Starting phenix.real_space_refine on Sat Jun 14 12:01:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yrn_34063/06_2025/7yrn_34063.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yrn_34063/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yrn_34063/06_2025/7yrn_34063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yrn_34063/06_2025/7yrn_34063.map" model { file = "/net/cci-nas-00/data/ceres_data/7yrn_34063/06_2025/7yrn_34063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yrn_34063/06_2025/7yrn_34063.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.57, per 1000 atoms: 0.60 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: 3.89 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.71 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: 5.08 Time building geometry restraints manager: 4.58 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: 0.11 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'K' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 57.150 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: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 36.260 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.100 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:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.320 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP I 96 HIS 0.002 0.000 HIS A 319 PHE 0.008 0.001 PHE I 92 TYR 0.007 0.001 TYR C 129 ARG 0.001 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00721 ( 9) link_NAG-ASN : angle 3.43651 ( 27) link_BETA1-4 : bond 0.00054 ( 3) link_BETA1-4 : angle 1.49169 ( 9) hydrogen bonds : bond 0.19539 ( 526) hydrogen bonds : angle 8.08117 ( 1389) SS BOND : bond 0.00115 ( 12) SS BOND : angle 0.74042 ( 24) covalent geometry : bond 0.00217 (16458) covalent geometry : angle 0.48159 (22326) *********************** 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 : 1.818 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: 1.0224 time to fit residues: 420.6510 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 : 1.794 ------------------------------------------------------------------------------- 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 162 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 150 optimal weight: 0.0980 chunk 58 optimal weight: 0.0470 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 0.4980 chunk 174 optimal weight: 1.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- 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 212 GLN ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.145319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.122569 restraints weight = 44141.471| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 3.06 r_work: 0.4115 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16482 Z= 0.158 Angle : 0.623 9.248 22386 Z= 0.322 Chirality : 0.046 0.329 2487 Planarity : 0.004 0.042 2817 Dihedral : 6.592 56.035 2463 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.39 % Favored : 94.14 % Rotamer: Outliers : 5.49 % Allowed : 13.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.19), residues: 1947 helix: 0.61 (0.28), residues: 309 sheet: 0.38 (0.20), residues: 636 loop : -1.29 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 431 HIS 0.004 0.001 HIS A 202 PHE 0.019 0.002 PHE B 486 TYR 0.014 0.001 TYR C 488 ARG 0.009 0.000 ARG C 225 Details of bonding type rmsd link_NAG-ASN : bond 0.00768 ( 9) link_NAG-ASN : angle 5.04511 ( 27) link_BETA1-4 : bond 0.00088 ( 3) link_BETA1-4 : angle 1.74850 ( 9) hydrogen bonds : bond 0.05216 ( 526) hydrogen bonds : angle 6.18674 ( 1389) SS BOND : bond 0.00361 ( 12) SS BOND : angle 1.33602 ( 24) covalent geometry : bond 0.00352 (16458) covalent geometry : angle 0.59578 (22326) *********************** 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 281 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 184 time to evaluate : 1.870 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: 0.8616 (OUTLIER) cc_final: 0.8206 (mtp) REVERT: A 222 HIS cc_start: 0.7122 (OUTLIER) cc_final: 0.6681 (p90) REVERT: A 326 GLU cc_start: 0.8399 (mp0) cc_final: 0.7981 (mp0) REVERT: A 682 GLU cc_start: 0.8530 (mp0) cc_final: 0.8154 (mp0) REVERT: D 40 MET cc_start: 0.4127 (ppp) cc_final: 0.3635 (ppp) REVERT: E 49 HIS cc_start: 0.4506 (m90) cc_final: 0.3960 (m90) REVERT: B 222 HIS cc_start: 0.7179 (OUTLIER) cc_final: 0.6808 (p90) REVERT: B 682 GLU cc_start: 0.8513 (mp0) cc_final: 0.8123 (mp0) REVERT: F 19 LYS cc_start: 0.7212 (mmtm) cc_final: 0.6980 (mppt) REVERT: F 40 MET cc_start: 0.2724 (ppp) cc_final: 0.2421 (ppp) REVERT: F 80 TYR cc_start: 0.6217 (m-80) cc_final: 0.5812 (m-80) REVERT: G 14 SER cc_start: 0.8211 (m) cc_final: 0.7671 (p) REVERT: G 17 ASP cc_start: 0.7218 (m-30) cc_final: 0.6778 (p0) REVERT: G 49 HIS cc_start: 0.4346 (m90) cc_final: 0.3681 (m90) REVERT: G 98 PHE cc_start: 0.5601 (OUTLIER) cc_final: 0.5157 (t80) REVERT: C 222 HIS cc_start: 0.7141 (OUTLIER) cc_final: 0.6834 (p90) REVERT: H 18 LEU cc_start: 0.7139 (mm) cc_final: 0.6705 (mm) REVERT: H 19 LYS cc_start: 0.7564 (mppt) cc_final: 0.7318 (mmtm) REVERT: H 39 GLN cc_start: 0.6354 (tt0) cc_final: 0.6132 (tt0) REVERT: H 40 MET cc_start: 0.4137 (ppp) cc_final: 0.3632 (ppp) REVERT: H 78 THR cc_start: 0.8287 (m) cc_final: 0.7633 (t) REVERT: I 45 LYS cc_start: 0.6651 (mmmt) cc_final: 0.5919 (ttpp) REVERT: I 49 HIS cc_start: 0.4274 (m90) cc_final: 0.3609 (m-70) REVERT: I 55 GLN cc_start: 0.7180 (OUTLIER) cc_final: 0.6811 (tt0) outliers start: 97 outliers final: 49 residues processed: 257 average time/residue: 1.0710 time to fit residues: 316.5805 Evaluate side-chains 215 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 160 time to evaluate : 2.397 ------------------------------------------------------------------------------- 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 7 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 222 HIS Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 222 HIS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 469 HIS Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 55 GLN Chi-restraints excluded: chain I residue 98 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 18 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 176 optimal weight: 0.1980 chunk 56 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 184 optimal weight: 8.9990 chunk 137 optimal weight: 0.0370 chunk 5 optimal weight: 0.5980 chunk 154 optimal weight: 1.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- 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** D 3 GLN ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN F 3 GLN F 82 HIS ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 GLN C 220 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.144746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.122727 restraints weight = 43693.025| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 3.07 r_work: 0.4082 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2104 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= 0.130 Angle : 0.556 8.711 22386 Z= 0.290 Chirality : 0.044 0.323 2487 Planarity : 0.003 0.038 2817 Dihedral : 6.395 59.258 2462 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.08 % Favored : 94.45 % Rotamer: Outliers : 5.21 % Allowed : 14.37 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.19), residues: 1947 helix: 0.64 (0.29), residues: 312 sheet: 0.30 (0.21), residues: 633 loop : -1.24 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 83 HIS 0.003 0.001 HIS A 202 PHE 0.018 0.001 PHE B 486 TYR 0.019 0.001 TYR E 32 ARG 0.007 0.000 ARG I 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00729 ( 9) link_NAG-ASN : angle 4.01825 ( 27) link_BETA1-4 : bond 0.00075 ( 3) link_BETA1-4 : angle 1.95613 ( 9) hydrogen bonds : bond 0.04363 ( 526) hydrogen bonds : angle 5.90615 ( 1389) SS BOND : bond 0.00290 ( 12) SS BOND : angle 1.08066 ( 24) covalent geometry : bond 0.00290 (16458) covalent geometry : angle 0.53602 (22326) *********************** 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 264 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 172 time to evaluate : 1.803 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: A 222 HIS cc_start: 0.7102 (OUTLIER) cc_final: 0.6637 (p90) REVERT: A 371 MET cc_start: 0.7840 (mtm) cc_final: 0.7489 (mtm) REVERT: A 682 GLU cc_start: 0.8544 (mp0) cc_final: 0.8303 (mp0) REVERT: D 40 MET cc_start: 0.4052 (ppp) cc_final: 0.3581 (ppp) REVERT: D 102 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7358 (mt) REVERT: E 32 TYR cc_start: 0.6964 (OUTLIER) cc_final: 0.6185 (t80) REVERT: E 49 HIS cc_start: 0.4572 (m90) cc_final: 0.3928 (m90) REVERT: F 40 MET cc_start: 0.2810 (ppp) cc_final: 0.2473 (ppp) REVERT: G 17 ASP cc_start: 0.7336 (m-30) cc_final: 0.6720 (p0) REVERT: G 49 HIS cc_start: 0.4640 (m90) cc_final: 0.4089 (m90) REVERT: G 98 PHE cc_start: 0.5615 (OUTLIER) cc_final: 0.5223 (t80) REVERT: H 19 LYS cc_start: 0.7333 (mppt) cc_final: 0.7123 (mptp) REVERT: H 39 GLN cc_start: 0.6517 (tt0) cc_final: 0.6232 (tt0) REVERT: H 40 MET cc_start: 0.4027 (ppp) cc_final: 0.3518 (ppp) REVERT: H 78 THR cc_start: 0.8249 (m) cc_final: 0.7006 (t) REVERT: H 80 TYR cc_start: 0.6657 (m-80) cc_final: 0.5810 (m-80) REVERT: I 49 HIS cc_start: 0.4438 (m90) cc_final: 0.4015 (m90) REVERT: I 89 GLN cc_start: 0.4437 (pm20) cc_final: 0.3455 (pp30) outliers start: 92 outliers final: 49 residues processed: 239 average time/residue: 1.0408 time to fit residues: 288.3993 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 : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 318 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 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 32 TYR Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 161 LEU 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 306 VAL 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 48 ILE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 188 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 186 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 337 GLN A 365 HIS ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN D 3 GLN B 337 GLN B 365 HIS ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN F 3 GLN ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.139044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.116141 restraints weight = 43715.553| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 3.07 r_work: 0.3966 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 16482 Z= 0.257 Angle : 0.690 10.262 22386 Z= 0.358 Chirality : 0.048 0.363 2487 Planarity : 0.005 0.047 2817 Dihedral : 6.961 59.439 2455 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.16 % Favored : 93.37 % Rotamer: Outliers : 5.49 % Allowed : 14.88 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.19), residues: 1947 helix: 0.36 (0.29), residues: 312 sheet: -0.02 (0.21), residues: 639 loop : -1.45 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 83 HIS 0.006 0.001 HIS G 49 PHE 0.028 0.003 PHE A 486 TYR 0.025 0.002 TYR D 99 ARG 0.007 0.001 ARG E 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00817 ( 9) link_NAG-ASN : angle 4.46182 ( 27) link_BETA1-4 : bond 0.00796 ( 3) link_BETA1-4 : angle 3.46184 ( 9) hydrogen bonds : bond 0.04703 ( 526) hydrogen bonds : angle 6.21393 ( 1389) SS BOND : bond 0.00410 ( 12) SS BOND : angle 1.62011 ( 24) covalent geometry : bond 0.00584 (16458) covalent geometry : angle 0.66754 (22326) *********************** 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 255 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 158 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.7331 (OUTLIER) cc_final: 0.6905 (p90) REVERT: A 371 MET cc_start: 0.7925 (mtm) cc_final: 0.7593 (mtm) REVERT: A 682 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8445 (mp0) REVERT: D 40 MET cc_start: 0.4083 (ppp) cc_final: 0.3604 (ppp) REVERT: D 102 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7550 (mt) REVERT: E 32 TYR cc_start: 0.7812 (OUTLIER) cc_final: 0.7548 (t80) REVERT: E 49 HIS cc_start: 0.4499 (m90) cc_final: 0.4006 (m90) REVERT: F 40 MET cc_start: 0.2690 (ppp) cc_final: 0.2306 (ppp) REVERT: F 80 TYR cc_start: 0.6304 (m-80) cc_final: 0.5847 (m-80) REVERT: G 49 HIS cc_start: 0.4742 (m90) cc_final: 0.4197 (m90) REVERT: G 82 ASP cc_start: 0.7181 (m-30) cc_final: 0.6860 (m-30) REVERT: G 98 PHE cc_start: 0.5815 (OUTLIER) cc_final: 0.5217 (t80) REVERT: H 18 LEU cc_start: 0.7112 (mm) cc_final: 0.6684 (mm) REVERT: H 40 MET cc_start: 0.4038 (ppp) cc_final: 0.3487 (ppp) REVERT: H 78 THR cc_start: 0.8189 (m) cc_final: 0.6965 (t) REVERT: H 80 TYR cc_start: 0.6620 (m-80) cc_final: 0.5813 (m-80) REVERT: I 45 LYS cc_start: 0.6269 (mmmt) cc_final: 0.5777 (ttpp) REVERT: I 49 HIS cc_start: 0.4766 (m90) cc_final: 0.4115 (m90) REVERT: I 89 GLN cc_start: 0.4726 (pm20) cc_final: 0.3672 (pp30) outliers start: 97 outliers final: 52 residues processed: 231 average time/residue: 0.9476 time to fit residues: 254.2812 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 : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 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 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 E residue 21 ILE Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 222 HIS Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 314 SER 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 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 C residue 161 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 105 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 365 HIS ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.140965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.118353 restraints weight = 44152.079| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 3.10 r_work: 0.4007 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16482 Z= 0.147 Angle : 0.589 8.942 22386 Z= 0.304 Chirality : 0.045 0.326 2487 Planarity : 0.004 0.045 2817 Dihedral : 6.597 59.816 2453 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.70 % Favored : 93.84 % Rotamer: Outliers : 4.64 % Allowed : 16.92 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.19), residues: 1947 helix: 0.48 (0.29), residues: 312 sheet: -0.16 (0.21), residues: 657 loop : -1.37 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 83 HIS 0.005 0.001 HIS A 365 PHE 0.021 0.002 PHE E 62 TYR 0.013 0.001 TYR E 32 ARG 0.011 0.000 ARG E 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00678 ( 9) link_NAG-ASN : angle 3.87915 ( 27) link_BETA1-4 : bond 0.00126 ( 3) link_BETA1-4 : angle 2.73319 ( 9) hydrogen bonds : bond 0.04080 ( 526) hydrogen bonds : angle 5.95984 ( 1389) SS BOND : bond 0.00277 ( 12) SS BOND : angle 1.50978 ( 24) covalent geometry : bond 0.00328 (16458) covalent geometry : angle 0.56935 (22326) *********************** 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 250 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 168 time to evaluate : 1.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.7213 (OUTLIER) cc_final: 0.6741 (p90) REVERT: A 371 MET cc_start: 0.7864 (mtm) cc_final: 0.7588 (mtm) REVERT: A 682 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8378 (mp0) REVERT: D 40 MET cc_start: 0.4033 (ppp) cc_final: 0.3473 (ppp) REVERT: D 102 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7470 (mt) REVERT: E 49 HIS cc_start: 0.4661 (m90) cc_final: 0.4037 (m90) REVERT: E 82 ASP cc_start: 0.7483 (m-30) cc_final: 0.7179 (m-30) REVERT: B 186 TYR cc_start: 0.7926 (m-80) cc_final: 0.7457 (m-80) REVERT: F 19 LYS cc_start: 0.7658 (mppt) cc_final: 0.7399 (mmtm) REVERT: F 40 MET cc_start: 0.2620 (ppp) cc_final: 0.2208 (ppp) REVERT: F 80 TYR cc_start: 0.6324 (m-80) cc_final: 0.5802 (m-80) REVERT: G 17 ASP cc_start: 0.7404 (m-30) cc_final: 0.6900 (p0) REVERT: G 45 LYS cc_start: 0.6397 (mmmt) cc_final: 0.5684 (ttpp) REVERT: G 49 HIS cc_start: 0.4734 (m90) cc_final: 0.4145 (m90) REVERT: G 82 ASP cc_start: 0.7067 (m-30) cc_final: 0.6791 (m-30) REVERT: H 18 LEU cc_start: 0.7074 (mm) cc_final: 0.6748 (mm) REVERT: H 40 MET cc_start: 0.3990 (ppp) cc_final: 0.3454 (ppp) REVERT: H 80 TYR cc_start: 0.6590 (m-80) cc_final: 0.5992 (m-80) REVERT: I 49 HIS cc_start: 0.4469 (m90) cc_final: 0.3967 (m90) REVERT: I 89 GLN cc_start: 0.4734 (pm20) cc_final: 0.3773 (pp30) outliers start: 82 outliers final: 47 residues processed: 227 average time/residue: 1.0117 time to fit residues: 261.5215 Evaluate side-chains 196 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 146 time to evaluate : 1.734 ------------------------------------------------------------------------------- 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 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 20 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 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 250 CYS 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 32 TYR Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain C residue 161 LEU 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 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 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 110 optimal weight: 1.9990 chunk 179 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 148 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 165 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 365 HIS ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 HIS ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 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 = 0.4390 r_free = 0.4390 target = 0.133373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.111018 restraints weight = 44346.797| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.97 r_work: 0.3879 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.091 16482 Z= 0.443 Angle : 0.910 10.839 22386 Z= 0.472 Chirality : 0.055 0.388 2487 Planarity : 0.006 0.061 2817 Dihedral : 8.226 59.438 2449 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.55 % Favored : 91.99 % Rotamer: Outliers : 5.55 % Allowed : 17.20 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.18), residues: 1947 helix: -0.32 (0.28), residues: 309 sheet: -0.87 (0.20), residues: 645 loop : -1.89 (0.18), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP F 83 HIS 0.009 0.002 HIS E 49 PHE 0.032 0.004 PHE E 92 TYR 0.032 0.003 TYR E 32 ARG 0.008 0.001 ARG I 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00904 ( 9) link_NAG-ASN : angle 5.22133 ( 27) link_BETA1-4 : bond 0.01324 ( 3) link_BETA1-4 : angle 4.63758 ( 9) hydrogen bonds : bond 0.05469 ( 526) hydrogen bonds : angle 7.04335 ( 1389) SS BOND : bond 0.00485 ( 12) SS BOND : angle 2.56214 ( 24) covalent geometry : bond 0.01001 (16458) covalent geometry : angle 0.88383 (22326) *********************** 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 247 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 149 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 682 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8450 (mp0) REVERT: D 19 LYS cc_start: 0.7640 (mppt) cc_final: 0.7305 (mmtm) REVERT: D 40 MET cc_start: 0.4115 (ppp) cc_final: 0.3588 (ppp) REVERT: D 78 THR cc_start: 0.8409 (m) cc_final: 0.7775 (t) REVERT: D 82 HIS cc_start: 0.7063 (t-90) cc_final: 0.6806 (t70) REVERT: D 102 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7663 (mt) REVERT: E 36 TYR cc_start: 0.3522 (m-80) cc_final: 0.0982 (m-10) REVERT: E 49 HIS cc_start: 0.4875 (m90) cc_final: 0.4190 (m90) REVERT: B 222 HIS cc_start: 0.7942 (OUTLIER) cc_final: 0.7404 (p90) REVERT: B 326 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8558 (pm20) REVERT: F 40 MET cc_start: 0.2724 (ppp) cc_final: 0.2360 (ppp) REVERT: F 80 TYR cc_start: 0.6460 (m-80) cc_final: 0.5928 (m-80) REVERT: G 17 ASP cc_start: 0.7225 (m-30) cc_final: 0.6726 (p0) REVERT: G 49 HIS cc_start: 0.5019 (m90) cc_final: 0.4596 (m90) REVERT: G 82 ASP cc_start: 0.6815 (m-30) cc_final: 0.6557 (m-30) REVERT: C 680 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7184 (tp) REVERT: H 29 PHE cc_start: 0.6023 (OUTLIER) cc_final: 0.5434 (p90) REVERT: H 40 MET cc_start: 0.4247 (ppp) cc_final: 0.3662 (ppp) REVERT: H 80 TYR cc_start: 0.6688 (m-80) cc_final: 0.6157 (m-80) REVERT: I 49 HIS cc_start: 0.4853 (m90) cc_final: 0.4240 (m90) REVERT: I 89 GLN cc_start: 0.5375 (pm20) cc_final: 0.4019 (pp30) outliers start: 98 outliers final: 52 residues processed: 228 average time/residue: 0.8531 time to fit residues: 230.7431 Evaluate side-chains 184 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 126 time to evaluate : 1.733 ------------------------------------------------------------------------------- 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 176 ILE Chi-restraints excluded: chain A residue 199 VAL 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 469 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 68 VAL 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 35 TRP Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 222 HIS Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain F residue 68 VAL 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 222 HIS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 365 HIS 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 C residue 653 ILE Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 29 PHE 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 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 114 optimal weight: 0.6980 chunk 52 optimal weight: 0.0980 chunk 1 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 49 optimal weight: 9.9990 chunk 169 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 A 485 GLN ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS B 365 HIS ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN C 222 HIS C 365 HIS H 3 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.139572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.117220 restraints weight = 43990.920| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 3.11 r_work: 0.3989 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16482 Z= 0.138 Angle : 0.640 11.042 22386 Z= 0.329 Chirality : 0.046 0.305 2487 Planarity : 0.004 0.050 2817 Dihedral : 6.982 57.589 2447 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.75 % Favored : 93.79 % Rotamer: Outliers : 3.51 % Allowed : 20.49 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.19), residues: 1947 helix: 0.17 (0.29), residues: 312 sheet: -0.77 (0.20), residues: 657 loop : -1.55 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 47 HIS 0.018 0.001 HIS B 365 PHE 0.041 0.002 PHE B 366 TYR 0.030 0.002 TYR C 364 ARG 0.003 0.000 ARG A 157 Details of bonding type rmsd link_NAG-ASN : bond 0.00728 ( 9) link_NAG-ASN : angle 3.85321 ( 27) link_BETA1-4 : bond 0.00052 ( 3) link_BETA1-4 : angle 2.77670 ( 9) hydrogen bonds : bond 0.04140 ( 526) hydrogen bonds : angle 6.25498 ( 1389) SS BOND : bond 0.00307 ( 12) SS BOND : angle 1.44935 ( 24) covalent geometry : bond 0.00299 (16458) covalent geometry : angle 0.62226 (22326) *********************** 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 231 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 169 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 682 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8432 (mp0) REVERT: D 19 LYS cc_start: 0.7543 (mppt) cc_final: 0.7320 (mmtm) REVERT: D 40 MET cc_start: 0.4185 (ppp) cc_final: 0.3601 (ppp) REVERT: D 102 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7657 (mt) REVERT: E 49 HIS cc_start: 0.4287 (m90) cc_final: 0.3717 (m90) REVERT: B 326 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8542 (pm20) REVERT: F 34 ILE cc_start: 0.7162 (mm) cc_final: 0.6636 (mp) REVERT: F 37 VAL cc_start: 0.5528 (m) cc_final: 0.5325 (p) REVERT: F 40 MET cc_start: 0.2890 (ppp) cc_final: 0.2450 (ppp) REVERT: F 80 TYR cc_start: 0.6492 (m-80) cc_final: 0.5914 (m-80) REVERT: G 17 ASP cc_start: 0.7165 (m-30) cc_final: 0.6840 (p0) REVERT: G 49 HIS cc_start: 0.4572 (m90) cc_final: 0.4148 (m90) REVERT: G 82 ASP cc_start: 0.6673 (m-30) cc_final: 0.6437 (m-30) REVERT: C 140 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8533 (t) REVERT: H 40 MET cc_start: 0.4322 (ppp) cc_final: 0.3796 (ppp) REVERT: H 80 TYR cc_start: 0.6786 (m-80) cc_final: 0.6216 (m-80) outliers start: 62 outliers final: 29 residues processed: 210 average time/residue: 0.8280 time to fit residues: 203.9590 Evaluate side-chains 181 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU 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 68 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain F residue 71 SER 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 140 VAL Chi-restraints excluded: chain C residue 161 LEU 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 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 72 VAL Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 105 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 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 222 HIS ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 HIS ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 485 GLN ** F 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN C 222 HIS C 485 GLN ** I 27 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.136174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.113534 restraints weight = 43861.138| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 3.08 r_work: 0.3926 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 16482 Z= 0.268 Angle : 0.722 9.587 22386 Z= 0.369 Chirality : 0.048 0.350 2487 Planarity : 0.005 0.046 2817 Dihedral : 6.992 58.187 2442 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.65 % Favored : 92.04 % Rotamer: Outliers : 3.62 % Allowed : 20.83 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.18), residues: 1947 helix: 0.11 (0.29), residues: 312 sheet: -0.95 (0.20), residues: 639 loop : -1.77 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 83 HIS 0.006 0.001 HIS E 49 PHE 0.031 0.003 PHE E 62 TYR 0.021 0.002 TYR C 494 ARG 0.005 0.001 ARG I 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 9) link_NAG-ASN : angle 4.33293 ( 27) link_BETA1-4 : bond 0.00544 ( 3) link_BETA1-4 : angle 3.63668 ( 9) hydrogen bonds : bond 0.04472 ( 526) hydrogen bonds : angle 6.50722 ( 1389) SS BOND : bond 0.00537 ( 12) SS BOND : angle 1.64326 ( 24) covalent geometry : bond 0.00607 (16458) covalent geometry : angle 0.70175 (22326) *********************** 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 210 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 146 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 682 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8457 (mp0) REVERT: D 19 LYS cc_start: 0.7619 (mppt) cc_final: 0.7382 (mmtm) REVERT: D 40 MET cc_start: 0.4243 (ppp) cc_final: 0.3680 (ppp) REVERT: D 78 THR cc_start: 0.8396 (m) cc_final: 0.7115 (t) REVERT: D 80 TYR cc_start: 0.6867 (m-80) cc_final: 0.6092 (m-80) REVERT: D 102 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7736 (mt) REVERT: E 32 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.7373 (t80) REVERT: E 36 TYR cc_start: 0.3455 (m-80) cc_final: 0.0921 (m-80) REVERT: E 49 HIS cc_start: 0.4684 (m90) cc_final: 0.4050 (m90) REVERT: F 34 ILE cc_start: 0.7365 (OUTLIER) cc_final: 0.6740 (mp) REVERT: F 40 MET cc_start: 0.2777 (ppp) cc_final: 0.2402 (ppp) REVERT: F 80 TYR cc_start: 0.6532 (m-80) cc_final: 0.5961 (m-80) REVERT: F 94 TYR cc_start: 0.8255 (m-10) cc_final: 0.7360 (m-10) REVERT: G 17 ASP cc_start: 0.7190 (m-30) cc_final: 0.6801 (p0) REVERT: G 49 HIS cc_start: 0.4853 (m90) cc_final: 0.4436 (m90) REVERT: G 82 ASP cc_start: 0.6826 (m-30) cc_final: 0.6583 (m-30) REVERT: H 40 MET cc_start: 0.4391 (ppp) cc_final: 0.3833 (ppp) REVERT: H 80 TYR cc_start: 0.6817 (m-80) cc_final: 0.6263 (m-80) REVERT: I 49 HIS cc_start: 0.4705 (m90) cc_final: 0.4262 (m-70) outliers start: 64 outliers final: 36 residues processed: 192 average time/residue: 0.9566 time to fit residues: 211.5647 Evaluate side-chains 176 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 1.705 ------------------------------------------------------------------------------- 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 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 68 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 71 SER 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 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 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 I residue 21 ILE Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 105 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 32 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN C 222 HIS I 27 GLN ** I 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.137106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.114768 restraints weight = 43971.728| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 3.07 r_work: 0.3940 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16482 Z= 0.212 Angle : 0.685 10.920 22386 Z= 0.347 Chirality : 0.047 0.330 2487 Planarity : 0.004 0.050 2817 Dihedral : 6.896 56.963 2442 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.78 % Favored : 92.91 % Rotamer: Outliers : 2.89 % Allowed : 21.39 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.18), residues: 1947 helix: 0.16 (0.29), residues: 312 sheet: -1.01 (0.20), residues: 639 loop : -1.77 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 83 HIS 0.005 0.001 HIS A 365 PHE 0.032 0.002 PHE B 486 TYR 0.019 0.002 TYR B 364 ARG 0.004 0.000 ARG I 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00577 ( 9) link_NAG-ASN : angle 4.08978 ( 27) link_BETA1-4 : bond 0.00356 ( 3) link_BETA1-4 : angle 3.30966 ( 9) hydrogen bonds : bond 0.04288 ( 526) hydrogen bonds : angle 6.44833 ( 1389) SS BOND : bond 0.00317 ( 12) SS BOND : angle 1.42586 ( 24) covalent geometry : bond 0.00480 (16458) covalent geometry : angle 0.66634 (22326) *********************** 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 193 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 142 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.7443 (OUTLIER) cc_final: 0.6892 (p90) REVERT: A 682 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8433 (mp0) REVERT: D 40 MET cc_start: 0.4178 (ppp) cc_final: 0.3626 (ppp) REVERT: D 78 THR cc_start: 0.8410 (m) cc_final: 0.7106 (t) REVERT: D 80 TYR cc_start: 0.6842 (m-80) cc_final: 0.6088 (m-80) REVERT: D 102 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7688 (mt) REVERT: E 36 TYR cc_start: 0.3259 (m-80) cc_final: 0.0911 (m-80) REVERT: E 49 HIS cc_start: 0.4464 (m90) cc_final: 0.3983 (m90) REVERT: B 326 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8508 (pm20) REVERT: F 34 ILE cc_start: 0.7297 (OUTLIER) cc_final: 0.6717 (mp) REVERT: F 40 MET cc_start: 0.2861 (ppp) cc_final: 0.2495 (ppp) REVERT: F 80 TYR cc_start: 0.6618 (m-80) cc_final: 0.6009 (m-80) REVERT: G 17 ASP cc_start: 0.7186 (m-30) cc_final: 0.6794 (p0) REVERT: G 45 LYS cc_start: 0.6160 (mmmt) cc_final: 0.5732 (tttm) REVERT: G 49 HIS cc_start: 0.4719 (m90) cc_final: 0.4300 (m90) REVERT: G 82 ASP cc_start: 0.6791 (m-30) cc_final: 0.6522 (m-30) REVERT: H 40 MET cc_start: 0.4400 (ppp) cc_final: 0.3842 (ppp) REVERT: H 80 TYR cc_start: 0.6793 (m-80) cc_final: 0.6244 (m-80) REVERT: I 49 HIS cc_start: 0.4580 (m90) cc_final: 0.4064 (m-70) outliers start: 51 outliers final: 32 residues processed: 178 average time/residue: 0.9995 time to fit residues: 207.4738 Evaluate side-chains 171 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 222 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 68 VAL 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 35 TRP Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 326 GLU 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 71 SER 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 159 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN C 222 HIS ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 GLN ** 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 = 0.4457 r_free = 0.4457 target = 0.137918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.115562 restraints weight = 44262.982| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 3.12 r_work: 0.3956 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16482 Z= 0.182 Angle : 0.672 11.407 22386 Z= 0.338 Chirality : 0.047 0.327 2487 Planarity : 0.004 0.045 2817 Dihedral : 6.709 57.454 2442 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.55 % Favored : 92.14 % Rotamer: Outliers : 2.72 % Allowed : 21.84 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.19), residues: 1947 helix: 0.28 (0.29), residues: 312 sheet: -1.04 (0.20), residues: 639 loop : -1.75 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 83 HIS 0.005 0.001 HIS A 365 PHE 0.031 0.002 PHE A 486 TYR 0.022 0.002 TYR B 201 ARG 0.004 0.000 ARG I 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00569 ( 9) link_NAG-ASN : angle 3.85541 ( 27) link_BETA1-4 : bond 0.00214 ( 3) link_BETA1-4 : angle 3.11742 ( 9) hydrogen bonds : bond 0.04103 ( 526) hydrogen bonds : angle 6.35178 ( 1389) SS BOND : bond 0.00343 ( 12) SS BOND : angle 1.34933 ( 24) covalent geometry : bond 0.00411 (16458) covalent geometry : angle 0.65535 (22326) ********************** 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 194 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.7337 (OUTLIER) cc_final: 0.6770 (p90) REVERT: A 682 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8422 (mp0) REVERT: D 40 MET cc_start: 0.4264 (ppp) cc_final: 0.3716 (ppp) REVERT: D 78 THR cc_start: 0.8367 (m) cc_final: 0.7057 (t) REVERT: D 80 TYR cc_start: 0.6819 (m-80) cc_final: 0.6052 (m-80) REVERT: D 102 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7688 (mt) REVERT: E 36 TYR cc_start: 0.3339 (m-80) cc_final: 0.0891 (m-80) REVERT: E 49 HIS cc_start: 0.4456 (m90) cc_final: 0.4067 (m90) REVERT: F 40 MET cc_start: 0.3049 (ppp) cc_final: 0.2685 (ppp) REVERT: F 80 TYR cc_start: 0.6569 (m-80) cc_final: 0.5955 (m-80) REVERT: G 17 ASP cc_start: 0.7185 (m-30) cc_final: 0.6800 (p0) REVERT: G 49 HIS cc_start: 0.4755 (m90) cc_final: 0.4330 (m90) REVERT: G 82 ASP cc_start: 0.6764 (m-30) cc_final: 0.6502 (m-30) REVERT: H 40 MET cc_start: 0.4379 (ppp) cc_final: 0.3821 (ppp) REVERT: H 80 TYR cc_start: 0.6844 (m-80) cc_final: 0.6245 (m-80) REVERT: I 49 HIS cc_start: 0.4367 (m90) cc_final: 0.3962 (m-70) outliers start: 48 outliers final: 34 residues processed: 181 average time/residue: 0.8850 time to fit residues: 187.6065 Evaluate side-chains 176 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 1.707 ------------------------------------------------------------------------------- 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 537 ILE Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain F residue 71 SER 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 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 Chi-restraints excluded: chain I residue 105 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 181 optimal weight: 4.9990 chunk 172 optimal weight: 0.0370 chunk 94 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 126 optimal weight: 0.2980 chunk 79 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 157 optimal weight: 0.1980 chunk 69 optimal weight: 0.1980 chunk 29 optimal weight: 9.9990 overall best weight: 0.3258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 222 HIS C 220 ASN C 222 HIS ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.139874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.117682 restraints weight = 44162.770| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 3.13 r_work: 0.3996 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16482 Z= 0.129 Angle : 0.645 11.367 22386 Z= 0.323 Chirality : 0.046 0.313 2487 Planarity : 0.004 0.046 2817 Dihedral : 6.446 58.350 2442 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.47 % Favored : 93.22 % Rotamer: Outliers : 2.60 % Allowed : 22.07 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.19), residues: 1947 helix: 0.44 (0.29), residues: 312 sheet: -1.02 (0.20), residues: 654 loop : -1.66 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 83 HIS 0.006 0.001 HIS A 365 PHE 0.039 0.002 PHE C 486 TYR 0.019 0.001 TYR B 364 ARG 0.003 0.000 ARG I 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00593 ( 9) link_NAG-ASN : angle 3.47542 ( 27) link_BETA1-4 : bond 0.00043 ( 3) link_BETA1-4 : angle 2.66034 ( 9) hydrogen bonds : bond 0.03916 ( 526) hydrogen bonds : angle 6.17872 ( 1389) SS BOND : bond 0.00320 ( 12) SS BOND : angle 1.19121 ( 24) covalent geometry : bond 0.00289 (16458) covalent geometry : angle 0.63078 (22326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13449.97 seconds wall clock time: 237 minutes 5.77 seconds (14225.77 seconds total)