Starting phenix.real_space_refine on Tue Dec 31 15:56:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yrn_34063/12_2024/7yrn_34063.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yrn_34063/12_2024/7yrn_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_34063/12_2024/7yrn_34063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yrn_34063/12_2024/7yrn_34063.map" model { file = "/net/cci-nas-00/data/ceres_data/7yrn_34063/12_2024/7yrn_34063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yrn_34063/12_2024/7yrn_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-5532/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: 10.08, per 1000 atoms: 0.63 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: 4.17 Conformation dependent library (CDL) restraints added in 2.1 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: 1.85 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: 5.38 Time building geometry restraints manager: 4.79 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 37.170 Find NCS groups from input model: 0.530 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:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.390 ------------------------------------------------------------------------------- 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 16458 Z= 0.143 Angle : 0.482 5.587 22326 Z= 0.269 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 *********************** 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 : 1.823 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: 1.0011 time to fit residues: 410.9639 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 : 1.906 ------------------------------------------------------------------------------- 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: 0.0570 chunk 58 optimal weight: 0.0470 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 0.4980 chunk 174 optimal weight: 0.7980 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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 247 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN C 485 GLN H 39 GLN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16458 Z= 0.216 Angle : 0.590 9.332 22326 Z= 0.313 Chirality : 0.046 0.326 2487 Planarity : 0.004 0.041 2817 Dihedral : 6.524 55.447 2463 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.34 % Favored : 94.20 % Rotamer: Outliers : 5.26 % Allowed : 13.92 % Favored : 80.81 % 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: 0.40 (0.28), residues: 327 sheet: 0.40 (0.20), residues: 636 loop : -1.25 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 83 HIS 0.003 0.001 HIS I 49 PHE 0.021 0.002 PHE B 486 TYR 0.013 0.001 TYR B 488 ARG 0.008 0.000 ARG C 225 *********************** 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 289 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 196 time to evaluate : 1.950 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: A 211 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8307 (mtp) REVERT: A 222 HIS cc_start: 0.7272 (OUTLIER) cc_final: 0.6896 (p90) REVERT: A 233 TRP cc_start: 0.7070 (t60) cc_final: 0.6842 (t60) REVERT: A 682 GLU cc_start: 0.8245 (mp0) cc_final: 0.7763 (mp0) REVERT: D 40 MET cc_start: 0.5054 (ppp) cc_final: 0.4724 (ppp) REVERT: B 175 GLU cc_start: 0.7080 (tt0) cc_final: 0.6870 (tt0) REVERT: B 222 HIS cc_start: 0.7280 (OUTLIER) cc_final: 0.6928 (p90) REVERT: B 682 GLU cc_start: 0.8326 (mp0) cc_final: 0.7870 (mp0) REVERT: F 40 MET cc_start: 0.4082 (ppp) cc_final: 0.3860 (ppp) REVERT: G 71 PHE cc_start: 0.4065 (m-80) cc_final: 0.3593 (m-80) REVERT: G 98 PHE cc_start: 0.6132 (OUTLIER) cc_final: 0.5566 (t80) REVERT: C 222 HIS cc_start: 0.7183 (OUTLIER) cc_final: 0.6896 (p90) REVERT: H 40 MET cc_start: 0.4865 (ppp) cc_final: 0.4567 (ppp) REVERT: H 78 THR cc_start: 0.7930 (m) cc_final: 0.7553 (t) REVERT: I 55 GLN cc_start: 0.5799 (OUTLIER) cc_final: 0.5469 (tt0) outliers start: 93 outliers final: 49 residues processed: 263 average time/residue: 0.9500 time to fit residues: 288.1586 Evaluate side-chains 214 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 159 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 222 HIS Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 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 C residue 140 VAL 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 96 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 145 optimal weight: 0.7980 chunk 118 optimal weight: 10.0000 chunk 48 optimal weight: 0.0370 chunk 174 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 59 optimal weight: 0.0030 chunk 140 optimal weight: 8.9990 overall best weight: 1.5672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 GLN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN D 82 HIS B 212 GLN B 220 ASN ** B 365 HIS ** 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** C 212 GLN C 220 ASN I 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16458 Z= 0.282 Angle : 0.585 6.531 22326 Z= 0.312 Chirality : 0.046 0.336 2487 Planarity : 0.004 0.046 2817 Dihedral : 6.673 59.602 2462 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.29 % Favored : 94.25 % Rotamer: Outliers : 5.43 % Allowed : 15.11 % Favored : 79.46 % 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: -0.68 (0.19), residues: 1947 helix: 0.59 (0.29), residues: 312 sheet: 0.27 (0.21), residues: 639 loop : -1.28 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 83 HIS 0.008 0.001 HIS E 49 PHE 0.020 0.002 PHE B 486 TYR 0.017 0.002 TYR G 32 ARG 0.007 0.001 ARG H 103 *********************** 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 262 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 166 time to evaluate : 1.708 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: A 222 HIS cc_start: 0.7385 (OUTLIER) cc_final: 0.6918 (p90) REVERT: A 371 MET cc_start: 0.7795 (mtm) cc_final: 0.7527 (mtm) REVERT: A 682 GLU cc_start: 0.8317 (mp0) cc_final: 0.7645 (mp0) REVERT: D 40 MET cc_start: 0.4958 (ppp) cc_final: 0.4623 (ppp) REVERT: D 68 VAL cc_start: 0.7285 (OUTLIER) cc_final: 0.6833 (t) REVERT: F 40 MET cc_start: 0.4285 (ppp) cc_final: 0.4039 (ppp) REVERT: G 32 TYR cc_start: 0.7272 (OUTLIER) cc_final: 0.6544 (t80) REVERT: G 98 PHE cc_start: 0.6367 (OUTLIER) cc_final: 0.5797 (t80) REVERT: H 40 MET cc_start: 0.4828 (ppp) cc_final: 0.4550 (ppp) REVERT: H 78 THR cc_start: 0.7909 (m) cc_final: 0.7181 (t) outliers start: 96 outliers final: 53 residues processed: 235 average time/residue: 0.9654 time to fit residues: 261.4061 Evaluate side-chains 199 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 142 time to evaluate : 1.845 ------------------------------------------------------------------------------- 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 374 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 199 VAL 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 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 32 TYR Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 469 HIS Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 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 55 GLN 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 172 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 117 optimal weight: 0.3980 chunk 175 optimal weight: 4.9990 chunk 185 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 166 optimal weight: 0.0010 chunk 50 optimal weight: 3.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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 692 GLN D 3 GLN B 220 ASN B 337 GLN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN F 3 GLN G 27 GLN C 212 GLN C 220 ASN ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 GLN C 692 GLN I 27 GLN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16458 Z= 0.250 Angle : 0.572 8.400 22326 Z= 0.303 Chirality : 0.045 0.336 2487 Planarity : 0.004 0.045 2817 Dihedral : 6.541 58.720 2456 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.96 % Favored : 93.58 % Rotamer: Outliers : 4.98 % Allowed : 16.30 % Favored : 78.72 % 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: -0.81 (0.19), residues: 1947 helix: 0.53 (0.29), residues: 312 sheet: 0.11 (0.20), residues: 663 loop : -1.36 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 83 HIS 0.005 0.001 HIS A 365 PHE 0.014 0.002 PHE F 64 TYR 0.014 0.002 TYR G 32 ARG 0.003 0.000 ARG A 150 *********************** 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 242 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 154 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.7380 (OUTLIER) cc_final: 0.6898 (p90) REVERT: A 371 MET cc_start: 0.7774 (mtm) cc_final: 0.7482 (mtm) REVERT: A 682 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8073 (mp0) REVERT: D 40 MET cc_start: 0.4836 (ppp) cc_final: 0.4530 (ppp) REVERT: E 32 TYR cc_start: 0.7148 (OUTLIER) cc_final: 0.6513 (t80) REVERT: B 326 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8877 (mp0) REVERT: F 40 MET cc_start: 0.4259 (ppp) cc_final: 0.3979 (ppp) REVERT: G 32 TYR cc_start: 0.7212 (OUTLIER) cc_final: 0.6053 (t80) REVERT: G 98 PHE cc_start: 0.6461 (OUTLIER) cc_final: 0.5863 (t80) REVERT: H 40 MET cc_start: 0.4876 (ppp) cc_final: 0.4583 (ppp) REVERT: I 89 GLN cc_start: 0.4043 (pm20) cc_final: 0.3655 (pp30) outliers start: 88 outliers final: 52 residues processed: 213 average time/residue: 0.9734 time to fit residues: 240.7158 Evaluate side-chains 201 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 143 time to evaluate : 2.851 ------------------------------------------------------------------------------- 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 211 MET Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 7 SER 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 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 251 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 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 32 TYR Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 55 GLN 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 154 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 158 optimal weight: 0.5980 chunk 128 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16458 Z= 0.218 Angle : 0.549 6.921 22326 Z= 0.291 Chirality : 0.045 0.329 2487 Planarity : 0.003 0.042 2817 Dihedral : 6.391 59.220 2451 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.91 % Favored : 93.73 % Rotamer: Outliers : 4.53 % Allowed : 17.77 % Favored : 77.70 % 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: -0.93 (0.19), residues: 1947 helix: 0.59 (0.29), residues: 312 sheet: -0.02 (0.21), residues: 645 loop : -1.44 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 83 HIS 0.005 0.001 HIS A 365 PHE 0.027 0.002 PHE C 486 TYR 0.015 0.001 TYR E 32 ARG 0.003 0.000 ARG A 150 *********************** 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 234 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 154 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.7353 (OUTLIER) cc_final: 0.6932 (p90) REVERT: A 371 MET cc_start: 0.7727 (mtm) cc_final: 0.7447 (mtm) REVERT: A 682 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: D 40 MET cc_start: 0.4825 (ppp) cc_final: 0.4435 (ppp) REVERT: E 32 TYR cc_start: 0.7130 (OUTLIER) cc_final: 0.6360 (t80) REVERT: B 186 TYR cc_start: 0.7966 (m-80) cc_final: 0.7470 (m-80) REVERT: F 40 MET cc_start: 0.4252 (ppp) cc_final: 0.3979 (ppp) REVERT: G 98 PHE cc_start: 0.6392 (OUTLIER) cc_final: 0.5955 (t80) REVERT: H 40 MET cc_start: 0.4887 (ppp) cc_final: 0.4592 (ppp) REVERT: I 89 GLN cc_start: 0.4018 (pm20) cc_final: 0.3595 (pp30) outliers start: 80 outliers final: 48 residues processed: 212 average time/residue: 0.9378 time to fit residues: 231.0863 Evaluate side-chains 192 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 140 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 167 GLU 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 35 TRP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 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 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 32 TYR Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 55 GLN 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 62 optimal weight: 0.9980 chunk 167 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 chunk 86 optimal weight: 0.0470 chunk 15 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 overall best weight: 1.5282 ------------------------------------------------------------------------------- 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** B 220 ASN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN G 27 GLN C 220 ASN ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN I 27 GLN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16458 Z= 0.266 Angle : 0.587 9.778 22326 Z= 0.308 Chirality : 0.046 0.334 2487 Planarity : 0.004 0.044 2817 Dihedral : 6.540 59.437 2451 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.63 % Favored : 93.01 % Rotamer: Outliers : 4.53 % Allowed : 18.85 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.53 (0.29), residues: 312 sheet: 0.01 (0.21), residues: 609 loop : -1.47 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 83 HIS 0.005 0.001 HIS G 49 PHE 0.027 0.002 PHE E 62 TYR 0.016 0.002 TYR B 494 ARG 0.006 0.001 ARG F 67 *********************** 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 231 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 151 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.7481 (OUTLIER) cc_final: 0.7094 (p90) REVERT: A 371 MET cc_start: 0.7733 (mtm) cc_final: 0.7491 (mtm) REVERT: A 682 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8055 (mp0) REVERT: D 40 MET cc_start: 0.4902 (ppp) cc_final: 0.4505 (ppp) REVERT: E 32 TYR cc_start: 0.7152 (OUTLIER) cc_final: 0.6350 (t80) REVERT: B 326 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8710 (mp0) REVERT: F 40 MET cc_start: 0.4254 (ppp) cc_final: 0.3986 (ppp) REVERT: G 98 PHE cc_start: 0.6605 (OUTLIER) cc_final: 0.6208 (t80) REVERT: H 40 MET cc_start: 0.4836 (ppp) cc_final: 0.4518 (ppp) REVERT: I 89 GLN cc_start: 0.4029 (pm20) cc_final: 0.3568 (pp30) outliers start: 80 outliers final: 51 residues processed: 210 average time/residue: 0.9022 time to fit residues: 220.3192 Evaluate side-chains 195 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 139 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain 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 70 ILE Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 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 37 VAL 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 55 GLN 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 179 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 135 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 103 optimal weight: 0.0270 chunk 185 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 112 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 GLN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16458 Z= 0.234 Angle : 0.570 9.181 22326 Z= 0.299 Chirality : 0.045 0.326 2487 Planarity : 0.004 0.043 2817 Dihedral : 6.319 58.814 2448 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.63 % Favored : 93.07 % Rotamer: Outliers : 4.24 % Allowed : 19.35 % Favored : 76.40 % 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: -0.98 (0.19), residues: 1947 helix: 0.62 (0.29), residues: 312 sheet: -0.07 (0.22), residues: 606 loop : -1.44 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 83 HIS 0.005 0.001 HIS A 365 PHE 0.014 0.002 PHE F 29 TYR 0.016 0.001 TYR E 32 ARG 0.003 0.000 ARG B 157 *********************** 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 225 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 150 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.8229 (ptm) cc_final: 0.7797 (pmm) REVERT: A 222 HIS cc_start: 0.7436 (OUTLIER) cc_final: 0.7011 (p90) REVERT: A 473 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7320 (ptm) REVERT: A 682 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8045 (mp0) REVERT: D 40 MET cc_start: 0.4908 (ppp) cc_final: 0.4523 (ppp) REVERT: F 40 MET cc_start: 0.4232 (ppp) cc_final: 0.3956 (ppp) REVERT: G 98 PHE cc_start: 0.6570 (OUTLIER) cc_final: 0.6217 (t80) REVERT: H 40 MET cc_start: 0.4880 (ppp) cc_final: 0.4572 (ppp) REVERT: I 89 GLN cc_start: 0.4032 (pm20) cc_final: 0.3596 (pp30) outliers start: 75 outliers final: 53 residues processed: 204 average time/residue: 0.8678 time to fit residues: 206.1326 Evaluate side-chains 198 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 141 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 70 ILE 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 140 VAL 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 391 CYS Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL 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 32 TYR Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 55 GLN Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 0.0470 chunk 110 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 overall best weight: 1.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN C 220 ASN ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16458 Z= 0.209 Angle : 0.580 12.165 22326 Z= 0.297 Chirality : 0.045 0.322 2487 Planarity : 0.003 0.044 2817 Dihedral : 6.214 58.120 2448 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.93 % Favored : 92.76 % Rotamer: Outliers : 3.96 % Allowed : 20.03 % 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: -0.98 (0.19), residues: 1947 helix: 0.68 (0.29), residues: 312 sheet: -0.20 (0.21), residues: 624 loop : -1.37 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 83 HIS 0.006 0.001 HIS A 365 PHE 0.023 0.002 PHE B 486 TYR 0.013 0.001 TYR B 494 ARG 0.002 0.000 ARG A 150 *********************** 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 225 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 155 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.7425 (OUTLIER) cc_final: 0.6983 (p90) REVERT: A 473 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7297 (ptm) REVERT: A 682 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: D 40 MET cc_start: 0.4943 (ppp) cc_final: 0.4578 (ppp) REVERT: B 326 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8740 (mp0) REVERT: F 40 MET cc_start: 0.4292 (ppp) cc_final: 0.4023 (ppp) REVERT: G 98 PHE cc_start: 0.6566 (OUTLIER) cc_final: 0.6231 (t80) REVERT: H 40 MET cc_start: 0.4947 (ppp) cc_final: 0.4652 (ppp) REVERT: I 89 GLN cc_start: 0.3894 (pm20) cc_final: 0.3503 (pp30) outliers start: 70 outliers final: 51 residues processed: 207 average time/residue: 0.8742 time to fit residues: 211.9422 Evaluate side-chains 198 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 142 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 70 ILE 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 140 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain 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 55 GLN Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 172 optimal weight: 0.0770 chunk 103 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 135 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 171 optimal weight: 5.9990 chunk 113 optimal weight: 0.0470 overall best weight: 1.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 HIS ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16458 Z= 0.275 Angle : 0.612 10.001 22326 Z= 0.315 Chirality : 0.046 0.331 2487 Planarity : 0.004 0.048 2817 Dihedral : 6.405 57.210 2448 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.99 % Favored : 92.71 % Rotamer: Outliers : 4.02 % Allowed : 19.98 % 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: -1.11 (0.19), residues: 1947 helix: 0.67 (0.29), residues: 312 sheet: -0.21 (0.21), residues: 591 loop : -1.51 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 83 HIS 0.005 0.001 HIS C 365 PHE 0.032 0.002 PHE E 62 TYR 0.016 0.002 TYR B 494 ARG 0.004 0.000 ARG A 150 *********************** 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 217 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 146 time to evaluate : 3.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.8286 (ptm) cc_final: 0.7840 (pmm) REVERT: A 222 HIS cc_start: 0.7511 (OUTLIER) cc_final: 0.7032 (p90) REVERT: A 473 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7307 (ptm) REVERT: A 682 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8029 (mp0) REVERT: D 40 MET cc_start: 0.4944 (ppp) cc_final: 0.4562 (ppp) REVERT: E 32 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.6190 (t80) REVERT: B 326 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8703 (mp0) REVERT: F 40 MET cc_start: 0.4321 (ppp) cc_final: 0.4026 (ppp) REVERT: H 40 MET cc_start: 0.5015 (ppp) cc_final: 0.4682 (ppp) REVERT: I 89 GLN cc_start: 0.4129 (pm20) cc_final: 0.3721 (pp30) outliers start: 71 outliers final: 50 residues processed: 200 average time/residue: 0.8423 time to fit residues: 197.4611 Evaluate side-chains 196 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 141 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 653 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 37 VAL 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 32 TYR Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 55 GLN 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 182 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 176 optimal weight: 0.0170 chunk 152 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 overall best weight: 1.5424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 HIS ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16458 Z= 0.270 Angle : 0.633 10.254 22326 Z= 0.322 Chirality : 0.046 0.327 2487 Planarity : 0.004 0.045 2817 Dihedral : 6.367 57.293 2446 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.88 % Favored : 92.81 % Rotamer: Outliers : 3.51 % Allowed : 20.66 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.19 (0.19), residues: 1947 helix: 0.58 (0.29), residues: 312 sheet: -0.37 (0.21), residues: 606 loop : -1.50 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 83 HIS 0.005 0.001 HIS B 365 PHE 0.038 0.002 PHE A 486 TYR 0.016 0.002 TYR B 494 ARG 0.003 0.000 ARG I 24 ********************** 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 204 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 142 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.6336 (tt) cc_final: 0.6115 (mm) REVERT: A 126 MET cc_start: 0.8298 (ptm) cc_final: 0.7864 (pmm) REVERT: A 222 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.7031 (p90) REVERT: A 473 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7291 (ptm) REVERT: A 682 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7984 (mp0) REVERT: D 40 MET cc_start: 0.5014 (ppp) cc_final: 0.4631 (ppp) REVERT: E 32 TYR cc_start: 0.7031 (OUTLIER) cc_final: 0.6375 (t80) REVERT: B 326 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8737 (mp0) REVERT: F 40 MET cc_start: 0.4352 (ppp) cc_final: 0.4059 (ppp) REVERT: F 94 TYR cc_start: 0.7196 (m-10) cc_final: 0.6342 (m-10) REVERT: G 32 TYR cc_start: 0.7450 (OUTLIER) cc_final: 0.6507 (t80) REVERT: H 40 MET cc_start: 0.5118 (ppp) cc_final: 0.4774 (ppp) REVERT: I 89 GLN cc_start: 0.4185 (pm20) cc_final: 0.3729 (pp30) outliers start: 62 outliers final: 50 residues processed: 189 average time/residue: 0.7980 time to fit residues: 177.9171 Evaluate side-chains 193 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 137 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 653 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 37 VAL 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 32 TYR Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 55 GLN 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 162 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 chunk 63 optimal weight: 0.5980 chunk 156 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 chunk 28 optimal weight: 8.9990 chunk 133 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS B 222 HIS ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS I 27 GLN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.141572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.118274 restraints weight = 44007.475| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 3.03 r_work: 0.4036 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16458 Z= 0.183 Angle : 0.600 10.242 22326 Z= 0.304 Chirality : 0.045 0.315 2487 Planarity : 0.003 0.044 2817 Dihedral : 6.138 57.395 2446 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.52 % Favored : 93.17 % Rotamer: Outliers : 3.17 % Allowed : 21.11 % 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: -1.14 (0.19), residues: 1947 helix: 0.70 (0.29), residues: 312 sheet: -0.39 (0.21), residues: 606 loop : -1.45 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 83 HIS 0.006 0.001 HIS B 365 PHE 0.037 0.002 PHE E 62 TYR 0.015 0.001 TYR A 206 ARG 0.002 0.000 ARG I 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5224.86 seconds wall clock time: 96 minutes 12.51 seconds (5772.51 seconds total)