031 47550 Z= 0.267 Chirality : 0.042 0.166 5364 Planarity : 0.004 0.057 6234 Dihedral : 7.953 57.919 4988 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.50 % Favored : 96.22 % Rotamer: Outliers : 1.67 % Allowed : 12.95 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.59 (0.14), residues: 4344 helix: 1.29 (0.13), residues: 1836 sheet: -0.26 (0.20), residues: 666 loop : -0.16 (0.17), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 766 TYR 0.011 0.001 TYR D 138 PHE 0.022 0.001 PHE A 152 TRP 0.007 0.001 TRP F 551 HIS 0.002 0.001 HIS D 317 Details of bonding type rmsd covalent geometry : bond 0.00256 (35148) covalent geometry : angle 0.52299 (47550) hydrogen bonds : bond 0.03700 ( 1464) hydrogen bonds : angle 4.32302 ( 4176) Misc. bond : bond 0.00144 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 178 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.6975 (tpt) cc_final: 0.6475 (tpt) REVERT: A 146 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.7953 (mp) REVERT: A 230 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8534 (t80) REVERT: B 84 MET cc_start: 0.6733 (tpt) cc_final: 0.6445 (tpt) REVERT: B 230 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8674 (m-80) REVERT: B 420 LEU cc_start: 0.9014 (mt) cc_final: 0.8766 (mt) REVERT: B 630 ASP cc_start: 0.8697 (p0) cc_final: 0.8482 (p0) REVERT: C 427 MET cc_start: 0.7748 (ppp) cc_final: 0.6711 (ppp) REVERT: D 84 MET cc_start: 0.6858 (tpt) cc_final: 0.6581 (tpt) REVERT: D 230 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8559 (t80) REVERT: E 60 LYS cc_start: 0.8316 (tptt) cc_final: 0.8098 (tptt) REVERT: E 84 MET cc_start: 0.7057 (tpt) cc_final: 0.6764 (tpt) REVERT: E 152 PHE cc_start: 0.8559 (p90) cc_final: 0.7975 (p90) REVERT: E 230 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8655 (m-80) REVERT: E 427 MET cc_start: 0.7346 (ppp) cc_final: 0.6606 (ppp) REVERT: F 153 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8438 (tm) REVERT: F 427 MET cc_start: 0.7587 (ppp) cc_final: 0.6611 (ppp) outliers start: 62 outliers final: 23 residues processed: 231 average time/residue: 0.2018 time to fit residues: 79.9692 Evaluate side-chains 193 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 230 PHE Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 192 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 380 optimal weight: 5.9990 chunk 311 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 371 optimal weight: 20.0000 chunk 356 optimal weight: 0.9980 chunk 313 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS B 115 HIS D 285 ASN E 285 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.113667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.068401 restraints weight = 69635.919| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.23 r_work: 0.2676 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 35154 Z= 0.216 Angle : 0.579 7.551 47550 Z= 0.294 Chirality : 0.045 0.189 5364 Planarity : 0.005 0.055 6234 Dihedral : 8.110 59.785 4988 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.27 % Favored : 96.45 % Rotamer: Outliers : 2.48 % Allowed : 12.36 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.14), residues: 4344 helix: 1.28 (0.13), residues: 1842 sheet: -0.15 (0.19), residues: 672 loop : -0.28 (0.16), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 766 TYR 0.009 0.001 TYR E 138 PHE 0.015 0.002 PHE F 506 TRP 0.009 0.002 TRP E 551 HIS 0.004 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00524 (35148) covalent geometry : angle 0.57889 (47550) hydrogen bonds : bond 0.04125 ( 1464) hydrogen bonds : angle 4.27742 ( 4176) Misc. bond : bond 0.00141 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 172 time to evaluate : 1.724 Fit side-chains REVERT: A 84 MET cc_start: 0.7024 (tpt) cc_final: 0.6678 (tpt) REVERT: A 230 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8560 (t80) REVERT: B 60 LYS cc_start: 0.8365 (tptt) cc_final: 0.8093 (mtmm) REVERT: B 84 MET cc_start: 0.6785 (tpt) cc_final: 0.6561 (tpt) REVERT: B 630 ASP cc_start: 0.8711 (p0) cc_final: 0.8476 (p0) REVERT: C 66 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7435 (mm-30) REVERT: C 427 MET cc_start: 0.7743 (ppp) cc_final: 0.6746 (ppp) REVERT: D 84 MET cc_start: 0.6523 (tpt) cc_final: 0.6100 (tpt) REVERT: D 230 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8555 (t80) REVERT: E 84 MET cc_start: 0.7027 (tpt) cc_final: 0.6793 (tpt) REVERT: E 152 PHE cc_start: 0.8413 (p90) cc_final: 0.7857 (p90) REVERT: E 427 MET cc_start: 0.7359 (ppp) cc_final: 0.6625 (ppp) REVERT: F 153 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8334 (tm) outliers start: 92 outliers final: 38 residues processed: 251 average time/residue: 0.1876 time to fit residues: 83.5456 Evaluate side-chains 204 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 230 PHE Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 230 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 273 optimal weight: 20.0000 chunk 166 optimal weight: 0.7980 chunk 373 optimal weight: 10.0000 chunk 299 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 343 optimal weight: 1.9990 chunk 318 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 ASN B 327 GLN D 115 HIS E 327 GLN F 285 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.114024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.068943 restraints weight = 69282.739| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.14 r_work: 0.2682 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35154 Z= 0.184 Angle : 0.558 7.570 47550 Z= 0.284 Chirality : 0.044 0.183 5364 Planarity : 0.004 0.064 6234 Dihedral : 7.887 58.016 4986 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.38 % Favored : 96.34 % Rotamer: Outliers : 1.51 % Allowed : 12.84 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.62 (0.14), residues: 4344 helix: 1.33 (0.13), residues: 1842 sheet: -0.10 (0.20), residues: 654 loop : -0.23 (0.16), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 766 TYR 0.012 0.001 TYR D 138 PHE 0.014 0.002 PHE A 152 TRP 0.009 0.002 TRP E 551 HIS 0.004 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00443 (35148) covalent geometry : angle 0.55831 (47550) hydrogen bonds : bond 0.03802 ( 1464) hydrogen bonds : angle 4.15559 ( 4176) Misc. bond : bond 0.00124 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 162 time to evaluate : 1.497 Fit side-chains REVERT: A 84 MET cc_start: 0.6537 (tpt) cc_final: 0.6128 (tpt) REVERT: A 230 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8488 (t80) REVERT: B 84 MET cc_start: 0.6960 (tpt) cc_final: 0.6557 (tpt) REVERT: B 427 MET cc_start: 0.7491 (ppp) cc_final: 0.6700 (ppp) REVERT: B 630 ASP cc_start: 0.8675 (p0) cc_final: 0.8445 (p0) REVERT: C 66 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7473 (mm-30) REVERT: C 427 MET cc_start: 0.7711 (ppp) cc_final: 0.6744 (ppp) REVERT: D 84 MET cc_start: 0.6537 (tpt) cc_final: 0.6122 (tpt) REVERT: D 230 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8520 (t80) REVERT: D 427 MET cc_start: 0.7570 (ppp) cc_final: 0.6822 (ppp) REVERT: E 84 MET cc_start: 0.7081 (tpt) cc_final: 0.6696 (tpt) REVERT: E 152 PHE cc_start: 0.8452 (p90) cc_final: 0.8008 (p90) REVERT: E 427 MET cc_start: 0.7321 (ppp) cc_final: 0.6605 (ppp) REVERT: F 153 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8381 (tm) REVERT: F 427 MET cc_start: 0.7654 (ppp) cc_final: 0.6720 (ppp) outliers start: 56 outliers final: 38 residues processed: 210 average time/residue: 0.1864 time to fit residues: 69.7127 Evaluate side-chains 199 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 10 optimal weight: 0.1980 chunk 55 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 313 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 159 optimal weight: 20.0000 chunk 418 optimal weight: 0.9990 chunk 258 optimal weight: 9.9990 chunk 409 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.114406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.069703 restraints weight = 69105.087| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 3.17 r_work: 0.2705 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 35154 Z= 0.127 Angle : 0.526 7.912 47550 Z= 0.267 Chirality : 0.043 0.155 5364 Planarity : 0.004 0.055 6234 Dihedral : 7.607 58.649 4986 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.82 % Favored : 96.02 % Rotamer: Outliers : 1.48 % Allowed : 13.25 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.73 (0.14), residues: 4344 helix: 1.43 (0.13), residues: 1842 sheet: -0.07 (0.20), residues: 654 loop : -0.17 (0.16), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 766 TYR 0.009 0.001 TYR D 138 PHE 0.017 0.001 PHE D 131 TRP 0.007 0.001 TRP E 551 HIS 0.003 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00310 (35148) covalent geometry : angle 0.52558 (47550) hydrogen bonds : bond 0.03427 ( 1464) hydrogen bonds : angle 4.03362 ( 4176) Misc. bond : bond 0.00109 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 163 time to evaluate : 1.520 Fit side-chains REVERT: A 84 MET cc_start: 0.6524 (tpt) cc_final: 0.6185 (tpt) REVERT: A 230 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8524 (t80) REVERT: A 427 MET cc_start: 0.7473 (ppp) cc_final: 0.6665 (ppp) REVERT: B 84 MET cc_start: 0.6881 (tpt) cc_final: 0.6583 (tpt) REVERT: B 427 MET cc_start: 0.7446 (ppp) cc_final: 0.6698 (ppp) REVERT: B 630 ASP cc_start: 0.8583 (p0) cc_final: 0.8360 (p0) REVERT: C 427 MET cc_start: 0.7702 (ppp) cc_final: 0.6766 (ppp) REVERT: C 473 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8701 (mm-40) REVERT: D 84 MET cc_start: 0.6474 (tpt) cc_final: 0.6165 (tpt) REVERT: D 230 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8564 (t80) REVERT: D 427 MET cc_start: 0.7552 (ppp) cc_final: 0.6790 (ppp) REVERT: E 84 MET cc_start: 0.6808 (tpt) cc_final: 0.6528 (tpt) REVERT: E 152 PHE cc_start: 0.8464 (p90) cc_final: 0.8065 (p90) REVERT: E 427 MET cc_start: 0.7270 (ppp) cc_final: 0.6576 (ppp) REVERT: F 153 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8405 (tm) REVERT: F 427 MET cc_start: 0.7629 (ppp) cc_final: 0.6744 (ppp) outliers start: 55 outliers final: 37 residues processed: 210 average time/residue: 0.1875 time to fit residues: 70.3848 Evaluate side-chains 196 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 410 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 383 optimal weight: 0.7980 chunk 347 optimal weight: 6.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.113781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.068843 restraints weight = 69260.054| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 3.08 r_work: 0.2670 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35154 Z= 0.183 Angle : 0.559 9.040 47550 Z= 0.282 Chirality : 0.044 0.154 5364 Planarity : 0.004 0.055 6234 Dihedral : 7.636 58.981 4986 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.59 % Favored : 96.27 % Rotamer: Outliers : 1.40 % Allowed : 13.57 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.72 (0.14), residues: 4344 helix: 1.42 (0.13), residues: 1842 sheet: -0.06 (0.20), residues: 654 loop : -0.18 (0.16), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 766 TYR 0.011 0.001 TYR E 138 PHE 0.025 0.002 PHE D 152 TRP 0.008 0.002 TRP E 551 HIS 0.004 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00444 (35148) covalent geometry : angle 0.55902 (47550) hydrogen bonds : bond 0.03705 ( 1464) hydrogen bonds : angle 4.03085 ( 4176) Misc. bond : bond 0.00101 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 160 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.8467 (t80) REVERT: B 84 MET cc_start: 0.6944 (tpt) cc_final: 0.6672 (tpt) REVERT: B 152 PHE cc_start: 0.8464 (p90) cc_final: 0.8252 (p90) REVERT: B 427 MET cc_start: 0.7486 (ppp) cc_final: 0.6733 (ppp) REVERT: B 630 ASP cc_start: 0.8669 (p0) cc_final: 0.8431 (p0) REVERT: C 66 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7463 (mm-30) REVERT: C 427 MET cc_start: 0.7701 (ppp) cc_final: 0.6788 (ppp) REVERT: D 84 MET cc_start: 0.6798 (tpt) cc_final: 0.6445 (tpt) REVERT: D 159 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7753 (ptm-80) REVERT: D 230 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8555 (t80) REVERT: D 427 MET cc_start: 0.7575 (ppp) cc_final: 0.6870 (ppp) REVERT: E 84 MET cc_start: 0.6918 (tpt) cc_final: 0.6609 (tpt) REVERT: E 152 PHE cc_start: 0.8527 (p90) cc_final: 0.8158 (p90) REVERT: E 427 MET cc_start: 0.7269 (ppp) cc_final: 0.6594 (ppp) REVERT: F 153 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8443 (tm) REVERT: F 427 MET cc_start: 0.7618 (ppp) cc_final: 0.6757 (ppp) REVERT: F 608 MET cc_start: 0.9215 (mtm) cc_final: 0.8831 (mtm) outliers start: 52 outliers final: 39 residues processed: 206 average time/residue: 0.2004 time to fit residues: 72.1887 Evaluate side-chains 199 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 346 optimal weight: 1.9990 chunk 226 optimal weight: 20.0000 chunk 284 optimal weight: 0.9980 chunk 322 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 315 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 96 optimal weight: 0.4980 chunk 232 optimal weight: 0.0980 chunk 78 optimal weight: 9.9990 chunk 252 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.114559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.070061 restraints weight = 69453.858| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.05 r_work: 0.2690 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35154 Z= 0.143 Angle : 0.535 13.310 47550 Z= 0.270 Chirality : 0.043 0.142 5364 Planarity : 0.004 0.055 6234 Dihedral : 7.453 59.571 4986 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.91 % Favored : 95.95 % Rotamer: Outliers : 1.43 % Allowed : 13.95 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.14), residues: 4344 helix: 1.47 (0.13), residues: 1842 sheet: -0.07 (0.20), residues: 654 loop : -0.16 (0.16), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 766 TYR 0.009 0.001 TYR E 138 PHE 0.022 0.001 PHE D 152 TRP 0.007 0.002 TRP E 551 HIS 0.003 0.001 HIS E 384 Details of bonding type rmsd covalent geometry : bond 0.00348 (35148) covalent geometry : angle 0.53526 (47550) hydrogen bonds : bond 0.03424 ( 1464) hydrogen bonds : angle 3.96831 ( 4176) Misc. bond : bond 0.00067 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 159 time to evaluate : 1.375 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.6475 (tpt) cc_final: 0.6049 (tpt) REVERT: A 115 HIS cc_start: 0.6791 (t70) cc_final: 0.6450 (t-90) REVERT: A 427 MET cc_start: 0.7489 (ppp) cc_final: 0.6718 (ppp) REVERT: B 84 MET cc_start: 0.6609 (tpt) cc_final: 0.6392 (tpt) REVERT: B 114 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8374 (mp) REVERT: B 427 MET cc_start: 0.7436 (ppp) cc_final: 0.6715 (ppp) REVERT: B 630 ASP cc_start: 0.8620 (p0) cc_final: 0.8375 (p0) REVERT: C 66 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7413 (mm-30) REVERT: C 427 MET cc_start: 0.7523 (ppp) cc_final: 0.6647 (ppp) REVERT: C 473 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8645 (mm-40) REVERT: D 84 MET cc_start: 0.6526 (tpt) cc_final: 0.6219 (tpt) REVERT: D 230 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8413 (t80) REVERT: D 427 MET cc_start: 0.7581 (ppp) cc_final: 0.6904 (ppp) REVERT: E 84 MET cc_start: 0.6563 (tpt) cc_final: 0.6348 (tpt) REVERT: E 152 PHE cc_start: 0.8439 (p90) cc_final: 0.8084 (p90) REVERT: E 427 MET cc_start: 0.7213 (ppp) cc_final: 0.6558 (ppp) REVERT: F 153 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8421 (tm) REVERT: F 427 MET cc_start: 0.7525 (ppp) cc_final: 0.6677 (ppp) REVERT: F 608 MET cc_start: 0.9219 (mtm) cc_final: 0.8847 (mtm) outliers start: 53 outliers final: 40 residues processed: 207 average time/residue: 0.1882 time to fit residues: 68.2128 Evaluate side-chains 198 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 153 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 304 optimal weight: 7.9990 chunk 164 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 84 optimal weight: 20.0000 chunk 255 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 297 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 376 optimal weight: 40.0000 chunk 187 optimal weight: 0.5980 chunk 158 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.113551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.068781 restraints weight = 68987.727| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.23 r_work: 0.2686 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 35154 Z= 0.154 Angle : 0.541 11.818 47550 Z= 0.272 Chirality : 0.043 0.143 5364 Planarity : 0.004 0.055 6234 Dihedral : 7.410 58.264 4986 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.78 % Favored : 96.09 % Rotamer: Outliers : 1.21 % Allowed : 14.03 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.79 (0.14), residues: 4344 helix: 1.53 (0.13), residues: 1836 sheet: -0.08 (0.20), residues: 654 loop : -0.18 (0.16), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 766 TYR 0.011 0.001 TYR E 138 PHE 0.033 0.001 PHE B 152 TRP 0.008 0.002 TRP E 551 HIS 0.003 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00376 (35148) covalent geometry : angle 0.54118 (47550) hydrogen bonds : bond 0.03486 ( 1464) hydrogen bonds : angle 3.94824 ( 4176) Misc. bond : bond 0.00079 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 153 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: A 427 MET cc_start: 0.7447 (ppp) cc_final: 0.6675 (ppp) REVERT: B 427 MET cc_start: 0.7517 (ppp) cc_final: 0.6793 (ppp) REVERT: B 630 ASP cc_start: 0.8646 (p0) cc_final: 0.8394 (p0) REVERT: C 66 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7412 (mm-30) REVERT: C 427 MET cc_start: 0.7682 (ppp) cc_final: 0.6779 (ppp) REVERT: D 84 MET cc_start: 0.6765 (tpt) cc_final: 0.6502 (tpt) REVERT: D 230 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8394 (t80) REVERT: D 427 MET cc_start: 0.7575 (ppp) cc_final: 0.6906 (ppp) REVERT: D 442 MET cc_start: 0.9067 (tpt) cc_final: 0.8795 (tpp) REVERT: E 152 PHE cc_start: 0.8437 (p90) cc_final: 0.8114 (p90) REVERT: E 427 MET cc_start: 0.7282 (ppp) cc_final: 0.6616 (ppp) REVERT: F 153 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8438 (tm) REVERT: F 427 MET cc_start: 0.7631 (ppp) cc_final: 0.6771 (ppp) REVERT: F 608 MET cc_start: 0.9185 (mtm) cc_final: 0.8811 (mtm) outliers start: 45 outliers final: 41 residues processed: 194 average time/residue: 0.1810 time to fit residues: 62.2280 Evaluate side-chains 193 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 118 optimal weight: 6.9990 chunk 407 optimal weight: 4.9990 chunk 206 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 233 optimal weight: 20.0000 chunk 170 optimal weight: 2.9990 chunk 329 optimal weight: 8.9990 chunk 246 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 360 optimal weight: 10.0000 chunk 358 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 327 GLN D 327 GLN E 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.111785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.066577 restraints weight = 69683.993| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.22 r_work: 0.2625 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 35154 Z= 0.280 Angle : 0.625 11.295 47550 Z= 0.315 Chirality : 0.046 0.144 5364 Planarity : 0.005 0.067 6234 Dihedral : 7.753 57.276 4986 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.80 % Favored : 96.06 % Rotamer: Outliers : 1.29 % Allowed : 13.97 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.65 (0.14), residues: 4344 helix: 1.43 (0.13), residues: 1824 sheet: -0.14 (0.20), residues: 666 loop : -0.27 (0.16), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 766 TYR 0.011 0.001 TYR A 138 PHE 0.027 0.002 PHE B 152 TRP 0.013 0.003 TRP E 551 HIS 0.004 0.001 HIS D 384 Details of bonding type rmsd covalent geometry : bond 0.00673 (35148) covalent geometry : angle 0.62524 (47550) hydrogen bonds : bond 0.04144 ( 1464) hydrogen bonds : angle 4.08167 ( 4176) Misc. bond : bond 0.00189 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 153 time to evaluate : 1.425 Fit side-chains REVERT: A 427 MET cc_start: 0.7521 (ppp) cc_final: 0.6910 (ppp) REVERT: B 84 MET cc_start: 0.7137 (tpt) cc_final: 0.6850 (tpt) REVERT: B 427 MET cc_start: 0.7553 (ppp) cc_final: 0.6835 (ppp) REVERT: C 66 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7445 (mm-30) REVERT: C 427 MET cc_start: 0.7691 (ppp) cc_final: 0.6796 (ppp) REVERT: D 84 MET cc_start: 0.6997 (tpt) cc_final: 0.6775 (tpt) REVERT: D 230 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8359 (t80) REVERT: D 427 MET cc_start: 0.7661 (ppp) cc_final: 0.7237 (ppp) REVERT: D 442 MET cc_start: 0.9133 (tpt) cc_final: 0.8878 (tpp) REVERT: E 427 MET cc_start: 0.7425 (ppp) cc_final: 0.6717 (ppp) REVERT: F 153 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8503 (tm) REVERT: F 427 MET cc_start: 0.7796 (ppp) cc_final: 0.6923 (ppp) REVERT: F 608 MET cc_start: 0.9195 (mtm) cc_final: 0.8925 (mtm) outliers start: 48 outliers final: 38 residues processed: 197 average time/residue: 0.1869 time to fit residues: 65.0506 Evaluate side-chains 186 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 559 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 287 optimal weight: 0.9990 chunk 329 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 79 optimal weight: 0.0070 chunk 338 optimal weight: 0.9990 chunk 394 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 386 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 133 optimal weight: 0.4980 overall best weight: 0.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.114541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.071112 restraints weight = 68743.431| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.42 r_work: 0.2696 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35154 Z= 0.108 Angle : 0.531 12.038 47550 Z= 0.267 Chirality : 0.043 0.142 5364 Planarity : 0.004 0.056 6234 Dihedral : 7.324 57.713 4986 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.78 % Favored : 96.09 % Rotamer: Outliers : 1.08 % Allowed : 14.40 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.14), residues: 4344 helix: 1.55 (0.13), residues: 1836 sheet: -0.15 (0.20), residues: 654 loop : -0.23 (0.16), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 83 TYR 0.010 0.001 TYR A 138 PHE 0.034 0.001 PHE E 152 TRP 0.006 0.001 TRP E 551 HIS 0.003 0.000 HIS F 384 Details of bonding type rmsd covalent geometry : bond 0.00266 (35148) covalent geometry : angle 0.53052 (47550) hydrogen bonds : bond 0.03222 ( 1464) hydrogen bonds : angle 3.92008 ( 4176) Misc. bond : bond 0.00009 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7968.10 seconds wall clock time: 137 minutes 26.08 seconds (8246.08 seconds total)