Starting phenix.real_space_refine on Sun Aug 24 01:47:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yrn_34063/08_2025/7yrn_34063.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yrn_34063/08_2025/7yrn_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_34063/08_2025/7yrn_34063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yrn_34063/08_2025/7yrn_34063.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yrn_34063/08_2025/7yrn_34063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yrn_34063/08_2025/7yrn_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-2.0-5787/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.39, per 1000 atoms: 0.27 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: 1.72 Conformation dependent library (CDL) restraints added in 811.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.68 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: 3.14 Time building geometry restraints manager: 2.22 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: 9238 15.02 - 30.03: 466 30.03 - 45.05: 149 45.05 - 60.07: 30 60.07 - 75.08: 8 Dihedral angle restraints: 9891 sinusoidal: 4053 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 9888 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: 4.760 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: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.840 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 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 : 10.423 75.084 6099 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 aren 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 covalent geometry : bond 0.00217 (16458) covalent geometry : angle 0.48159 (22326) SS BOND : bond 0.00115 ( 12) SS BOND : angle 0.74042 ( 24) hydrogen bonds : bond 0.19539 ( 526) hydrogen bonds : angle 8.08117 ( 1389) link_BETA1-4 : bond 0.00054 ( 3) link_BETA1-4 : angle 1.49169 ( 9) link_NAG-ASN : bond 0.00721 ( 9) link_NAG-ASN : angle 3.43651 ( 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 : 0.660 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: 0.5099 time to fit residues: 208.0297 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 : 0.629 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 212 GLN A 220 ASN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 H 39 GLN I 38 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.145217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.122418 restraints weight = 44031.892| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 3.01 r_work: 0.4113 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16482 Z= 0.159 Angle : 0.625 9.090 22386 Z= 0.322 Chirality : 0.046 0.331 2487 Planarity : 0.004 0.042 2817 Dihedral : 6.625 55.852 2463 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.44 % Favored : 94.09 % Rotamer: Outliers : 5.43 % Allowed : 13.81 % Favored : 80.76 % 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 aren not related in a simple way. whole: -0.65 (0.19), residues: 1947 helix: 0.57 (0.28), residues: 309 sheet: 0.30 (0.20), residues: 642 loop : -1.26 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 225 TYR 0.013 0.001 TYR C 488 PHE 0.020 0.002 PHE B 486 TRP 0.016 0.001 TRP B 431 HIS 0.004 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00353 (16458) covalent geometry : angle 0.59725 (22326) SS BOND : bond 0.00769 ( 12) SS BOND : angle 1.33759 ( 24) hydrogen bonds : bond 0.05138 ( 526) hydrogen bonds : angle 6.18773 ( 1389) link_BETA1-4 : bond 0.00368 ( 3) link_BETA1-4 : angle 1.79003 ( 9) link_NAG-ASN : bond 0.00882 ( 9) link_NAG-ASN : angle 5.15153 ( 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 284 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 188 time to evaluate : 0.668 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: 0.8615 (OUTLIER) cc_final: 0.8210 (mtp) REVERT: A 222 HIS cc_start: 0.7140 (OUTLIER) cc_final: 0.6697 (p90) REVERT: A 326 GLU cc_start: 0.8404 (mp0) cc_final: 0.7978 (mp0) REVERT: A 682 GLU cc_start: 0.8513 (mp0) cc_final: 0.8141 (mp0) REVERT: D 40 MET cc_start: 0.4086 (ppp) cc_final: 0.3591 (ppp) REVERT: E 49 HIS cc_start: 0.4550 (m90) cc_final: 0.4027 (m90) REVERT: B 222 HIS cc_start: 0.7185 (OUTLIER) cc_final: 0.6819 (p90) REVERT: B 682 GLU cc_start: 0.8507 (mp0) cc_final: 0.8113 (mp0) REVERT: F 19 LYS cc_start: 0.7219 (mmtm) cc_final: 0.6981 (mppt) REVERT: F 40 MET cc_start: 0.2694 (ppp) cc_final: 0.2385 (ppp) REVERT: F 80 TYR cc_start: 0.6242 (m-80) cc_final: 0.5894 (m-80) REVERT: G 14 SER cc_start: 0.8205 (m) cc_final: 0.7664 (p) REVERT: G 17 ASP cc_start: 0.7226 (m-30) cc_final: 0.6785 (p0) REVERT: G 49 HIS cc_start: 0.4331 (m90) cc_final: 0.3641 (m90) REVERT: G 98 PHE cc_start: 0.5552 (OUTLIER) cc_final: 0.5112 (t80) REVERT: C 222 HIS cc_start: 0.7144 (OUTLIER) cc_final: 0.6837 (p90) REVERT: H 18 LEU cc_start: 0.7148 (mm) cc_final: 0.6715 (mm) REVERT: H 19 LYS cc_start: 0.7606 (mppt) cc_final: 0.7372 (mmtm) REVERT: H 39 GLN cc_start: 0.6357 (tt0) cc_final: 0.6141 (tt0) REVERT: H 40 MET cc_start: 0.4110 (ppp) cc_final: 0.3605 (ppp) REVERT: H 78 THR cc_start: 0.8265 (m) cc_final: 0.7620 (t) REVERT: I 45 LYS cc_start: 0.6628 (mmmt) cc_final: 0.5900 (ttpp) REVERT: I 49 HIS cc_start: 0.4307 (m90) cc_final: 0.3639 (m-70) REVERT: I 55 GLN cc_start: 0.7180 (OUTLIER) cc_final: 0.6828 (tt0) outliers start: 96 outliers final: 46 residues processed: 260 average time/residue: 0.4793 time to fit residues: 142.4587 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 : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL 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 21 ILE Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 105 ASP 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 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 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: 5.9990 chunk 20 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 GLN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN A 365 HIS D 3 GLN B 212 GLN B 337 GLN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN F 3 GLN F 82 HIS ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 GLN ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN I 38 GLN ** I 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.138921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.114993 restraints weight = 44355.105| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 3.06 r_work: 0.3985 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 16482 Z= 0.270 Angle : 0.691 10.487 22386 Z= 0.359 Chirality : 0.048 0.363 2487 Planarity : 0.005 0.045 2817 Dihedral : 7.186 59.355 2461 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.75 % Favored : 93.79 % Rotamer: Outliers : 5.72 % Allowed : 14.37 % Favored : 79.91 % 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 aren not related in a simple way. whole: -0.92 (0.19), residues: 1947 helix: 0.34 (0.29), residues: 312 sheet: 0.01 (0.21), residues: 651 loop : -1.35 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG I 24 TYR 0.025 0.002 TYR D 99 PHE 0.021 0.003 PHE B 486 TRP 0.017 0.002 TRP F 108 HIS 0.006 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00611 (16458) covalent geometry : angle 0.66648 (22326) SS BOND : bond 0.00355 ( 12) SS BOND : angle 1.58412 ( 24) hydrogen bonds : bond 0.04982 ( 526) hydrogen bonds : angle 6.28825 ( 1389) link_BETA1-4 : bond 0.00832 ( 3) link_BETA1-4 : angle 3.45833 ( 9) link_NAG-ASN : bond 0.00803 ( 9) link_NAG-ASN : angle 4.73389 ( 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 261 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 160 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.7397 (OUTLIER) cc_final: 0.6978 (p90) REVERT: A 371 MET cc_start: 0.7875 (mtm) cc_final: 0.7558 (mtm) REVERT: A 682 GLU cc_start: 0.8652 (mp0) cc_final: 0.8209 (mp0) REVERT: D 40 MET cc_start: 0.4087 (ppp) cc_final: 0.3591 (ppp) REVERT: E 49 HIS cc_start: 0.4573 (m90) cc_final: 0.4001 (m90) REVERT: F 40 MET cc_start: 0.2698 (ppp) cc_final: 0.2372 (ppp) REVERT: F 80 TYR cc_start: 0.6327 (m-80) cc_final: 0.5883 (m-80) REVERT: F 82 HIS cc_start: 0.7384 (t-170) cc_final: 0.7182 (t70) REVERT: G 49 HIS cc_start: 0.4855 (m90) cc_final: 0.4177 (m90) REVERT: G 98 PHE cc_start: 0.5802 (OUTLIER) cc_final: 0.5249 (t80) REVERT: H 18 LEU cc_start: 0.7172 (mm) cc_final: 0.6687 (mm) REVERT: H 37 VAL cc_start: 0.5477 (m) cc_final: 0.5219 (p) REVERT: H 40 MET cc_start: 0.4082 (ppp) cc_final: 0.3533 (ppp) REVERT: H 78 THR cc_start: 0.8226 (m) cc_final: 0.7000 (t) REVERT: H 80 TYR cc_start: 0.6718 (m-80) cc_final: 0.5871 (m-80) REVERT: I 49 HIS cc_start: 0.4635 (m90) cc_final: 0.4100 (m90) REVERT: I 89 GLN cc_start: 0.4987 (pm20) cc_final: 0.3853 (pp30) outliers start: 101 outliers final: 55 residues processed: 229 average time/residue: 0.4726 time to fit residues: 124.0780 Evaluate side-chains 195 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 138 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 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 A residue 653 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 21 ILE 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 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 60 TYR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 35 TRP 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 162 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: 0.7980 chunk 180 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 156 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 178 optimal weight: 0.5980 chunk 38 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 HIS ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN 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** F 3 GLN C 212 GLN C 220 ASN C 485 GLN C 692 GLN H 82 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.141852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.119227 restraints weight = 43991.391| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 3.10 r_work: 0.4021 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16482 Z= 0.135 Angle : 0.577 8.752 22386 Z= 0.298 Chirality : 0.045 0.327 2487 Planarity : 0.004 0.048 2817 Dihedral : 6.673 59.068 2458 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.55 % Favored : 93.99 % Rotamer: Outliers : 4.75 % Allowed : 15.68 % Favored : 79.57 % 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 aren not related in a simple way. whole: -0.93 (0.19), residues: 1947 helix: 0.41 (0.29), residues: 312 sheet: 0.00 (0.21), residues: 639 loop : -1.37 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG G 24 TYR 0.016 0.001 TYR D 60 PHE 0.014 0.002 PHE E 62 TRP 0.014 0.001 TRP H 83 HIS 0.005 0.001 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00304 (16458) covalent geometry : angle 0.55750 (22326) SS BOND : bond 0.00274 ( 12) SS BOND : angle 1.15024 ( 24) hydrogen bonds : bond 0.04167 ( 526) hydrogen bonds : angle 5.98044 ( 1389) link_BETA1-4 : bond 0.00086 ( 3) link_BETA1-4 : angle 2.49762 ( 9) link_NAG-ASN : bond 0.00685 ( 9) link_NAG-ASN : angle 3.96267 ( 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 248 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 164 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.7881 (mtm) cc_final: 0.7634 (mtm) REVERT: A 682 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8379 (mp0) REVERT: D 40 MET cc_start: 0.4119 (ppp) cc_final: 0.3555 (ppp) REVERT: D 102 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7471 (mt) REVERT: E 49 HIS cc_start: 0.4436 (m90) cc_final: 0.3897 (m90) REVERT: F 19 LYS cc_start: 0.7726 (mppt) cc_final: 0.7464 (mmtm) REVERT: F 40 MET cc_start: 0.2722 (ppp) cc_final: 0.2339 (ppp) REVERT: F 80 TYR cc_start: 0.6353 (m-80) cc_final: 0.5819 (m-80) REVERT: G 17 ASP cc_start: 0.7350 (m-30) cc_final: 0.6875 (p0) REVERT: G 45 LYS cc_start: 0.6397 (mmmt) cc_final: 0.5699 (ttpp) REVERT: G 49 HIS cc_start: 0.4314 (m90) cc_final: 0.3763 (m90) REVERT: G 98 PHE cc_start: 0.5826 (OUTLIER) cc_final: 0.5570 (t80) REVERT: H 18 LEU cc_start: 0.7009 (mm) cc_final: 0.6619 (mm) REVERT: H 40 MET cc_start: 0.4119 (ppp) cc_final: 0.3583 (ppp) REVERT: H 78 THR cc_start: 0.8320 (m) cc_final: 0.7112 (t) REVERT: H 80 TYR cc_start: 0.6606 (m-80) cc_final: 0.5803 (m-80) REVERT: I 45 LYS cc_start: 0.6131 (mmmt) cc_final: 0.5637 (ttpp) REVERT: I 49 HIS cc_start: 0.4613 (m90) cc_final: 0.4112 (m90) REVERT: I 89 GLN cc_start: 0.4679 (pm20) cc_final: 0.3802 (pp30) outliers start: 84 outliers final: 42 residues processed: 223 average time/residue: 0.4500 time to fit residues: 115.6788 Evaluate side-chains 195 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 150 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 199 VAL 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 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 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 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 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 98 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 169 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 146 optimal weight: 0.1980 chunk 10 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 69 optimal weight: 0.0770 chunk 130 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.6544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** G 27 GLN C 220 ASN ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 GLN H 3 GLN I 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.139880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.116232 restraints weight = 43985.888| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 3.02 r_work: 0.4001 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3084 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= 0.188 Angle : 0.603 9.213 22386 Z= 0.311 Chirality : 0.046 0.340 2487 Planarity : 0.004 0.043 2817 Dihedral : 6.667 59.656 2452 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.01 % Favored : 93.58 % Rotamer: Outliers : 4.75 % Allowed : 16.92 % Favored : 78.32 % 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 aren not related in a simple way. whole: -1.06 (0.19), residues: 1947 helix: 0.42 (0.29), residues: 312 sheet: -0.13 (0.21), residues: 639 loop : -1.47 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 24 TYR 0.021 0.002 TYR C 364 PHE 0.016 0.002 PHE E 92 TRP 0.026 0.002 TRP D 83 HIS 0.005 0.001 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00428 (16458) covalent geometry : angle 0.58273 (22326) SS BOND : bond 0.00251 ( 12) SS BOND : angle 1.20455 ( 24) hydrogen bonds : bond 0.04208 ( 526) hydrogen bonds : angle 6.02234 ( 1389) link_BETA1-4 : bond 0.00289 ( 3) link_BETA1-4 : angle 3.05647 ( 9) link_NAG-ASN : bond 0.00679 ( 9) link_NAG-ASN : angle 4.02520 ( 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 249 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 165 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.7303 (OUTLIER) cc_final: 0.6870 (p90) REVERT: A 371 MET cc_start: 0.7879 (mtm) cc_final: 0.7640 (mtm) REVERT: A 682 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8382 (mp0) REVERT: D 40 MET cc_start: 0.4133 (ppp) cc_final: 0.3657 (ppp) REVERT: D 83 TRP cc_start: 0.5115 (t-100) cc_final: 0.4409 (t-100) REVERT: D 102 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7478 (mt) REVERT: E 32 TYR cc_start: 0.7344 (OUTLIER) cc_final: 0.5906 (t80) REVERT: E 49 HIS cc_start: 0.4607 (m90) cc_final: 0.4000 (m90) REVERT: E 82 ASP cc_start: 0.7451 (m-30) cc_final: 0.7175 (m-30) REVERT: F 40 MET cc_start: 0.2670 (ppp) cc_final: 0.2327 (ppp) REVERT: F 80 TYR cc_start: 0.6326 (m-80) cc_final: 0.5742 (m-80) REVERT: G 17 ASP cc_start: 0.7316 (m-30) cc_final: 0.6905 (p0) REVERT: G 49 HIS cc_start: 0.4432 (m90) cc_final: 0.3930 (m90) REVERT: G 98 PHE cc_start: 0.5850 (OUTLIER) cc_final: 0.5546 (t80) REVERT: H 18 LEU cc_start: 0.7033 (mm) cc_final: 0.6650 (mm) REVERT: H 40 MET cc_start: 0.4137 (ppp) cc_final: 0.3577 (ppp) REVERT: H 80 TYR cc_start: 0.6601 (m-80) cc_final: 0.5997 (m-80) REVERT: I 49 HIS cc_start: 0.4553 (m90) cc_final: 0.4129 (m90) REVERT: I 89 GLN cc_start: 0.4759 (pm20) cc_final: 0.3696 (pp30) outliers start: 84 outliers final: 44 residues processed: 222 average time/residue: 0.4410 time to fit residues: 113.1507 Evaluate side-chains 194 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 537 ILE Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain D residue 34 ILE 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 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 98 PHE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 211 MET 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: 4.9990 chunk 44 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 166 optimal weight: 0.0000 chunk 10 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** F 3 GLN F 82 HIS C 165 ASN C 220 ASN ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.141442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.118012 restraints weight = 44020.235| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 3.03 r_work: 0.4030 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16482 Z= 0.131 Angle : 0.572 8.585 22386 Z= 0.294 Chirality : 0.044 0.322 2487 Planarity : 0.003 0.043 2817 Dihedral : 6.266 59.162 2448 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.16 % Favored : 93.48 % Rotamer: Outliers : 4.07 % Allowed : 18.45 % Favored : 77.48 % 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 aren not related in a simple way. whole: -1.01 (0.19), residues: 1947 helix: 0.51 (0.29), residues: 312 sheet: -0.02 (0.22), residues: 606 loop : -1.47 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 150 TYR 0.012 0.001 TYR B 494 PHE 0.020 0.001 PHE E 62 TRP 0.025 0.001 TRP F 83 HIS 0.005 0.001 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00294 (16458) covalent geometry : angle 0.55493 (22326) SS BOND : bond 0.00218 ( 12) SS BOND : angle 0.96648 ( 24) hydrogen bonds : bond 0.03904 ( 526) hydrogen bonds : angle 5.93057 ( 1389) link_BETA1-4 : bond 0.00047 ( 3) link_BETA1-4 : angle 2.59623 ( 9) link_NAG-ASN : bond 0.00668 ( 9) link_NAG-ASN : angle 3.69166 ( 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 237 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 165 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.7159 (OUTLIER) cc_final: 0.6747 (p90) REVERT: A 682 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: D 40 MET cc_start: 0.4176 (ppp) cc_final: 0.3615 (ppp) REVERT: D 83 TRP cc_start: 0.5038 (t-100) cc_final: 0.4361 (t-100) REVERT: D 102 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7472 (mt) REVERT: E 49 HIS cc_start: 0.4448 (m90) cc_final: 0.3881 (m90) REVERT: E 82 ASP cc_start: 0.7474 (m-30) cc_final: 0.7230 (m-30) REVERT: B 326 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8515 (mp0) REVERT: F 37 VAL cc_start: 0.5667 (m) cc_final: 0.5448 (p) REVERT: F 40 MET cc_start: 0.2848 (ppp) cc_final: 0.2464 (ppp) REVERT: F 80 TYR cc_start: 0.6305 (m-80) cc_final: 0.5701 (m-80) REVERT: G 17 ASP cc_start: 0.7227 (m-30) cc_final: 0.6892 (p0) REVERT: G 45 LYS cc_start: 0.6253 (mmmt) cc_final: 0.5644 (ttpp) REVERT: G 49 HIS cc_start: 0.4562 (m90) cc_final: 0.4129 (m90) REVERT: G 98 PHE cc_start: 0.5824 (OUTLIER) cc_final: 0.5575 (t80) REVERT: H 18 LEU cc_start: 0.7047 (mm) cc_final: 0.6654 (mm) REVERT: H 40 MET cc_start: 0.4194 (ppp) cc_final: 0.3652 (ppp) REVERT: H 80 TYR cc_start: 0.6684 (m-80) cc_final: 0.6071 (m-80) REVERT: I 45 LYS cc_start: 0.6134 (mmmt) cc_final: 0.5616 (tttp) REVERT: I 49 HIS cc_start: 0.4295 (m90) cc_final: 0.4069 (m90) REVERT: I 89 GLN cc_start: 0.4662 (pm20) cc_final: 0.3760 (pp30) outliers start: 72 outliers final: 48 residues processed: 218 average time/residue: 0.4344 time to fit residues: 109.8036 Evaluate side-chains 203 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 150 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 211 MET 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 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 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 326 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 171 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 139 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 186 optimal weight: 20.0000 chunk 159 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** E 27 GLN B 220 ASN B 365 HIS ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 GLN H 3 GLN ** 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 = 0.4445 r_free = 0.4445 target = 0.137057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.114228 restraints weight = 43923.893| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 3.08 r_work: 0.3938 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 16482 Z= 0.283 Angle : 0.709 9.846 22386 Z= 0.366 Chirality : 0.048 0.353 2487 Planarity : 0.005 0.045 2817 Dihedral : 7.031 58.524 2448 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.99 % Favored : 92.71 % Rotamer: Outliers : 4.81 % Allowed : 18.00 % 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 aren not related in a simple way. whole: -1.37 (0.19), residues: 1947 helix: 0.31 (0.29), residues: 312 sheet: -0.49 (0.21), residues: 633 loop : -1.59 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 150 TYR 0.021 0.002 TYR B 494 PHE 0.035 0.003 PHE C 486 TRP 0.039 0.002 TRP F 83 HIS 0.007 0.001 HIS E 49 Details of bonding type rmsd covalent geometry : bond 0.00644 (16458) covalent geometry : angle 0.68826 (22326) SS BOND : bond 0.00265 ( 12) SS BOND : angle 1.42210 ( 24) hydrogen bonds : bond 0.04554 ( 526) hydrogen bonds : angle 6.37194 ( 1389) link_BETA1-4 : bond 0.00724 ( 3) link_BETA1-4 : angle 3.73095 ( 9) link_NAG-ASN : bond 0.00693 ( 9) link_NAG-ASN : angle 4.35159 ( 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 236 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 151 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.7473 (OUTLIER) cc_final: 0.7037 (p90) REVERT: A 473 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7300 (ptm) REVERT: A 682 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8460 (mp0) REVERT: D 40 MET cc_start: 0.4115 (ppp) cc_final: 0.3612 (ppp) REVERT: D 102 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7656 (mt) REVERT: E 32 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.7155 (t80) REVERT: E 49 HIS cc_start: 0.4637 (m90) cc_final: 0.3999 (m90) REVERT: F 37 VAL cc_start: 0.5338 (m) cc_final: 0.5093 (p) REVERT: F 40 MET cc_start: 0.2720 (ppp) cc_final: 0.2326 (ppp) REVERT: F 80 TYR cc_start: 0.6423 (m-80) cc_final: 0.5893 (m-80) REVERT: G 17 ASP cc_start: 0.7261 (m-30) cc_final: 0.6806 (p0) REVERT: G 49 HIS cc_start: 0.4766 (m90) cc_final: 0.4278 (m90) REVERT: H 18 LEU cc_start: 0.7082 (mm) cc_final: 0.6725 (mm) REVERT: H 40 MET cc_start: 0.4248 (ppp) cc_final: 0.3670 (ppp) REVERT: H 80 TYR cc_start: 0.6700 (m-80) cc_final: 0.6097 (m-80) REVERT: I 49 HIS cc_start: 0.4622 (m90) cc_final: 0.4219 (m90) REVERT: I 89 GLN cc_start: 0.4783 (pm20) cc_final: 0.3536 (pp30) outliers start: 85 outliers final: 49 residues processed: 214 average time/residue: 0.4229 time to fit residues: 105.5639 Evaluate side-chains 191 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 137 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 211 MET 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 653 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 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 104 LEU 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 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 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 161 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 211 MET 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 78 optimal weight: 0.7980 chunk 167 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 176 optimal weight: 0.0270 chunk 30 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 184 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** 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** ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 365 HIS B 485 GLN C 220 ASN C 365 HIS ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.140800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.118221 restraints weight = 44347.026| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 3.13 r_work: 0.4012 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3538 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= 0.130 Angle : 0.604 10.864 22386 Z= 0.305 Chirality : 0.045 0.314 2487 Planarity : 0.004 0.046 2817 Dihedral : 6.404 59.731 2446 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.27 % Favored : 93.43 % Rotamer: Outliers : 3.45 % Allowed : 20.26 % Favored : 76.29 % 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 aren not related in a simple way. whole: -1.18 (0.19), residues: 1947 helix: 0.53 (0.29), residues: 312 sheet: -0.33 (0.21), residues: 606 loop : -1.50 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 191 TYR 0.017 0.001 TYR C 364 PHE 0.031 0.002 PHE A 486 TRP 0.030 0.001 TRP F 83 HIS 0.005 0.001 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00292 (16458) covalent geometry : angle 0.58834 (22326) SS BOND : bond 0.00229 ( 12) SS BOND : angle 0.96133 ( 24) hydrogen bonds : bond 0.03855 ( 526) hydrogen bonds : angle 5.97206 ( 1389) link_BETA1-4 : bond 0.00078 ( 3) link_BETA1-4 : angle 2.77792 ( 9) link_NAG-ASN : bond 0.00679 ( 9) link_NAG-ASN : angle 3.63789 ( 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 232 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 171 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.8037 (ptm) cc_final: 0.7763 (pmm) REVERT: A 682 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: D 40 MET cc_start: 0.4131 (ppp) cc_final: 0.3564 (ppp) REVERT: D 80 TYR cc_start: 0.6917 (m-80) cc_final: 0.6323 (m-80) REVERT: D 102 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7607 (mt) REVERT: E 49 HIS cc_start: 0.4575 (m90) cc_final: 0.4010 (m90) REVERT: B 121 LEU cc_start: 0.6402 (OUTLIER) cc_final: 0.6114 (mm) REVERT: B 326 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8398 (pm20) REVERT: F 40 MET cc_start: 0.2853 (ppp) cc_final: 0.2380 (ppp) REVERT: F 80 TYR cc_start: 0.6427 (m-80) cc_final: 0.5868 (m-80) REVERT: F 94 TYR cc_start: 0.7988 (m-10) cc_final: 0.7033 (m-10) REVERT: G 17 ASP cc_start: 0.7277 (m-30) cc_final: 0.6902 (p0) REVERT: G 49 HIS cc_start: 0.4260 (m90) cc_final: 0.3866 (m90) REVERT: H 18 LEU cc_start: 0.7084 (mm) cc_final: 0.6741 (mm) REVERT: H 40 MET cc_start: 0.4289 (ppp) cc_final: 0.3741 (ppp) REVERT: H 80 TYR cc_start: 0.6799 (m-80) cc_final: 0.6164 (m-80) outliers start: 61 outliers final: 38 residues processed: 218 average time/residue: 0.4197 time to fit residues: 106.7857 Evaluate side-chains 191 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 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 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 B residue 121 LEU 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 537 ILE Chi-restraints excluded: chain F residue 34 ILE 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 161 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 242 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 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 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: 6.9990 chunk 102 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 172 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 212 GLN ** 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** F 3 GLN C 220 ASN ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.138935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.116340 restraints weight = 44232.243| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 3.09 r_work: 0.3971 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16482 Z= 0.197 Angle : 0.655 10.551 22386 Z= 0.330 Chirality : 0.046 0.334 2487 Planarity : 0.004 0.043 2817 Dihedral : 6.503 58.578 2444 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.52 % Favored : 93.17 % Rotamer: Outliers : 3.40 % Allowed : 20.77 % Favored : 75.83 % 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 aren not related in a simple way. whole: -1.27 (0.19), residues: 1947 helix: 0.50 (0.29), residues: 312 sheet: -0.41 (0.21), residues: 606 loop : -1.56 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.017 0.002 TYR B 494 PHE 0.041 0.002 PHE E 62 TRP 0.037 0.002 TRP F 83 HIS 0.006 0.001 HIS I 49 Details of bonding type rmsd covalent geometry : bond 0.00448 (16458) covalent geometry : angle 0.63821 (22326) SS BOND : bond 0.00266 ( 12) SS BOND : angle 1.16890 ( 24) hydrogen bonds : bond 0.04052 ( 526) hydrogen bonds : angle 6.09413 ( 1389) link_BETA1-4 : bond 0.00421 ( 3) link_BETA1-4 : angle 3.14970 ( 9) link_NAG-ASN : bond 0.00621 ( 9) link_NAG-ASN : angle 3.86213 ( 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 208 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 148 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.8037 (ptm) cc_final: 0.7810 (pmm) REVERT: A 682 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8356 (mp0) REVERT: D 40 MET cc_start: 0.4168 (ppp) cc_final: 0.3582 (ppp) REVERT: D 80 TYR cc_start: 0.6920 (m-80) cc_final: 0.6337 (m-80) REVERT: D 102 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7671 (mt) REVERT: E 32 TYR cc_start: 0.7550 (OUTLIER) cc_final: 0.7096 (t80) REVERT: E 49 HIS cc_start: 0.4696 (m90) cc_final: 0.4079 (m90) REVERT: B 121 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.6324 (mt) REVERT: B 326 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8599 (pm20) REVERT: F 40 MET cc_start: 0.2882 (ppp) cc_final: 0.2484 (ppp) REVERT: F 80 TYR cc_start: 0.6461 (m-80) cc_final: 0.5900 (m-80) REVERT: G 17 ASP cc_start: 0.7208 (m-30) cc_final: 0.6856 (p0) REVERT: G 49 HIS cc_start: 0.4525 (m90) cc_final: 0.4079 (m90) REVERT: H 18 LEU cc_start: 0.7072 (mm) cc_final: 0.6692 (mm) REVERT: H 40 MET cc_start: 0.4333 (ppp) cc_final: 0.3782 (ppp) REVERT: H 80 TYR cc_start: 0.6760 (m-80) cc_final: 0.6145 (m-80) REVERT: I 49 HIS cc_start: 0.4820 (m90) cc_final: 0.4584 (m-70) outliers start: 60 outliers final: 37 residues processed: 196 average time/residue: 0.4126 time to fit residues: 94.5793 Evaluate side-chains 182 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 121 LEU 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 537 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 115 ILE 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 242 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 115 ILE 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: 4.9990 chunk 122 optimal weight: 0.9980 chunk 187 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 146 optimal weight: 1.9990 chunk 108 optimal weight: 0.0040 chunk 112 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 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 F 3 GLN F 82 HIS ** G 34 ASN ** 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** I 27 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 = 0.4487 r_free = 0.4487 target = 0.139942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.116475 restraints weight = 44055.136| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 3.01 r_work: 0.4000 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16482 Z= 0.161 Angle : 0.648 11.923 22386 Z= 0.325 Chirality : 0.046 0.324 2487 Planarity : 0.004 0.044 2817 Dihedral : 6.449 59.691 2444 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.52 % Favored : 93.17 % Rotamer: Outliers : 3.00 % Allowed : 21.17 % Favored : 75.83 % 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 aren not related in a simple way. whole: -1.28 (0.19), residues: 1947 helix: 0.51 (0.29), residues: 312 sheet: -0.40 (0.22), residues: 591 loop : -1.56 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 150 TYR 0.016 0.002 TYR D 60 PHE 0.032 0.002 PHE B 486 TRP 0.034 0.002 TRP F 83 HIS 0.005 0.001 HIS B 365 Details of bonding type rmsd covalent geometry : bond 0.00364 (16458) covalent geometry : angle 0.63247 (22326) SS BOND : bond 0.00262 ( 12) SS BOND : angle 1.10065 ( 24) hydrogen bonds : bond 0.03900 ( 526) hydrogen bonds : angle 6.02213 ( 1389) link_BETA1-4 : bond 0.00148 ( 3) link_BETA1-4 : angle 2.90880 ( 9) link_NAG-ASN : bond 0.00622 ( 9) link_NAG-ASN : angle 3.68765 ( 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 206 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 153 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.8020 (ptm) cc_final: 0.7779 (pmm) REVERT: A 222 HIS cc_start: 0.7254 (OUTLIER) cc_final: 0.6846 (p90) REVERT: A 682 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: D 19 LYS cc_start: 0.7758 (mppt) cc_final: 0.7537 (mmpt) REVERT: D 40 MET cc_start: 0.4238 (ppp) cc_final: 0.3696 (ppp) REVERT: D 80 TYR cc_start: 0.6919 (m-80) cc_final: 0.6325 (m-80) REVERT: D 102 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7630 (mt) REVERT: E 32 TYR cc_start: 0.7291 (OUTLIER) cc_final: 0.6814 (t80) REVERT: E 49 HIS cc_start: 0.4623 (m90) cc_final: 0.4165 (m90) REVERT: B 126 MET cc_start: 0.8160 (ptm) cc_final: 0.7868 (pmm) REVERT: F 40 MET cc_start: 0.3022 (ppp) cc_final: 0.2534 (ppp) REVERT: F 80 TYR cc_start: 0.6417 (m-80) cc_final: 0.5830 (m-80) REVERT: F 94 TYR cc_start: 0.8060 (m-10) cc_final: 0.7175 (m-10) REVERT: G 17 ASP cc_start: 0.7084 (m-30) cc_final: 0.6799 (p0) REVERT: G 45 LYS cc_start: 0.6155 (mmmt) cc_final: 0.5704 (tmmt) REVERT: G 49 HIS cc_start: 0.4539 (m90) cc_final: 0.4146 (m90) REVERT: C 126 MET cc_start: 0.8116 (ptm) cc_final: 0.7797 (pmm) REVERT: H 18 LEU cc_start: 0.7030 (mm) cc_final: 0.6656 (mm) REVERT: H 40 MET cc_start: 0.4479 (ppp) cc_final: 0.3926 (ppp) REVERT: H 80 TYR cc_start: 0.6768 (m-80) cc_final: 0.6149 (m-80) REVERT: I 49 HIS cc_start: 0.4633 (m90) cc_final: 0.4320 (m-70) outliers start: 53 outliers final: 40 residues processed: 196 average time/residue: 0.3877 time to fit residues: 89.5469 Evaluate side-chains 191 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 537 ILE Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain D residue 34 ILE 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 105 ASP Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 485 GLN 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 72 VAL Chi-restraints excluded: chain F residue 115 ILE 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 242 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 115 ILE 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: 1.9990 chunk 108 optimal weight: 0.4980 chunk 165 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 152 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 GLN ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS ** G 34 ASN ** 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** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.139815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.117366 restraints weight = 43759.533| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 3.05 r_work: 0.3988 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.200 16482 Z= 0.250 Angle : 0.973 59.199 22386 Z= 0.513 Chirality : 0.049 0.874 2487 Planarity : 0.004 0.056 2817 Dihedral : 6.448 59.686 2444 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.57 % Favored : 93.12 % Rotamer: Outliers : 2.66 % Allowed : 21.51 % Favored : 75.83 % Cbeta Deviations : 0.11 % 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 aren not related in a simple way. whole: -1.29 (0.19), residues: 1947 helix: 0.49 (0.29), residues: 312 sheet: -0.41 (0.22), residues: 591 loop : -1.57 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 24 TYR 0.015 0.002 TYR B 494 PHE 0.032 0.002 PHE B 486 TRP 0.030 0.002 TRP F 83 HIS 0.005 0.001 HIS B 365 Details of bonding type rmsd covalent geometry : bond 0.00514 (16458) covalent geometry : angle 0.96378 (22326) SS BOND : bond 0.00284 ( 12) SS BOND : angle 1.08334 ( 24) hydrogen bonds : bond 0.03921 ( 526) hydrogen bonds : angle 6.02439 ( 1389) link_BETA1-4 : bond 0.00603 ( 3) link_BETA1-4 : angle 2.94014 ( 9) link_NAG-ASN : bond 0.00660 ( 9) link_NAG-ASN : angle 3.70371 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6253.66 seconds wall clock time: 107 minutes 51.19 seconds (6471.19 seconds total)