Starting phenix.real_space_refine on Fri Jul 3 20:37:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yrn_34063/07_2026/7yrn_34063.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yrn_34063/07_2026/7yrn_34063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yrn_34063/07_2026/7yrn_34063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yrn_34063/07_2026/7yrn_34063.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7yrn_34063/07_2026/7yrn_34063.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yrn_34063/07_2026/7yrn_34063.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yrn_34063/07_2026/7yrn_34063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yrn_34063/07_2026/7yrn_34063.map" } resolution = 2.99 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= 0.001 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: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 10185 2.51 5 N 2709 2.21 5 O 3123 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16080 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3562 Classifications: {'peptide': 434} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 423} Chain breaks: 2 Chain: "D" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 917 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "B" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3562 Classifications: {'peptide': 434} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 423} Chain breaks: 2 Chain: "F" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 917 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "G" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "C" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3562 Classifications: {'peptide': 434} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 423} Chain breaks: 2 Chain: "H" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 917 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "I" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.00, per 1000 atoms: 0.19 Number of scatterers: 16080 At special positions: 0 Unit cell: (160.072, 148.088, 152.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 3123 8.00 N 2709 7.00 C 10185 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 250 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 391 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 250 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 391 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 250 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 391 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 801 " - " ASN A 302 " " NAG A 802 " - " ASN A 281 " " NAG B 801 " - " ASN B 302 " " NAG B 802 " - " ASN B 281 " " NAG C 801 " - " ASN C 302 " " NAG C 802 " - " ASN C 281 " " NAG J 1 " - " ASN A 208 " " NAG K 1 " - " ASN B 208 " " NAG L 1 " - " ASN C 208 " Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 430.7 milliseconds 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3756 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 27 sheets defined 20.1% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 172 through 183 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 405 removed outlier: 3.924A pdb=" N ASP A 394 " --> pdb=" O ASP A 390 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU A 395 " --> pdb=" O CYS A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 524 removed outlier: 3.591A pdb=" N THR A 490 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU A 491 " --> pdb=" O THR A 487 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA A 505 " --> pdb=" O GLN A 501 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 534 removed outlier: 4.349A pdb=" N ILE A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 674 Processing helix chain 'A' and resid 679 through 696 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.847A pdb=" N PHE E 83 " --> pdb=" O LEU E 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 183 Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 389 through 405 removed outlier: 3.921A pdb=" N ASP B 394 " --> pdb=" O ASP B 390 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU B 395 " --> pdb=" O CYS B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 524 removed outlier: 3.587A pdb=" N THR B 490 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 491 " --> pdb=" O THR B 487 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG B 497 " --> pdb=" O GLY B 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU B 504 " --> pdb=" O ALA B 500 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA B 505 " --> pdb=" O GLN B 501 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS B 522 " --> pdb=" O LYS B 518 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 523 " --> pdb=" O GLU B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 534 removed outlier: 4.353A pdb=" N ILE B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 674 removed outlier: 3.500A pdb=" N SER B 674 " --> pdb=" O LYS B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 696 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.857A pdb=" N PHE G 83 " --> pdb=" O LEU G 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 183 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 386 through 388 No H-bonds generated for 'chain 'C' and resid 386 through 388' Processing helix chain 'C' and resid 389 through 405 removed outlier: 3.926A pdb=" N ASP C 394 " --> pdb=" O ASP C 390 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU C 395 " --> pdb=" O CYS C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 524 removed outlier: 3.591A pdb=" N THR C 490 " --> pdb=" O PHE C 486 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU C 491 " --> pdb=" O THR C 487 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG C 497 " --> pdb=" O GLY C 493 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU C 504 " --> pdb=" O ALA C 500 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA C 505 " --> pdb=" O GLN C 501 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS C 522 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 523 " --> pdb=" O GLU C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 534 removed outlier: 4.352A pdb=" N ILE C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 673 Processing helix chain 'C' and resid 679 through 696 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.866A pdb=" N PHE I 83 " --> pdb=" O LEU I 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 373 through 377 removed outlier: 6.889A pdb=" N VAL A 128 " --> pdb=" O TRP A 349 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ALA A 351 " --> pdb=" O MET A 126 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N MET A 126 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N GLU A 353 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLY A 124 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU A 123 " --> pdb=" O ILE A 434 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 155 removed outlier: 6.501A pdb=" N LYS A 145 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR A 168 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 147 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR A 166 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE A 149 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 164 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ARG A 151 " --> pdb=" O LEU A 162 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 158 through 169 current: chain 'A' and resid 224 through 227 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 224 through 227 current: chain 'A' and resid 266 through 267 removed outlier: 3.638A pdb=" N PHE A 266 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 274 " --> pdb=" O PHE A 266 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 273 through 274 current: chain 'A' and resid 316 through 326 Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 186 Processing sheet with id=AA4, first strand: chain 'A' and resid 188 through 193 Processing sheet with id=AA5, first strand: chain 'D' and resid 18 through 22 Processing sheet with id=AA6, first strand: chain 'D' and resid 45 through 51 removed outlier: 5.725A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.690A pdb=" N ASP E 105 " --> pdb=" O LEU E 11 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.447A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN E 34 " --> pdb=" O GLN E 89 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 373 through 377 removed outlier: 5.205A pdb=" N PHE B 348 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LYS B 130 " --> pdb=" O PHE B 348 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG B 354 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLY B 124 " --> pdb=" O ARG B 354 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU B 123 " --> pdb=" O ILE B 434 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 136 through 155 removed outlier: 6.489A pdb=" N LYS B 145 " --> pdb=" O TYR B 168 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR B 168 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU B 147 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR B 166 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE B 149 " --> pdb=" O SER B 164 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER B 164 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ARG B 151 " --> pdb=" O LEU B 162 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 158 through 169 current: chain 'B' and resid 224 through 227 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 224 through 227 current: chain 'B' and resid 266 through 267 removed outlier: 3.633A pdb=" N PHE B 266 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 274 " --> pdb=" O PHE B 266 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 273 through 274 current: chain 'B' and resid 316 through 326 Processing sheet with id=AB3, first strand: chain 'B' and resid 184 through 186 Processing sheet with id=AB4, first strand: chain 'B' and resid 188 through 193 Processing sheet with id=AB5, first strand: chain 'F' and resid 18 through 22 Processing sheet with id=AB6, first strand: chain 'F' and resid 45 through 51 removed outlier: 5.685A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.685A pdb=" N ASP G 105 " --> pdb=" O LEU G 11 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 53 through 54 removed outlier: 6.450A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN G 34 " --> pdb=" O GLN G 89 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN G 89 " --> pdb=" O ASN G 34 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 373 through 377 removed outlier: 5.213A pdb=" N PHE C 348 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LYS C 130 " --> pdb=" O PHE C 348 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ARG C 354 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLY C 124 " --> pdb=" O ARG C 354 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU C 123 " --> pdb=" O ILE C 434 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 136 through 155 removed outlier: 6.490A pdb=" N LYS C 145 " --> pdb=" O TYR C 168 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR C 168 " --> pdb=" O LYS C 145 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU C 147 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR C 166 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N PHE C 149 " --> pdb=" O SER C 164 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER C 164 " --> pdb=" O PHE C 149 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG C 151 " --> pdb=" O LEU C 162 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 158 through 169 current: chain 'C' and resid 224 through 227 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 224 through 227 current: chain 'C' and resid 266 through 267 removed outlier: 3.637A pdb=" N PHE C 266 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 274 " --> pdb=" O PHE C 266 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 273 through 274 current: chain 'C' and resid 316 through 326 Processing sheet with id=AC3, first strand: chain 'C' and resid 184 through 186 Processing sheet with id=AC4, first strand: chain 'C' and resid 188 through 193 Processing sheet with id=AC5, first strand: chain 'H' and resid 18 through 22 Processing sheet with id=AC6, first strand: chain 'H' and resid 45 through 51 removed outlier: 5.693A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AC8, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.681A pdb=" N ASP I 105 " --> pdb=" O LEU I 11 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.432A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN I 34 " --> pdb=" O GLN I 89 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN I 89 " --> pdb=" O ASN I 34 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1389 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5133 1.34 - 1.46: 4152 1.46 - 1.58: 7074 1.58 - 1.69: 0 1.69 - 1.81: 99 Bond restraints: 16458 Sorted by residual: bond pdb=" C1 NAG B 801 " pdb=" O5 NAG B 801 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.99e+00 bond pdb=" C1 NAG C 801 " pdb=" O5 NAG C 801 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C1 NAG A 801 " pdb=" O5 NAG A 801 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.87e+00 bond pdb=" C1 NAG A 802 " pdb=" O5 NAG A 802 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.83e+00 ... (remaining 16453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 21570 1.12 - 2.23: 602 2.23 - 3.35: 120 3.35 - 4.47: 19 4.47 - 5.59: 15 Bond angle restraints: 22326 Sorted by residual: angle pdb=" C SER E 93 " pdb=" CA SER E 93 " pdb=" CB SER E 93 " ideal model delta sigma weight residual 110.42 116.01 -5.59 1.99e+00 2.53e-01 7.88e+00 angle pdb=" C SER G 93 " pdb=" CA SER G 93 " pdb=" CB SER G 93 " ideal model delta sigma weight residual 110.42 115.99 -5.57 1.99e+00 2.53e-01 7.84e+00 angle pdb=" C SER I 93 " pdb=" CA SER I 93 " pdb=" CB SER I 93 " ideal model delta sigma weight residual 110.42 115.99 -5.57 1.99e+00 2.53e-01 7.83e+00 angle pdb=" CA TYR D 60 " pdb=" CB TYR D 60 " pdb=" CG TYR D 60 " ideal model delta sigma weight residual 113.90 118.85 -4.95 1.80e+00 3.09e-01 7.56e+00 angle pdb=" CA TYR H 60 " pdb=" CB TYR H 60 " pdb=" CG TYR H 60 " ideal model delta sigma weight residual 113.90 118.70 -4.80 1.80e+00 3.09e-01 7.11e+00 ... (remaining 22321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.02: 9022 15.02 - 30.03: 460 30.03 - 45.05: 119 45.05 - 60.07: 30 60.07 - 75.08: 8 Dihedral angle restraints: 9639 sinusoidal: 3801 harmonic: 5838 Sorted by residual: dihedral pdb=" N CYS A 391 " pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sinusoidal sigma weight residual 60.00 0.14 59.86 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N CYS B 391 " pdb=" CA CYS B 391 " pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " ideal model delta sinusoidal sigma weight residual 60.00 0.22 59.78 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N CYS C 391 " pdb=" CA CYS C 391 " pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " ideal model delta sinusoidal sigma weight residual 60.00 0.50 59.50 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 9636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2186 0.062 - 0.123: 289 0.123 - 0.185: 9 0.185 - 0.246: 0 0.246 - 0.308: 3 Chirality restraints: 2487 Sorted by residual: chirality pdb=" C1 NAG B 802 " pdb=" ND2 ASN B 281 " pdb=" C2 NAG B 802 " pdb=" O5 NAG B 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 281 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C1 NAG C 802 " pdb=" ND2 ASN C 281 " pdb=" C2 NAG C 802 " pdb=" O5 NAG C 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 2484 not shown) Planarity restraints: 2826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 112 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO H 113 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO H 113 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 113 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 112 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.16e+00 pdb=" N PRO F 113 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO F 113 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 113 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 112 " -0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO D 113 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO D 113 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 113 " -0.020 5.00e-02 4.00e+02 ... (remaining 2823 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 4477 2.81 - 3.33: 14938 3.33 - 3.85: 27206 3.85 - 4.38: 31722 4.38 - 4.90: 54097 Nonbonded interactions: 132440 Sorted by model distance: nonbonded pdb=" OE2 GLU B 422 " pdb=" OG SER B 471 " model vdw 2.284 3.040 nonbonded pdb=" OE2 GLU C 422 " pdb=" OG SER C 471 " model vdw 2.285 3.040 nonbonded pdb=" OE2 GLU A 422 " pdb=" OG SER A 471 " model vdw 2.286 3.040 nonbonded pdb=" OD2 ASP A 660 " pdb=" OG SER B 363 " model vdw 2.297 3.040 nonbonded pdb=" OG SER A 363 " pdb=" OD2 ASP C 660 " model vdw 2.307 3.040 ... (remaining 132435 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.270 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 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 : 0.002 0.028 16482 Z= 0.117 Angle : 0.497 8.519 22386 Z= 0.272 Chirality : 0.041 0.308 2487 Planarity : 0.003 0.038 2817 Dihedral : 10.285 75.084 5847 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.80 % Favored : 93.73 % Rotamer: Outliers : 4.02 % Allowed : 7.75 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -0.60 (0.19), residues: 1947 helix: -0.07 (0.29), residues: 315 sheet: 0.35 (0.20), residues: 660 loop : -1.01 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 18 TYR 0.007 0.001 TYR C 129 PHE 0.008 0.001 PHE I 92 TRP 0.008 0.001 TRP I 96 HIS 0.002 0.000 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.12 (16458) covalent geometry : angle 0.48159 / 0.27 (22326) SS BOND : bond 0.00115 / 0.08 ( 12) SS BOND : angle 0.74042 / 0.47 ( 24) hydrogen bonds : bond 0.19539 / 12.94 ( 526) hydrogen bonds : angle 8.08117 / 5.56 ( 1389) link_BETA1-4 : bond 0.00054 / 0.03 ( 3) link_BETA1-4 : angle 1.49169 / 0.70 ( 9) link_NAG-ASN : bond 0.00721 / 0.39 ( 9) link_NAG-ASN : angle 3.43651 / 2.31 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 308 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 40 MET cc_start: 0.4986 (ppp) cc_final: 0.4590 (ppp) REVERT: B 186 TYR cc_start: 0.8036 (m-80) cc_final: 0.7834 (m-80) REVERT: F 78 THR cc_start: 0.7797 (m) cc_final: 0.7079 (t) REVERT: G 98 PHE cc_start: 0.6346 (OUTLIER) cc_final: 0.5575 (t80) REVERT: C 186 TYR cc_start: 0.8098 (m-80) cc_final: 0.7817 (m-80) REVERT: H 40 MET cc_start: 0.4819 (ppp) cc_final: 0.4543 (ppp) REVERT: H 78 THR cc_start: 0.7902 (m) cc_final: 0.7553 (t) outliers start: 71 outliers final: 18 residues processed: 361 average time/residue: 0.3731 time to fit residues: 153.7969 Evaluate side-chains 196 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 469 HIS Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain I residue 98 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.0000 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 ASN A 212 GLN A 220 ASN A 485 GLN D 3 GLN ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN B 220 ASN B 247 ASN B 485 GLN F 3 GLN F 106 ASN C 212 GLN C 220 ASN C 247 ASN C 485 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.145608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.123021 restraints weight = 44075.683| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 2.96 r_work: 0.4120 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16482 Z= 0.160 Angle : 0.624 9.474 22386 Z= 0.322 Chirality : 0.046 0.310 2487 Planarity : 0.004 0.044 2817 Dihedral : 5.330 57.007 2211 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.39 % Favored : 94.14 % Rotamer: Outliers : 5.38 % Allowed : 13.64 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -0.63 (0.19), residues: 1947 helix: 0.62 (0.28), residues: 309 sheet: 0.32 (0.20), residues: 642 loop : -1.26 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 225 TYR 0.013 0.001 TYR C 488 PHE 0.020 0.002 PHE B 486 TRP 0.014 0.001 TRP B 431 HIS 0.004 0.001 HIS I 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (16458) covalent geometry : angle 0.59572 / 0.32 (22326) SS BOND : bond 0.00219 / 0.12 ( 12) SS BOND : angle 1.37150 / 0.86 ( 24) hydrogen bonds : bond 0.05484 / 3.81 ( 526) hydrogen bonds : angle 6.22818 / 4.20 ( 1389) link_BETA1-4 : bond 0.00169 / 0.09 ( 3) link_BETA1-4 : angle 1.83717 / 0.95 ( 9) link_NAG-ASN : bond 0.00782 / 0.43 ( 9) link_NAG-ASN : angle 5.17822 / 2.97 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 183 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8164 (mtp) REVERT: A 222 HIS cc_start: 0.7114 (OUTLIER) cc_final: 0.6676 (p90) REVERT: A 326 GLU cc_start: 0.8369 (mp0) cc_final: 0.7972 (mp0) REVERT: A 682 GLU cc_start: 0.8477 (mp0) cc_final: 0.8105 (mp0) REVERT: D 40 MET cc_start: 0.4122 (ppp) cc_final: 0.3630 (ppp) REVERT: E 49 HIS cc_start: 0.4557 (m90) cc_final: 0.4028 (m90) REVERT: B 222 HIS cc_start: 0.7159 (OUTLIER) cc_final: 0.6795 (p90) REVERT: B 682 GLU cc_start: 0.8495 (mp0) cc_final: 0.8123 (mp0) REVERT: F 40 MET cc_start: 0.2715 (ppp) cc_final: 0.2413 (ppp) REVERT: F 80 TYR cc_start: 0.6229 (m-80) cc_final: 0.5827 (m-80) REVERT: G 14 SER cc_start: 0.8198 (m) cc_final: 0.7654 (p) REVERT: G 17 ASP cc_start: 0.7231 (m-30) cc_final: 0.6781 (p0) REVERT: G 49 HIS cc_start: 0.4453 (m90) cc_final: 0.3730 (m90) REVERT: G 98 PHE cc_start: 0.5585 (OUTLIER) cc_final: 0.5136 (t80) REVERT: C 222 HIS cc_start: 0.7100 (OUTLIER) cc_final: 0.6792 (p90) REVERT: H 18 LEU cc_start: 0.7117 (mm) cc_final: 0.6654 (mm) REVERT: H 19 LYS cc_start: 0.7487 (mppt) cc_final: 0.7185 (mmtm) REVERT: H 40 MET cc_start: 0.4125 (ppp) cc_final: 0.3649 (ppp) REVERT: H 78 THR cc_start: 0.8290 (m) cc_final: 0.7638 (t) REVERT: I 45 LYS cc_start: 0.6635 (mmmt) cc_final: 0.5871 (ttpp) REVERT: I 49 HIS cc_start: 0.4278 (m90) cc_final: 0.3596 (m-70) REVERT: I 55 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.6744 (tt0) outliers start: 95 outliers final: 51 residues processed: 256 average time/residue: 0.3740 time to fit residues: 110.1224 Evaluate side-chains 215 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 158 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 222 HIS Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 222 HIS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 469 HIS Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 55 GLN Chi-restraints excluded: chain I residue 98 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 156 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 24 optimal weight: 9.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 GLN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN B 337 GLN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN ** F 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 GLN ** I 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.140265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.116458 restraints weight = 44349.170| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 3.07 r_work: 0.4010 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16482 Z= 0.227 Angle : 0.654 9.907 22386 Z= 0.341 Chirality : 0.047 0.338 2487 Planarity : 0.004 0.044 2817 Dihedral : 5.589 59.630 2210 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.55 % Favored : 93.99 % Rotamer: Outliers : 5.55 % Allowed : 14.09 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -0.77 (0.19), residues: 1947 helix: 0.50 (0.29), residues: 312 sheet: 0.17 (0.21), residues: 639 loop : -1.31 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 150 TYR 0.021 0.002 TYR D 99 PHE 0.023 0.002 PHE B 486 TRP 0.025 0.002 TRP D 83 HIS 0.005 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.23 (16458) covalent geometry : angle 0.63216 / 0.34 (22326) SS BOND : bond 0.00336 / 0.21 ( 12) SS BOND : angle 1.39652 / 0.86 ( 24) hydrogen bonds : bond 0.04834 / 3.37 ( 526) hydrogen bonds : angle 6.16224 / 4.22 ( 1389) link_BETA1-4 : bond 0.00409 / 0.21 ( 3) link_BETA1-4 : angle 3.07922 / 1.43 ( 9) link_NAG-ASN : bond 0.00736 / 0.40 ( 9) link_NAG-ASN : angle 4.36835 / 2.85 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 160 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.6877 (p90) REVERT: A 371 MET cc_start: 0.7870 (mtm) cc_final: 0.7548 (mtm) REVERT: A 682 GLU cc_start: 0.8593 (mp0) cc_final: 0.8051 (mp0) REVERT: D 40 MET cc_start: 0.4094 (ppp) cc_final: 0.3599 (ppp) REVERT: D 102 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7460 (mt) REVERT: E 49 HIS cc_start: 0.4671 (m90) cc_final: 0.4057 (m90) REVERT: F 40 MET cc_start: 0.2687 (ppp) cc_final: 0.2364 (ppp) REVERT: F 80 TYR cc_start: 0.6257 (m-80) cc_final: 0.5839 (m-80) REVERT: G 32 TYR cc_start: 0.7653 (OUTLIER) cc_final: 0.6681 (t80) REVERT: G 49 HIS cc_start: 0.4918 (m90) cc_final: 0.4224 (m90) REVERT: G 98 PHE cc_start: 0.5811 (OUTLIER) cc_final: 0.5239 (t80) REVERT: H 18 LEU cc_start: 0.7138 (mm) cc_final: 0.6628 (mm) REVERT: H 19 LYS cc_start: 0.7324 (mppt) cc_final: 0.7109 (mptp) REVERT: H 37 VAL cc_start: 0.5407 (m) cc_final: 0.5176 (p) REVERT: H 40 MET cc_start: 0.4112 (ppp) cc_final: 0.3576 (ppp) REVERT: H 78 THR cc_start: 0.8319 (m) cc_final: 0.7101 (t) REVERT: H 80 TYR cc_start: 0.6687 (m-80) cc_final: 0.5824 (m-80) REVERT: I 49 HIS cc_start: 0.4469 (m90) cc_final: 0.4022 (m90) REVERT: I 89 GLN cc_start: 0.4763 (pm20) cc_final: 0.3751 (pp30) outliers start: 98 outliers final: 55 residues processed: 230 average time/residue: 0.3731 time to fit residues: 99.0236 Evaluate side-chains 200 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 141 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 469 HIS Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 98 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 35 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 129 optimal weight: 0.0870 chunk 156 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 38 optimal weight: 0.0980 chunk 140 optimal weight: 0.9990 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 ASN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 HIS A 692 GLN D 3 GLN B 220 ASN ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN F 3 GLN ** F 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 GLN C 220 ASN C 485 GLN H 39 GLN I 38 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.143030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.120597 restraints weight = 43990.521| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 3.14 r_work: 0.4036 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16482 Z= 0.120 Angle : 0.559 8.836 22386 Z= 0.289 Chirality : 0.044 0.313 2487 Planarity : 0.003 0.044 2817 Dihedral : 5.256 58.736 2206 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.65 % Favored : 93.89 % Rotamer: Outliers : 4.53 % Allowed : 15.62 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -0.77 (0.19), residues: 1947 helix: 0.56 (0.29), residues: 312 sheet: 0.16 (0.21), residues: 660 loop : -1.36 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 150 TYR 0.012 0.001 TYR E 32 PHE 0.014 0.001 PHE E 62 TRP 0.014 0.001 TRP H 83 HIS 0.005 0.001 HIS A 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (16458) covalent geometry : angle 0.54162 / 0.29 (22326) SS BOND : bond 0.00298 / 0.19 ( 12) SS BOND : angle 1.00620 / 0.59 ( 24) hydrogen bonds : bond 0.04080 / 2.84 ( 526) hydrogen bonds : angle 5.87386 / 4.02 ( 1389) link_BETA1-4 : bond 0.00080 / 0.04 ( 3) link_BETA1-4 : angle 2.25799 / 1.07 ( 9) link_NAG-ASN : bond 0.00694 / 0.39 ( 9) link_NAG-ASN : angle 3.71788 / 2.43 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 165 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.7815 (mtm) cc_final: 0.7555 (mtm) REVERT: A 682 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8388 (mp0) REVERT: D 40 MET cc_start: 0.3949 (ppp) cc_final: 0.3400 (ppp) REVERT: D 102 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7415 (mt) REVERT: E 49 HIS cc_start: 0.4539 (m90) cc_final: 0.4009 (m90) REVERT: F 19 LYS cc_start: 0.7572 (mppt) cc_final: 0.7330 (mppt) REVERT: F 40 MET cc_start: 0.2708 (ppp) cc_final: 0.2325 (ppp) REVERT: G 17 ASP cc_start: 0.7355 (m-30) cc_final: 0.6881 (p0) REVERT: G 45 LYS cc_start: 0.6443 (mmmt) cc_final: 0.5673 (tttt) REVERT: G 49 HIS cc_start: 0.4419 (m90) cc_final: 0.3850 (m90) REVERT: G 98 PHE cc_start: 0.5712 (OUTLIER) cc_final: 0.5332 (t80) REVERT: H 18 LEU cc_start: 0.7133 (mm) cc_final: 0.6721 (mm) REVERT: H 40 MET cc_start: 0.4086 (ppp) cc_final: 0.3575 (ppp) REVERT: H 78 THR cc_start: 0.8152 (m) cc_final: 0.6918 (t) REVERT: H 80 TYR cc_start: 0.6579 (m-80) cc_final: 0.5749 (m-80) REVERT: I 45 LYS cc_start: 0.6102 (mmmt) cc_final: 0.5539 (ttpp) REVERT: I 49 HIS cc_start: 0.4806 (m90) cc_final: 0.4296 (m90) REVERT: I 89 GLN cc_start: 0.4559 (pm20) cc_final: 0.3716 (pp30) outliers start: 80 outliers final: 43 residues processed: 222 average time/residue: 0.3502 time to fit residues: 90.5700 Evaluate side-chains 192 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 146 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 98 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 169 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 146 optimal weight: 0.2980 chunk 10 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN A 365 HIS ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 GLN C 692 GLN H 3 GLN ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.139508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.115646 restraints weight = 44024.482| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 3.03 r_work: 0.3993 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16482 Z= 0.219 Angle : 0.632 9.509 22386 Z= 0.326 Chirality : 0.046 0.342 2487 Planarity : 0.004 0.045 2817 Dihedral : 5.400 59.975 2201 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.16 % Favored : 93.43 % Rotamer: Outliers : 4.64 % Allowed : 16.53 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.19), residues: 1947 helix: 0.49 (0.29), residues: 312 sheet: -0.08 (0.21), residues: 636 loop : -1.45 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 150 TYR 0.019 0.002 TYR C 364 PHE 0.017 0.002 PHE E 92 TRP 0.014 0.002 TRP H 83 HIS 0.006 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.22 (16458) covalent geometry : angle 0.61114 / 0.32 (22326) SS BOND : bond 0.00263 / 0.16 ( 12) SS BOND : angle 1.25293 / 0.76 ( 24) hydrogen bonds : bond 0.04324 / 3.01 ( 526) hydrogen bonds : angle 6.06013 / 4.16 ( 1389) link_BETA1-4 : bond 0.00438 / 0.22 ( 3) link_BETA1-4 : angle 3.32433 / 1.54 ( 9) link_NAG-ASN : bond 0.00712 / 0.39 ( 9) link_NAG-ASN : angle 4.09477 / 2.71 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 156 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.7321 (OUTLIER) cc_final: 0.6899 (p90) REVERT: A 371 MET cc_start: 0.7901 (mtm) cc_final: 0.7605 (mtm) REVERT: A 682 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8371 (mp0) REVERT: D 40 MET cc_start: 0.4092 (ppp) cc_final: 0.3621 (ppp) REVERT: D 102 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7451 (mt) REVERT: E 32 TYR cc_start: 0.7408 (OUTLIER) cc_final: 0.6165 (t80) REVERT: E 49 HIS cc_start: 0.4580 (m90) cc_final: 0.4014 (m90) REVERT: E 82 ASP cc_start: 0.7495 (m-30) cc_final: 0.7214 (m-30) REVERT: F 40 MET cc_start: 0.2727 (ppp) cc_final: 0.2390 (ppp) REVERT: F 80 TYR cc_start: 0.6308 (m-80) cc_final: 0.5751 (m-80) REVERT: G 17 ASP cc_start: 0.7351 (m-30) cc_final: 0.6890 (p0) REVERT: G 49 HIS cc_start: 0.4760 (m90) cc_final: 0.4202 (m90) REVERT: G 82 ASP cc_start: 0.7100 (m-30) cc_final: 0.6743 (m-30) REVERT: G 98 PHE cc_start: 0.5840 (OUTLIER) cc_final: 0.5468 (t80) REVERT: G 104 LEU cc_start: 0.4994 (OUTLIER) cc_final: 0.4570 (pt) REVERT: H 18 LEU cc_start: 0.7035 (mm) cc_final: 0.6607 (mm) REVERT: H 40 MET cc_start: 0.4116 (ppp) cc_final: 0.3558 (ppp) REVERT: H 80 TYR cc_start: 0.6629 (m-80) cc_final: 0.5996 (m-80) REVERT: I 49 HIS cc_start: 0.4718 (m90) cc_final: 0.4094 (m90) REVERT: I 89 GLN cc_start: 0.4631 (pm20) cc_final: 0.3611 (pp30) outliers start: 82 outliers final: 47 residues processed: 215 average time/residue: 0.3736 time to fit residues: 92.9907 Evaluate side-chains 192 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 139 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 485 GLN Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 HIS ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 365 HIS ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN ** F 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** I 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.140720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.118000 restraints weight = 44011.629| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 3.11 r_work: 0.4006 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16482 Z= 0.152 Angle : 0.586 8.648 22386 Z= 0.302 Chirality : 0.045 0.323 2487 Planarity : 0.004 0.044 2817 Dihedral : 5.105 59.734 2198 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.32 % Favored : 93.32 % Rotamer: Outliers : 4.36 % Allowed : 18.05 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.19), residues: 1947 helix: 0.53 (0.29), residues: 312 sheet: 0.00 (0.22), residues: 606 loop : -1.48 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 150 TYR 0.014 0.001 TYR B 494 PHE 0.015 0.002 PHE E 62 TRP 0.021 0.001 TRP F 83 HIS 0.005 0.001 HIS C 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (16458) covalent geometry : angle 0.56787 / 0.30 (22326) SS BOND : bond 0.00220 / 0.13 ( 12) SS BOND : angle 1.02482 / 0.61 ( 24) hydrogen bonds : bond 0.04003 / 2.79 ( 526) hydrogen bonds : angle 5.97172 / 4.08 ( 1389) link_BETA1-4 : bond 0.00065 / 0.03 ( 3) link_BETA1-4 : angle 2.80125 / 1.31 ( 9) link_NAG-ASN : bond 0.00670 / 0.37 ( 9) link_NAG-ASN : angle 3.77547 / 2.49 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 158 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.7188 (OUTLIER) cc_final: 0.6776 (p90) REVERT: A 682 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: D 40 MET cc_start: 0.4030 (ppp) cc_final: 0.3474 (ppp) REVERT: D 102 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7451 (mt) REVERT: E 32 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.5929 (t80) REVERT: E 49 HIS cc_start: 0.4663 (m90) cc_final: 0.3973 (m90) REVERT: E 82 ASP cc_start: 0.7452 (m-30) cc_final: 0.7195 (m-30) REVERT: F 37 VAL cc_start: 0.5451 (m) cc_final: 0.5241 (p) REVERT: F 40 MET cc_start: 0.2693 (ppp) cc_final: 0.2324 (ppp) REVERT: F 80 TYR cc_start: 0.6312 (m-80) cc_final: 0.5726 (m-80) REVERT: G 17 ASP cc_start: 0.7279 (m-30) cc_final: 0.6827 (p0) REVERT: G 49 HIS cc_start: 0.4756 (m90) cc_final: 0.4305 (m90) REVERT: G 82 ASP cc_start: 0.7039 (m-30) cc_final: 0.6778 (m-30) REVERT: G 98 PHE cc_start: 0.5766 (OUTLIER) cc_final: 0.5447 (t80) REVERT: H 18 LEU cc_start: 0.7029 (mm) cc_final: 0.6633 (mm) REVERT: H 40 MET cc_start: 0.4056 (ppp) cc_final: 0.3494 (ppp) REVERT: H 80 TYR cc_start: 0.6692 (m-80) cc_final: 0.6051 (m-80) REVERT: I 45 LYS cc_start: 0.6071 (mmmt) cc_final: 0.5557 (tttp) REVERT: I 49 HIS cc_start: 0.4589 (m90) cc_final: 0.4124 (m90) outliers start: 77 outliers final: 48 residues processed: 216 average time/residue: 0.4175 time to fit residues: 103.9069 Evaluate side-chains 197 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 144 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 171 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 188 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 186 optimal weight: 0.2980 chunk 159 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 ASN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 HIS ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN I 27 GLN I 55 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.140555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.117954 restraints weight = 43762.542| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 3.07 r_work: 0.4000 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16482 Z= 0.158 Angle : 0.586 8.703 22386 Z= 0.301 Chirality : 0.045 0.326 2487 Planarity : 0.004 0.043 2817 Dihedral : 5.107 59.488 2198 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.52 % Favored : 93.17 % Rotamer: Outliers : 4.07 % Allowed : 18.73 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.19), residues: 1947 helix: 0.59 (0.29), residues: 312 sheet: -0.09 (0.22), residues: 606 loop : -1.50 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 157 TYR 0.020 0.001 TYR C 364 PHE 0.017 0.002 PHE A 486 TRP 0.031 0.001 TRP F 83 HIS 0.005 0.001 HIS C 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (16458) covalent geometry : angle 0.56800 / 0.30 (22326) SS BOND : bond 0.00225 / 0.14 ( 12) SS BOND : angle 1.05463 / 0.64 ( 24) hydrogen bonds : bond 0.03941 / 2.75 ( 526) hydrogen bonds : angle 5.92571 / 4.07 ( 1389) link_BETA1-4 : bond 0.00112 / 0.06 ( 3) link_BETA1-4 : angle 2.89400 / 1.36 ( 9) link_NAG-ASN : bond 0.00666 / 0.37 ( 9) link_NAG-ASN : angle 3.72861 / 2.46 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 151 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.7238 (OUTLIER) cc_final: 0.6819 (p90) REVERT: A 473 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7260 (ptm) REVERT: A 682 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8359 (mp0) REVERT: D 40 MET cc_start: 0.4081 (ppp) cc_final: 0.3526 (ppp) REVERT: D 102 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7457 (mt) REVERT: E 32 TYR cc_start: 0.7151 (OUTLIER) cc_final: 0.6070 (t80) REVERT: E 49 HIS cc_start: 0.4532 (m90) cc_final: 0.3860 (m90) REVERT: E 82 ASP cc_start: 0.7302 (m-30) cc_final: 0.7060 (m-30) REVERT: B 326 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8559 (mp0) REVERT: F 37 VAL cc_start: 0.5617 (m) cc_final: 0.5397 (p) REVERT: F 40 MET cc_start: 0.2755 (ppp) cc_final: 0.2361 (ppp) REVERT: F 80 TYR cc_start: 0.6375 (m-80) cc_final: 0.5835 (m-80) REVERT: G 17 ASP cc_start: 0.7218 (m-30) cc_final: 0.6804 (p0) REVERT: G 49 HIS cc_start: 0.4675 (m90) cc_final: 0.4276 (m90) REVERT: G 82 ASP cc_start: 0.6900 (m-30) cc_final: 0.6634 (m-30) REVERT: G 98 PHE cc_start: 0.6000 (OUTLIER) cc_final: 0.5726 (t80) REVERT: H 18 LEU cc_start: 0.7039 (mm) cc_final: 0.6647 (mm) REVERT: H 40 MET cc_start: 0.4086 (ppp) cc_final: 0.3526 (ppp) REVERT: H 80 TYR cc_start: 0.6724 (m-80) cc_final: 0.6050 (m-80) REVERT: I 49 HIS cc_start: 0.4504 (m90) cc_final: 0.3969 (m90) outliers start: 72 outliers final: 49 residues processed: 205 average time/residue: 0.3765 time to fit residues: 90.3621 Evaluate side-chains 204 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 148 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 78 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 176 optimal weight: 0.0980 chunk 30 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 184 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 HIS ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** I 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.139198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.116488 restraints weight = 44187.100| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 3.12 r_work: 0.3970 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16482 Z= 0.199 Angle : 0.639 9.200 22386 Z= 0.326 Chirality : 0.046 0.338 2487 Planarity : 0.004 0.045 2817 Dihedral : 5.267 59.731 2198 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.78 % Favored : 92.91 % Rotamer: Outliers : 4.24 % Allowed : 18.68 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.19), residues: 1947 helix: 0.54 (0.29), residues: 312 sheet: -0.38 (0.21), residues: 636 loop : -1.49 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 67 TYR 0.018 0.002 TYR C 364 PHE 0.026 0.002 PHE E 62 TRP 0.036 0.002 TRP D 83 HIS 0.005 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (16458) covalent geometry : angle 0.62057 / 0.32 (22326) SS BOND : bond 0.00242 / 0.15 ( 12) SS BOND : angle 1.21857 / 0.75 ( 24) hydrogen bonds : bond 0.04073 / 2.82 ( 526) hydrogen bonds : angle 6.08035 / 4.19 ( 1389) link_BETA1-4 : bond 0.00379 / 0.19 ( 3) link_BETA1-4 : angle 3.21030 / 1.49 ( 9) link_NAG-ASN : bond 0.00673 / 0.37 ( 9) link_NAG-ASN : angle 3.90922 / 2.57 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 156 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.7317 (OUTLIER) cc_final: 0.6874 (p90) REVERT: A 473 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7319 (ptm) REVERT: A 682 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8429 (mp0) REVERT: D 40 MET cc_start: 0.4122 (ppp) cc_final: 0.3550 (ppp) REVERT: D 80 TYR cc_start: 0.6836 (m-80) cc_final: 0.6257 (m-80) REVERT: D 102 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7576 (mt) REVERT: E 32 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.6676 (t80) REVERT: E 49 HIS cc_start: 0.4612 (m90) cc_final: 0.3901 (m90) REVERT: E 61 ARG cc_start: 0.7436 (pmm-80) cc_final: 0.7168 (pmm-80) REVERT: B 326 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8606 (mp0) REVERT: F 37 VAL cc_start: 0.5456 (m) cc_final: 0.5231 (p) REVERT: F 40 MET cc_start: 0.2887 (ppp) cc_final: 0.2488 (ppp) REVERT: F 80 TYR cc_start: 0.6430 (m-80) cc_final: 0.5886 (m-80) REVERT: G 17 ASP cc_start: 0.7257 (m-30) cc_final: 0.6814 (p0) REVERT: G 32 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.6749 (t80) REVERT: G 45 LYS cc_start: 0.6328 (mmmt) cc_final: 0.5737 (ttpp) REVERT: G 49 HIS cc_start: 0.4668 (m90) cc_final: 0.4257 (m90) REVERT: G 82 ASP cc_start: 0.6806 (m-30) cc_final: 0.6548 (m-30) REVERT: H 18 LEU cc_start: 0.7056 (mm) cc_final: 0.6697 (mm) REVERT: H 40 MET cc_start: 0.4269 (ppp) cc_final: 0.3683 (ppp) REVERT: H 80 TYR cc_start: 0.6771 (m-80) cc_final: 0.6153 (m-80) REVERT: I 45 LYS cc_start: 0.6154 (mmmt) cc_final: 0.5733 (ttpp) REVERT: I 49 HIS cc_start: 0.4579 (m90) cc_final: 0.4191 (m90) outliers start: 75 outliers final: 48 residues processed: 211 average time/residue: 0.3762 time to fit residues: 92.7998 Evaluate side-chains 201 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 146 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 105 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 186 optimal weight: 0.0070 chunk 102 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 chunk 142 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 HIS ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 222 HIS ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN C 222 HIS C 365 HIS C 485 GLN I 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.140484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.117020 restraints weight = 44055.940| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 3.06 r_work: 0.4007 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16482 Z= 0.143 Angle : 0.615 10.590 22386 Z= 0.311 Chirality : 0.045 0.323 2487 Planarity : 0.004 0.046 2817 Dihedral : 5.046 59.389 2196 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.68 % Favored : 93.01 % Rotamer: Outliers : 3.85 % Allowed : 19.24 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.19), residues: 1947 helix: 0.62 (0.29), residues: 312 sheet: -0.29 (0.21), residues: 606 loop : -1.50 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 157 TYR 0.018 0.001 TYR C 364 PHE 0.037 0.002 PHE A 486 TRP 0.030 0.002 TRP F 83 HIS 0.006 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (16458) covalent geometry : angle 0.59916 / 0.31 (22326) SS BOND : bond 0.00247 / 0.16 ( 12) SS BOND : angle 1.06514 / 0.65 ( 24) hydrogen bonds : bond 0.03887 / 2.68 ( 526) hydrogen bonds : angle 5.98219 / 4.11 ( 1389) link_BETA1-4 : bond 0.00139 / 0.07 ( 3) link_BETA1-4 : angle 2.83818 / 1.33 ( 9) link_NAG-ASN : bond 0.00670 / 0.37 ( 9) link_NAG-ASN : angle 3.63955 / 2.39 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 159 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.7199 (OUTLIER) cc_final: 0.6773 (p90) REVERT: A 473 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7257 (ptm) REVERT: A 682 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8355 (mp0) REVERT: D 40 MET cc_start: 0.4219 (ppp) cc_final: 0.3705 (ppp) REVERT: D 80 TYR cc_start: 0.6896 (m-80) cc_final: 0.6334 (m-80) REVERT: D 102 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7555 (mt) REVERT: E 32 TYR cc_start: 0.7235 (OUTLIER) cc_final: 0.6302 (t80) REVERT: E 49 HIS cc_start: 0.4552 (m90) cc_final: 0.3943 (m90) REVERT: B 326 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8538 (mp0) REVERT: F 40 MET cc_start: 0.2966 (ppp) cc_final: 0.2564 (ppp) REVERT: F 80 TYR cc_start: 0.6416 (m-80) cc_final: 0.5892 (m-80) REVERT: F 94 TYR cc_start: 0.8175 (m-10) cc_final: 0.7067 (m-10) REVERT: G 17 ASP cc_start: 0.7175 (m-30) cc_final: 0.6817 (p0) REVERT: G 49 HIS cc_start: 0.4420 (m90) cc_final: 0.4020 (m90) REVERT: G 82 ASP cc_start: 0.6902 (m-30) cc_final: 0.6623 (m-30) REVERT: C 121 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6233 (mt) REVERT: C 186 TYR cc_start: 0.8140 (m-80) cc_final: 0.7937 (m-80) REVERT: H 18 LEU cc_start: 0.7029 (mm) cc_final: 0.6613 (mm) REVERT: H 40 MET cc_start: 0.4357 (ppp) cc_final: 0.3778 (ppp) REVERT: H 80 TYR cc_start: 0.6728 (m-80) cc_final: 0.6106 (m-80) REVERT: I 45 LYS cc_start: 0.6231 (mmmt) cc_final: 0.5707 (tttm) REVERT: I 49 HIS cc_start: 0.4377 (m90) cc_final: 0.4054 (m90) outliers start: 68 outliers final: 45 residues processed: 210 average time/residue: 0.3703 time to fit residues: 91.2976 Evaluate side-chains 201 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 149 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 151 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 146 optimal weight: 0.2980 chunk 108 optimal weight: 0.1980 chunk 112 optimal weight: 0.0370 chunk 120 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 HIS ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN C 220 ASN ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.142279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.119898 restraints weight = 44011.945| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 3.13 r_work: 0.4031 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16482 Z= 0.120 Angle : 0.610 11.747 22386 Z= 0.306 Chirality : 0.045 0.314 2487 Planarity : 0.004 0.046 2817 Dihedral : 4.935 58.218 2196 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.57 % Favored : 93.12 % Rotamer: Outliers : 2.94 % Allowed : 20.43 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.19), residues: 1947 helix: 0.74 (0.29), residues: 312 sheet: -0.22 (0.21), residues: 591 loop : -1.52 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 157 TYR 0.016 0.001 TYR C 364 PHE 0.029 0.002 PHE E 62 TRP 0.029 0.002 TRP F 83 HIS 0.005 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (16458) covalent geometry : angle 0.59705 / 0.30 (22326) SS BOND : bond 0.00254 / 0.15 ( 12) SS BOND : angle 0.93729 / 0.57 ( 24) hydrogen bonds : bond 0.03747 / 2.59 ( 526) hydrogen bonds : angle 5.82686 / 4.00 ( 1389) link_BETA1-4 : bond 0.00215 / 0.11 ( 3) link_BETA1-4 : angle 2.50851 / 1.16 ( 9) link_NAG-ASN : bond 0.00682 / 0.38 ( 9) link_NAG-ASN : angle 3.32180 / 2.17 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 160 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.7909 (pmm) cc_final: 0.7666 (pmm) REVERT: A 682 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8326 (mp0) REVERT: D 40 MET cc_start: 0.4106 (ppp) cc_final: 0.3565 (ppp) REVERT: D 80 TYR cc_start: 0.6893 (m-80) cc_final: 0.6300 (m-80) REVERT: D 102 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7460 (mt) REVERT: E 32 TYR cc_start: 0.6859 (OUTLIER) cc_final: 0.6101 (t80) REVERT: E 49 HIS cc_start: 0.4450 (m90) cc_final: 0.3997 (m90) REVERT: B 326 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8242 (pm20) REVERT: F 40 MET cc_start: 0.2916 (ppp) cc_final: 0.2434 (ppp) REVERT: F 80 TYR cc_start: 0.6543 (m-80) cc_final: 0.6000 (m-80) REVERT: G 17 ASP cc_start: 0.7184 (m-30) cc_final: 0.6902 (p0) REVERT: G 45 LYS cc_start: 0.6283 (mmmt) cc_final: 0.5773 (tmmt) REVERT: G 49 HIS cc_start: 0.4552 (m90) cc_final: 0.4190 (m90) REVERT: G 82 ASP cc_start: 0.6745 (m-30) cc_final: 0.6490 (m-30) REVERT: G 98 PHE cc_start: 0.5849 (OUTLIER) cc_final: 0.5384 (t80) REVERT: C 121 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5958 (mt) REVERT: C 126 MET cc_start: 0.8058 (ptm) cc_final: 0.7781 (pmm) REVERT: C 186 TYR cc_start: 0.8117 (m-80) cc_final: 0.7882 (m-80) REVERT: H 18 LEU cc_start: 0.7022 (mm) cc_final: 0.6610 (mm) REVERT: H 40 MET cc_start: 0.4285 (ppp) cc_final: 0.3744 (ppp) REVERT: H 80 TYR cc_start: 0.6809 (m-80) cc_final: 0.6165 (m-80) REVERT: I 45 LYS cc_start: 0.6262 (mmmt) cc_final: 0.5802 (tttm) REVERT: I 89 GLN cc_start: 0.3627 (pm20) cc_final: 0.2139 (pp30) outliers start: 52 outliers final: 40 residues processed: 199 average time/residue: 0.3582 time to fit residues: 83.8493 Evaluate side-chains 196 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 176 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 188 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN D 82 HIS B 365 HIS ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS C 220 ASN C 365 HIS C 485 GLN H 3 GLN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.141137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.119112 restraints weight = 43782.853| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.96 r_work: 0.4024 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16482 Z= 0.151 Angle : 0.634 11.549 22386 Z= 0.316 Chirality : 0.045 0.319 2487 Planarity : 0.004 0.044 2817 Dihedral : 4.911 57.869 2194 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.68 % Favored : 93.01 % Rotamer: Outliers : 3.17 % Allowed : 20.49 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.19), residues: 1947 helix: 0.74 (0.29), residues: 312 sheet: -0.26 (0.21), residues: 591 loop : -1.50 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 157 TYR 0.014 0.001 TYR B 364 PHE 0.032 0.002 PHE B 486 TRP 0.034 0.002 TRP F 83 HIS 0.008 0.001 HIS I 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (16458) covalent geometry : angle 0.61927 / 0.31 (22326) SS BOND : bond 0.00237 / 0.14 ( 12) SS BOND : angle 1.23135 / 0.74 ( 24) hydrogen bonds : bond 0.03777 / 2.61 ( 526) hydrogen bonds : angle 5.86437 / 4.01 ( 1389) link_BETA1-4 : bond 0.00072 / 0.04 ( 3) link_BETA1-4 : angle 2.77733 / 1.29 ( 9) link_NAG-ASN : bond 0.00658 / 0.36 ( 9) link_NAG-ASN : angle 3.45318 / 2.27 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5217.85 seconds wall clock time: 89 minutes 56.65 seconds (5396.65 seconds total)