Starting phenix.real_space_refine on Sun Jul 28 04:34:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y53_33611/07_2024/7y53_33611.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y53_33611/07_2024/7y53_33611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y53_33611/07_2024/7y53_33611.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y53_33611/07_2024/7y53_33611.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y53_33611/07_2024/7y53_33611.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y53_33611/07_2024/7y53_33611.cif" } resolution = 3.61 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= 0.004 sd= 0.058 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 230 5.16 5 C 27256 2.51 5 N 7466 2.21 5 O 7990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Z PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B GLU 470": "OE1" <-> "OE2" Residue "B GLU 561": "OE1" <-> "OE2" Residue "B GLU 578": "OE1" <-> "OE2" Residue "B GLU 607": "OE1" <-> "OE2" Residue "C GLU 721": "OE1" <-> "OE2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D GLU 194": "OE1" <-> "OE2" Residue "D GLU 291": "OE1" <-> "OE2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "E GLU 435": "OE1" <-> "OE2" Residue "E GLU 477": "OE1" <-> "OE2" Residue "E GLU 554": "OE1" <-> "OE2" Residue "E GLU 556": "OE1" <-> "OE2" Residue "F GLU 132": "OE1" <-> "OE2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F GLU 218": "OE1" <-> "OE2" Residue "F GLU 402": "OE1" <-> "OE2" Residue "F GLU 483": "OE1" <-> "OE2" Residue "F PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 42966 Number of models: 1 Model: "" Number of chains: 16 Chain: "W" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 13, 'TRANS': 211} Chain: "X" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 13, 'TRANS': 211} Chain: "Y" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 13, 'TRANS': 211} Chain: "Z" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 13, 'TRANS': 211} Chain: "A" Number of atoms: 5846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5846 Classifications: {'peptide': 745} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 703} Chain: "B" Number of atoms: 5846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5846 Classifications: {'peptide': 745} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 703} Chain: "C" Number of atoms: 5809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5809 Classifications: {'peptide': 741} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 38, 'TRANS': 699} Chain: "D" Number of atoms: 5829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5829 Classifications: {'peptide': 743} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 701} Chain: "E" Number of atoms: 5911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 5911 Classifications: {'peptide': 753} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 710} Chain: "F" Number of atoms: 5921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5921 Classifications: {'peptide': 755} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 712} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 21.73, per 1000 atoms: 0.51 Number of scatterers: 42966 At special positions: 0 Unit cell: (178.2, 166.1, 198, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 230 16.00 P 24 15.00 O 7990 8.00 N 7466 7.00 C 27256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.90 Conformation dependent library (CDL) restraints added in 8.4 seconds 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10018 Finding SS restraints... Secondary structure from input PDB file: 245 helices and 30 sheets defined 52.0% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.94 Creating SS restraints... Processing helix chain 'W' and resid 2 through 10 Processing helix chain 'W' and resid 12 through 32 Proline residue: W 26 - end of helix Processing helix chain 'W' and resid 35 through 39 Processing helix chain 'W' and resid 42 through 49 Processing helix chain 'W' and resid 56 through 60 Processing helix chain 'W' and resid 68 through 89 removed outlier: 4.145A pdb=" N THR W 84 " --> pdb=" O TYR W 80 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG W 85 " --> pdb=" O GLN W 81 " (cutoff:3.500A) Processing helix chain 'W' and resid 94 through 116 removed outlier: 4.164A pdb=" N TYR W 98 " --> pdb=" O ARG W 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 122 through 137 Processing helix chain 'W' and resid 154 through 166 Processing helix chain 'W' and resid 169 through 188 removed outlier: 4.462A pdb=" N GLU W 173 " --> pdb=" O SER W 169 " (cutoff:3.500A) Processing helix chain 'W' and resid 188 through 194 removed outlier: 3.810A pdb=" N MET W 192 " --> pdb=" O PHE W 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 203 through 210 removed outlier: 3.638A pdb=" N TYR W 207 " --> pdb=" O PRO W 203 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 11 removed outlier: 3.597A pdb=" N ILE X 11 " --> pdb=" O TRP X 7 " (cutoff:3.500A) Processing helix chain 'X' and resid 12 through 31 Proline residue: X 26 - end of helix Processing helix chain 'X' and resid 35 through 39 Processing helix chain 'X' and resid 42 through 49 Processing helix chain 'X' and resid 56 through 61 Processing helix chain 'X' and resid 68 through 89 removed outlier: 4.028A pdb=" N THR X 84 " --> pdb=" O TYR X 80 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG X 85 " --> pdb=" O GLN X 81 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY X 89 " --> pdb=" O ARG X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 94 through 116 Processing helix chain 'X' and resid 122 through 137 removed outlier: 3.667A pdb=" N ILE X 126 " --> pdb=" O MET X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 154 through 166 Processing helix chain 'X' and resid 169 through 188 removed outlier: 4.281A pdb=" N GLU X 173 " --> pdb=" O SER X 169 " (cutoff:3.500A) Processing helix chain 'X' and resid 188 through 194 removed outlier: 3.867A pdb=" N MET X 192 " --> pdb=" O PHE X 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 203 through 210 removed outlier: 3.786A pdb=" N TYR X 207 " --> pdb=" O PRO X 203 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 11 removed outlier: 3.863A pdb=" N ILE Y 11 " --> pdb=" O TRP Y 7 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 31 Proline residue: Y 26 - end of helix Processing helix chain 'Y' and resid 35 through 39 Processing helix chain 'Y' and resid 42 through 49 Processing helix chain 'Y' and resid 52 through 58 removed outlier: 4.400A pdb=" N ILE Y 56 " --> pdb=" O ILE Y 52 " (cutoff:3.500A) Processing helix chain 'Y' and resid 68 through 88 removed outlier: 3.850A pdb=" N TYR Y 72 " --> pdb=" O THR Y 68 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR Y 84 " --> pdb=" O TYR Y 80 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ARG Y 85 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU Y 86 " --> pdb=" O TYR Y 82 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 116 removed outlier: 3.538A pdb=" N TYR Y 98 " --> pdb=" O ARG Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 122 through 137 Processing helix chain 'Y' and resid 154 through 166 removed outlier: 3.611A pdb=" N ILE Y 165 " --> pdb=" O GLY Y 161 " (cutoff:3.500A) Processing helix chain 'Y' and resid 169 through 188 removed outlier: 3.548A pdb=" N GLU Y 173 " --> pdb=" O SER Y 169 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU Y 178 " --> pdb=" O LEU Y 174 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL Y 179 " --> pdb=" O ILE Y 175 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY Y 180 " --> pdb=" O GLY Y 176 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N HIS Y 181 " --> pdb=" O ASN Y 177 " (cutoff:3.500A) Processing helix chain 'Y' and resid 188 through 194 removed outlier: 3.977A pdb=" N MET Y 192 " --> pdb=" O PHE Y 188 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2 through 11 Processing helix chain 'Z' and resid 12 through 32 removed outlier: 3.590A pdb=" N ALA Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA Z 21 " --> pdb=" O TYR Z 17 " (cutoff:3.500A) Proline residue: Z 26 - end of helix Processing helix chain 'Z' and resid 35 through 40 removed outlier: 3.975A pdb=" N PHE Z 40 " --> pdb=" O ALA Z 37 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 49 Processing helix chain 'Z' and resid 52 through 59 removed outlier: 4.548A pdb=" N ILE Z 56 " --> pdb=" O ILE Z 52 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR Z 59 " --> pdb=" O PRO Z 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 68 through 89 removed outlier: 4.105A pdb=" N TYR Z 72 " --> pdb=" O THR Z 68 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG Z 85 " --> pdb=" O GLN Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 94 through 116 Processing helix chain 'Z' and resid 121 through 137 removed outlier: 3.737A pdb=" N LEU Z 125 " --> pdb=" O LEU Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 154 through 166 Processing helix chain 'Z' and resid 170 through 188 removed outlier: 3.897A pdb=" N GLY Z 176 " --> pdb=" O ASN Z 172 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL Z 179 " --> pdb=" O ILE Z 175 " (cutoff:3.500A) Processing helix chain 'Z' and resid 189 through 194 removed outlier: 3.924A pdb=" N ASP Z 193 " --> pdb=" O ARG Z 189 " (cutoff:3.500A) Processing helix chain 'Z' and resid 203 through 210 removed outlier: 3.731A pdb=" N TYR Z 207 " --> pdb=" O PRO Z 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 49 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 85 through 93 removed outlier: 3.582A pdb=" N ARG A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 removed outlier: 3.651A pdb=" N VAL A 123 " --> pdb=" O ASP A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'A' and resid 202 through 206 removed outlier: 4.004A pdb=" N ILE A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 226 Proline residue: A 223 - end of helix removed outlier: 4.269A pdb=" N HIS A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 234 removed outlier: 3.829A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 263 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 295 removed outlier: 3.907A pdb=" N SER A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 319 through 334 Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.501A pdb=" N ARG A 358 " --> pdb=" O PRO A 355 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG A 359 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.605A pdb=" N VAL A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.707A pdb=" N LYS A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.542A pdb=" N ASN A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.766A pdb=" N GLN A 458 " --> pdb=" O TRP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 removed outlier: 3.787A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 505 removed outlier: 3.737A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 Processing helix chain 'A' and resid 543 through 550 Processing helix chain 'A' and resid 557 through 569 removed outlier: 3.875A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 587 Processing helix chain 'A' and resid 593 through 610 Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.781A pdb=" N ILE A 629 " --> pdb=" O PRO A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 651 No H-bonds generated for 'chain 'A' and resid 649 through 651' Processing helix chain 'A' and resid 652 through 662 Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.534A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 713 removed outlier: 3.619A pdb=" N LEU A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 742 removed outlier: 4.043A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 765 removed outlier: 4.262A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 85 through 92 removed outlier: 3.501A pdb=" N ARG B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 123 removed outlier: 3.600A pdb=" N VAL B 123 " --> pdb=" O ASP B 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 129 through 134 removed outlier: 3.608A pdb=" N VAL B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'B' and resid 202 through 206 removed outlier: 4.127A pdb=" N ILE B 206 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.809A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 234 Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'B' and resid 281 through 295 removed outlier: 4.119A pdb=" N ASN B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 319 through 334 Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.885A pdb=" N ARG B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 407 through 426 removed outlier: 3.636A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 445 Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 removed outlier: 3.507A pdb=" N LYS B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.815A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 536 Processing helix chain 'B' and resid 543 through 550 Processing helix chain 'B' and resid 555 through 569 Processing helix chain 'B' and resid 580 through 587 Processing helix chain 'B' and resid 593 through 610 removed outlier: 3.712A pdb=" N GLY B 610 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 661 removed outlier: 3.571A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.570A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 714 removed outlier: 3.631A pdb=" N ALA B 694 " --> pdb=" O ILE B 690 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 742 removed outlier: 3.957A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 765 removed outlier: 3.715A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 85 through 93 removed outlier: 3.674A pdb=" N ARG C 89 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 124 removed outlier: 3.690A pdb=" N GLU C 124 " --> pdb=" O ASP C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 134 through 140 Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.837A pdb=" N VAL C 201 " --> pdb=" O SER C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 226 removed outlier: 5.257A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 234 removed outlier: 3.713A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 removed outlier: 3.583A pdb=" N ILE C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 281 through 295 removed outlier: 3.972A pdb=" N ASN C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 319 through 335 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.584A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.941A pdb=" N ARG C 359 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.692A pdb=" N THR C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 425 Processing helix chain 'C' and resid 440 through 445 Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.594A pdb=" N GLN C 458 " --> pdb=" O TRP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 499 removed outlier: 4.005A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.546A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.604A pdb=" N CYS C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 removed outlier: 3.865A pdb=" N TRP C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 580 through 586 removed outlier: 3.559A pdb=" N ARG C 586 " --> pdb=" O ILE C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 610 removed outlier: 4.100A pdb=" N ARG C 599 " --> pdb=" O GLY C 595 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE C 601 " --> pdb=" O ALA C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 661 removed outlier: 3.597A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 657 " --> pdb=" O ARG C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 716 Processing helix chain 'C' and resid 732 through 741 removed outlier: 3.921A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 763 removed outlier: 3.631A pdb=" N ILE C 752 " --> pdb=" O SER C 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 50 Processing helix chain 'D' and resid 85 through 93 Processing helix chain 'D' and resid 120 through 123 removed outlier: 4.023A pdb=" N VAL D 123 " --> pdb=" O ASP D 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 120 through 123' Processing helix chain 'D' and resid 129 through 134 removed outlier: 3.811A pdb=" N VAL D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 129 through 134' Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.747A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 226 removed outlier: 5.031A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 234 removed outlier: 3.850A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 removed outlier: 3.555A pdb=" N ILE D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 276 Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.734A pdb=" N ASN D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 309 Processing helix chain 'D' and resid 319 through 334 Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.765A pdb=" N ILE D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.776A pdb=" N ARG D 359 " --> pdb=" O ALA D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 395 through 402 removed outlier: 4.022A pdb=" N VAL D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 427 Processing helix chain 'D' and resid 438 through 443 removed outlier: 4.175A pdb=" N MET D 442 " --> pdb=" O ASP D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.580A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 499 removed outlier: 3.932A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 507 removed outlier: 4.024A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 536 Processing helix chain 'D' and resid 543 through 550 Processing helix chain 'D' and resid 556 through 569 Processing helix chain 'D' and resid 580 through 587 Processing helix chain 'D' and resid 593 through 610 Processing helix chain 'D' and resid 625 through 629 removed outlier: 3.670A pdb=" N ILE D 628 " --> pdb=" O ARG D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 661 Processing helix chain 'D' and resid 672 through 679 removed outlier: 3.506A pdb=" N THR D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 716 Processing helix chain 'D' and resid 732 through 740 Processing helix chain 'D' and resid 749 through 763 removed outlier: 3.830A pdb=" N ARG D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 49 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 85 through 93 Processing helix chain 'E' and resid 120 through 123 Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.746A pdb=" N ASP E 205 " --> pdb=" O GLY E 202 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 202 through 206' Processing helix chain 'E' and resid 209 through 226 removed outlier: 5.134A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 234 removed outlier: 3.515A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 270 through 276 removed outlier: 3.700A pdb=" N ILE E 274 " --> pdb=" O ASN E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 295 removed outlier: 3.558A pdb=" N ASN E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 4.023A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 334 Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.897A pdb=" N ARG E 359 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 403 Processing helix chain 'E' and resid 407 through 426 removed outlier: 3.833A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 444 removed outlier: 3.974A pdb=" N SER E 444 " --> pdb=" O VAL E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 458 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 499 removed outlier: 3.712A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 506 removed outlier: 4.201A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 536 Processing helix chain 'E' and resid 543 through 552 Processing helix chain 'E' and resid 556 through 559 Processing helix chain 'E' and resid 560 through 569 Processing helix chain 'E' and resid 580 through 587 Processing helix chain 'E' and resid 593 through 610 removed outlier: 3.591A pdb=" N VAL E 600 " --> pdb=" O ALA E 596 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE E 601 " --> pdb=" O ALA E 597 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 629 Processing helix chain 'E' and resid 652 through 662 Processing helix chain 'E' and resid 673 through 679 removed outlier: 4.411A pdb=" N THR E 679 " --> pdb=" O LEU E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 714 removed outlier: 4.245A pdb=" N LEU E 687 " --> pdb=" O SER E 683 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 738 removed outlier: 3.788A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 766 removed outlier: 4.240A pdb=" N ILE E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG E 753 " --> pdb=" O ASP E 749 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU E 762 " --> pdb=" O PHE E 758 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 50 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 85 through 92 removed outlier: 3.579A pdb=" N ARG F 89 " --> pdb=" O ASN F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 123 removed outlier: 3.715A pdb=" N VAL F 123 " --> pdb=" O ASP F 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 120 through 123' Processing helix chain 'F' and resid 129 through 134 Processing helix chain 'F' and resid 134 through 139 Processing helix chain 'F' and resid 209 through 226 removed outlier: 3.726A pdb=" N MET F 219 " --> pdb=" O GLN F 215 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 228 through 234 Processing helix chain 'F' and resid 250 through 263 removed outlier: 3.502A pdb=" N ILE F 254 " --> pdb=" O GLY F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 277 removed outlier: 4.020A pdb=" N ILE F 274 " --> pdb=" O ASN F 270 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET F 275 " --> pdb=" O GLY F 271 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 removed outlier: 4.238A pdb=" N SER F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 309 Processing helix chain 'F' and resid 319 through 335 Processing helix chain 'F' and resid 374 through 385 removed outlier: 3.617A pdb=" N LEU F 378 " --> pdb=" O ALA F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 407 through 425 removed outlier: 3.725A pdb=" N LYS F 425 " --> pdb=" O GLN F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 443 removed outlier: 3.793A pdb=" N MET F 442 " --> pdb=" O ASP F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.521A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 499 removed outlier: 3.664A pdb=" N ARG F 487 " --> pdb=" O GLU F 483 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 507 removed outlier: 3.915A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 536 Processing helix chain 'F' and resid 543 through 553 removed outlier: 3.979A pdb=" N GLY F 553 " --> pdb=" O THR F 549 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 569 removed outlier: 4.342A pdb=" N VAL F 559 " --> pdb=" O SER F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 587 Processing helix chain 'F' and resid 593 through 610 Processing helix chain 'F' and resid 650 through 661 removed outlier: 3.789A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.705A pdb=" N LEU F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 716 removed outlier: 3.582A pdb=" N ASN F 716 " --> pdb=" O GLU F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 742 removed outlier: 3.623A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 765 removed outlier: 3.894A pdb=" N ILE F 752 " --> pdb=" O SER F 748 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER F 765 " --> pdb=" O THR F 761 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'W' and resid 246 through 247 removed outlier: 6.152A pdb=" N ILE A 114 " --> pdb=" O HIS A 183 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 141 through 142 Processing sheet with id=AA3, first strand: chain 'X' and resid 246 through 247 removed outlier: 3.561A pdb=" N PHE X 246 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE B 114 " --> pdb=" O HIS B 183 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG B 113 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N THR B 168 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 26 through 29 removed outlier: 5.996A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 100 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 removed outlier: 3.547A pdb=" N CYS A 174 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 267 through 270 removed outlier: 3.542A pdb=" N PHE A 302 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 542 removed outlier: 3.649A pdb=" N ILE A 540 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 25 through 29 removed outlier: 8.091A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 145 through 146 removed outlier: 3.676A pdb=" N CYS B 174 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 267 through 269 removed outlier: 3.517A pdb=" N PHE B 302 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 538 through 542 removed outlier: 7.041A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 24 through 29 removed outlier: 7.592A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N LYS C 81 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N SER C 42 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL C 39 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP C 74 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU C 41 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS C 69 " --> pdb=" O VAL C 57 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 145 through 147 removed outlier: 4.544A pdb=" N ALA C 177 " --> pdb=" O GLY C 111 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ARG C 113 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 10.233A pdb=" N ASP C 179 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N HIS C 115 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 10.297A pdb=" N VAL C 181 " --> pdb=" O HIS C 115 " (cutoff:3.500A) removed outlier: 10.446A pdb=" N LEU C 117 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N HIS C 183 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 267 through 270 removed outlier: 6.625A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 540 through 542 removed outlier: 5.855A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 25 through 30 removed outlier: 3.635A pdb=" N ARG D 83 " --> pdb=" O SER D 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 151 through 155 removed outlier: 3.782A pdb=" N PHE D 152 " --> pdb=" O PHE D 163 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR D 168 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG D 113 " --> pdb=" O THR D 168 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 145 through 146 removed outlier: 3.854A pdb=" N CYS D 174 " --> pdb=" O ILE D 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 267 through 269 removed outlier: 6.650A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 538 through 542 removed outlier: 7.347A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 25 through 29 removed outlier: 8.503A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL E 39 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS E 69 " --> pdb=" O VAL E 57 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 117 through 118 Processing sheet with id=AC5, first strand: chain 'E' and resid 145 through 146 Processing sheet with id=AC6, first strand: chain 'E' and resid 267 through 269 removed outlier: 6.050A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE E 241 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR E 347 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU E 243 " --> pdb=" O THR E 347 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 538 through 542 removed outlier: 7.121A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL E 514 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N THR E 623 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE E 516 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 25 through 29 removed outlier: 7.873A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N MET F 84 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASP F 29 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL F 39 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN F 103 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 151 through 155 removed outlier: 5.607A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG F 113 " --> pdb=" O ASP F 169 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AD2, first strand: chain 'F' and resid 267 through 269 removed outlier: 3.866A pdb=" N PHE F 302 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 538 through 542 removed outlier: 7.295A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY F 513 " --> pdb=" O LEU F 639 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR F 517 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1881 hydrogen bonds defined for protein. 5433 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: 17.24 Time building geometry restraints manager: 17.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14347 1.34 - 1.46: 9294 1.46 - 1.59: 19795 1.59 - 1.71: 36 1.71 - 1.83: 380 Bond restraints: 43852 Sorted by residual: bond pdb=" C VAL C 728 " pdb=" N PRO C 729 " ideal model delta sigma weight residual 1.336 1.373 -0.037 1.08e-02 8.57e+03 1.19e+01 bond pdb=" C SER F 664 " pdb=" N PRO F 665 " ideal model delta sigma weight residual 1.326 1.359 -0.032 1.44e-02 4.82e+03 5.04e+00 bond pdb=" CA ASP F 725 " pdb=" CB ASP F 725 " ideal model delta sigma weight residual 1.524 1.548 -0.024 1.33e-02 5.65e+03 3.38e+00 bond pdb=" C TYR E 495 " pdb=" N PRO E 496 " ideal model delta sigma weight residual 1.335 1.353 -0.019 1.28e-02 6.10e+03 2.14e+00 bond pdb=" CA GLU B 34 " pdb=" CB GLU B 34 " ideal model delta sigma weight residual 1.518 1.547 -0.029 2.08e-02 2.31e+03 1.98e+00 ... (remaining 43847 not shown) Histogram of bond angle deviations from ideal: 97.30 - 105.05: 1048 105.05 - 112.80: 23110 112.80 - 120.55: 19148 120.55 - 128.30: 15810 128.30 - 136.05: 276 Bond angle restraints: 59392 Sorted by residual: angle pdb=" N VAL E 559 " pdb=" CA VAL E 559 " pdb=" C VAL E 559 " ideal model delta sigma weight residual 112.90 107.84 5.06 9.60e-01 1.09e+00 2.77e+01 angle pdb=" N VAL B 220 " pdb=" CA VAL B 220 " pdb=" C VAL B 220 " ideal model delta sigma weight residual 113.71 109.27 4.44 9.50e-01 1.11e+00 2.18e+01 angle pdb=" CB ARG F 713 " pdb=" CG ARG F 713 " pdb=" CD ARG F 713 " ideal model delta sigma weight residual 111.30 121.97 -10.67 2.30e+00 1.89e-01 2.15e+01 angle pdb=" C LEU B 492 " pdb=" N VAL B 493 " pdb=" CA VAL B 493 " ideal model delta sigma weight residual 122.77 117.97 4.80 1.05e+00 9.07e-01 2.09e+01 angle pdb=" C GLU B 34 " pdb=" CA GLU B 34 " pdb=" CB GLU B 34 " ideal model delta sigma weight residual 115.79 110.43 5.36 1.19e+00 7.06e-01 2.03e+01 ... (remaining 59387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.04: 26153 35.04 - 70.08: 473 70.08 - 105.12: 68 105.12 - 140.15: 19 140.15 - 175.19: 2 Dihedral angle restraints: 26715 sinusoidal: 11199 harmonic: 15516 Sorted by residual: dihedral pdb=" CA ASP F 726 " pdb=" C ASP F 726 " pdb=" N PRO F 727 " pdb=" CA PRO F 727 " ideal model delta harmonic sigma weight residual -180.00 -141.89 -38.11 0 5.00e+00 4.00e-02 5.81e+01 dihedral pdb=" O1B ADP F 902 " pdb=" O3A ADP F 902 " pdb=" PB ADP F 902 " pdb=" PA ADP F 902 " ideal model delta sinusoidal sigma weight residual 300.00 124.80 175.19 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP E 901 " pdb=" O5' ADP E 901 " pdb=" PA ADP E 901 " pdb=" O2A ADP E 901 " ideal model delta sinusoidal sigma weight residual 300.00 148.45 151.55 1 2.00e+01 2.50e-03 4.51e+01 ... (remaining 26712 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 5236 0.055 - 0.111: 1151 0.111 - 0.166: 169 0.166 - 0.221: 10 0.221 - 0.276: 1 Chirality restraints: 6567 Sorted by residual: chirality pdb=" CB ILE F 300 " pdb=" CA ILE F 300 " pdb=" CG1 ILE F 300 " pdb=" CG2 ILE F 300 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA MET D 427 " pdb=" N MET D 427 " pdb=" C MET D 427 " pdb=" CB MET D 427 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ARG D 711 " pdb=" N ARG D 711 " pdb=" C ARG D 711 " pdb=" CB ARG D 711 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.49e-01 ... (remaining 6564 not shown) Planarity restraints: 7737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 726 " -0.081 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO F 727 " 0.217 5.00e-02 4.00e+02 pdb=" CA PRO F 727 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO F 727 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 551 " 0.023 2.00e-02 2.50e+03 2.92e-02 2.13e+01 pdb=" CG TRP C 551 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP C 551 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP C 551 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 551 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP C 551 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 551 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 551 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 551 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP C 551 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA F 297 " 0.063 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO F 298 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO F 298 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO F 298 " 0.051 5.00e-02 4.00e+02 ... (remaining 7734 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 766 2.68 - 3.23: 42251 3.23 - 3.79: 64631 3.79 - 4.34: 81772 4.34 - 4.90: 133125 Nonbonded interactions: 322545 Sorted by model distance: nonbonded pdb=" OG1 THR Y 202 " pdb=" OH TYR Y 207 " model vdw 2.119 2.440 nonbonded pdb=" O ASN C 624 " pdb=" OH TYR C 755 " model vdw 2.123 2.440 nonbonded pdb=" O ASN B 624 " pdb=" OH TYR B 755 " model vdw 2.139 2.440 nonbonded pdb=" OG SER D 664 " pdb=" O LYS F 505 " model vdw 2.156 2.440 nonbonded pdb=" NH2 ARG E 653 " pdb=" O THR E 679 " model vdw 2.173 2.520 ... (remaining 322540 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 763 or resid 901 through 902)) selection = (chain 'B' and (resid 23 through 763 or resid 901 through 902)) selection = chain 'C' selection = (chain 'D' and (resid 23 through 763 or resid 901 through 902)) selection = (chain 'E' and (resid 23 through 763 or resid 901 through 902)) selection = (chain 'F' and (resid 23 through 763 or resid 901 through 902)) } ncs_group { reference = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.050 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: 0.030 Extract box with map and model: 1.800 Check model and map are aligned: 0.330 Set scattering table: 0.400 Process input model: 109.280 Find NCS groups from input model: 3.370 Set up NCS constraints: 0.220 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:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 0.004 0.067 43852 Z= 0.238 Angle : 0.709 10.669 59392 Z= 0.367 Chirality : 0.046 0.276 6567 Planarity : 0.005 0.125 7737 Dihedral : 15.238 175.193 16697 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.63 % Favored : 90.95 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.33 % 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: -0.33 (0.12), residues: 5362 helix: 0.89 (0.11), residues: 2374 sheet: 0.21 (0.21), residues: 691 loop : -1.55 (0.13), residues: 2297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP C 551 HIS 0.010 0.001 HIS E 499 PHE 0.045 0.001 PHE C 552 TYR 0.029 0.001 TYR C 755 ARG 0.018 0.001 ARG D 711 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 4.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 82 TYR cc_start: 0.8089 (m-80) cc_final: 0.7681 (m-80) REVERT: W 106 TRP cc_start: 0.7038 (t60) cc_final: 0.6793 (t60) REVERT: X 57 THR cc_start: 0.6454 (p) cc_final: 0.6215 (p) REVERT: Y 116 MET cc_start: 0.5638 (mmp) cc_final: 0.5239 (mmm) REVERT: Y 192 MET cc_start: 0.6109 (ptt) cc_final: 0.5828 (ptt) REVERT: Z 127 MET cc_start: 0.8995 (pmm) cc_final: 0.8148 (pmm) REVERT: Z 163 ASN cc_start: 0.8419 (t0) cc_final: 0.8192 (p0) REVERT: Z 173 GLU cc_start: 0.8623 (mp0) cc_final: 0.8108 (mp0) REVERT: Z 198 ASN cc_start: 0.8092 (t0) cc_final: 0.7845 (t0) REVERT: B 561 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7587 (tm-30) REVERT: C 244 TYR cc_start: 0.7932 (p90) cc_final: 0.7661 (p90) REVERT: C 531 ILE cc_start: 0.9238 (tp) cc_final: 0.9033 (tp) REVERT: D 720 MET cc_start: 0.0445 (mtp) cc_final: 0.0175 (mtm) REVERT: E 46 MET cc_start: 0.6860 (mtp) cc_final: 0.5230 (tpt) REVERT: E 244 TYR cc_start: 0.7468 (p90) cc_final: 0.6806 (p90) REVERT: E 561 GLU cc_start: 0.7574 (pm20) cc_final: 0.7273 (pm20) REVERT: F 244 TYR cc_start: 0.7827 (p90) cc_final: 0.7583 (p90) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.5030 time to fit residues: 376.2336 Evaluate side-chains 330 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 4.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 450 optimal weight: 10.0000 chunk 404 optimal weight: 0.8980 chunk 224 optimal weight: 0.3980 chunk 138 optimal weight: 6.9990 chunk 273 optimal weight: 7.9990 chunk 216 optimal weight: 3.9990 chunk 418 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 254 optimal weight: 6.9990 chunk 311 optimal weight: 50.0000 chunk 484 optimal weight: 0.8980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 181 HIS ** Z 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 HIS F 404 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 43852 Z= 0.224 Angle : 0.660 9.739 59392 Z= 0.322 Chirality : 0.045 0.240 6567 Planarity : 0.005 0.096 7737 Dihedral : 9.325 166.734 6027 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.00 % Favored : 91.57 % Rotamer: Outliers : 0.81 % Allowed : 7.77 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.33 % 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: -0.21 (0.12), residues: 5362 helix: 0.97 (0.11), residues: 2462 sheet: 0.33 (0.21), residues: 665 loop : -1.58 (0.14), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP E 551 HIS 0.007 0.001 HIS F 404 PHE 0.020 0.001 PHE B 360 TYR 0.048 0.001 TYR D 495 ARG 0.007 0.000 ARG E 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 359 time to evaluate : 4.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 38 TYR cc_start: 0.3081 (OUTLIER) cc_final: 0.2021 (t80) REVERT: W 82 TYR cc_start: 0.7937 (m-80) cc_final: 0.7623 (m-80) REVERT: W 106 TRP cc_start: 0.7042 (t60) cc_final: 0.6776 (t60) REVERT: X 57 THR cc_start: 0.6415 (p) cc_final: 0.6213 (p) REVERT: X 192 MET cc_start: 0.8967 (ppp) cc_final: 0.8663 (ppp) REVERT: Z 1 MET cc_start: 0.4276 (ttt) cc_final: 0.3662 (tmm) REVERT: Z 163 ASN cc_start: 0.8481 (t0) cc_final: 0.8277 (p0) REVERT: Z 173 GLU cc_start: 0.8920 (mp0) cc_final: 0.8165 (mp0) REVERT: Z 192 MET cc_start: 0.7663 (ptt) cc_final: 0.7393 (ptp) REVERT: Z 198 ASN cc_start: 0.8152 (t0) cc_final: 0.7951 (t0) REVERT: B 561 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7565 (tm-30) REVERT: C 244 TYR cc_start: 0.7892 (p90) cc_final: 0.7670 (p90) REVERT: C 702 SER cc_start: 0.8755 (t) cc_final: 0.8252 (p) REVERT: D 508 MET cc_start: 0.4175 (OUTLIER) cc_final: 0.2584 (tmm) REVERT: D 651 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7350 (tttm) REVERT: D 720 MET cc_start: 0.0445 (mtp) cc_final: 0.0173 (mtm) REVERT: E 46 MET cc_start: 0.6891 (mtp) cc_final: 0.5326 (tpt) REVERT: E 244 TYR cc_start: 0.7501 (p90) cc_final: 0.7218 (p90) REVERT: E 315 LYS cc_start: 0.8620 (tppt) cc_final: 0.8292 (tptt) REVERT: E 427 MET cc_start: 0.8541 (tmm) cc_final: 0.8306 (tmm) REVERT: E 608 MET cc_start: 0.8655 (tmm) cc_final: 0.8365 (tmm) REVERT: F 244 TYR cc_start: 0.7810 (p90) cc_final: 0.7542 (p90) REVERT: F 740 MET cc_start: 0.8661 (tmm) cc_final: 0.8388 (tmm) outliers start: 37 outliers final: 20 residues processed: 376 average time/residue: 0.5043 time to fit residues: 321.7048 Evaluate side-chains 354 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 331 time to evaluate : 4.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 TYR Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain Y residue 117 ASP Chi-restraints excluded: chain Y residue 169 SER Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 269 optimal weight: 7.9990 chunk 150 optimal weight: 0.0980 chunk 403 optimal weight: 0.9990 chunk 330 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 485 optimal weight: 6.9990 chunk 524 optimal weight: 6.9990 chunk 432 optimal weight: 5.9990 chunk 481 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 chunk 389 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 172 ASN ** Z 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS D 499 HIS D 603 GLN ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 HIS ** E 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 43852 Z= 0.187 Angle : 0.624 11.691 59392 Z= 0.300 Chirality : 0.044 0.178 6567 Planarity : 0.004 0.093 7737 Dihedral : 8.974 151.836 6027 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.93 % Favored : 91.64 % Rotamer: Outliers : 0.94 % Allowed : 10.92 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.33 % 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: -0.13 (0.12), residues: 5362 helix: 1.05 (0.11), residues: 2477 sheet: 0.32 (0.20), residues: 669 loop : -1.56 (0.14), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 551 HIS 0.011 0.001 HIS E 404 PHE 0.019 0.001 PHE D 552 TYR 0.025 0.001 TYR D 495 ARG 0.009 0.000 ARG X 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 356 time to evaluate : 4.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 38 TYR cc_start: 0.3143 (OUTLIER) cc_final: 0.2314 (t80) REVERT: W 78 PHE cc_start: 0.8987 (m-80) cc_final: 0.8778 (m-80) REVERT: W 82 TYR cc_start: 0.7910 (m-80) cc_final: 0.7506 (m-80) REVERT: W 106 TRP cc_start: 0.6998 (t60) cc_final: 0.6743 (t60) REVERT: W 127 MET cc_start: 0.7973 (tmm) cc_final: 0.7473 (tmm) REVERT: X 57 THR cc_start: 0.6474 (p) cc_final: 0.6251 (p) REVERT: X 192 MET cc_start: 0.9018 (ppp) cc_final: 0.8625 (ppp) REVERT: Y 172 ASN cc_start: 0.8303 (m110) cc_final: 0.7771 (p0) REVERT: Z 1 MET cc_start: 0.4476 (ttt) cc_final: 0.3778 (tmm) REVERT: Z 173 GLU cc_start: 0.8931 (mp0) cc_final: 0.8236 (mp0) REVERT: Z 192 MET cc_start: 0.7728 (ptt) cc_final: 0.7404 (ptp) REVERT: Z 198 ASN cc_start: 0.8103 (t0) cc_final: 0.7884 (t0) REVERT: A 286 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8532 (tt) REVERT: B 561 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7581 (tm-30) REVERT: C 702 SER cc_start: 0.8812 (t) cc_final: 0.8294 (p) REVERT: D 508 MET cc_start: 0.4474 (OUTLIER) cc_final: 0.2793 (tmm) REVERT: D 651 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7339 (tttm) REVERT: D 678 MET cc_start: 0.8114 (tpp) cc_final: 0.7864 (tpp) REVERT: E 46 MET cc_start: 0.6824 (mtp) cc_final: 0.5267 (tpt) REVERT: E 244 TYR cc_start: 0.7495 (p90) cc_final: 0.7203 (p90) REVERT: E 379 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: E 427 MET cc_start: 0.8520 (tmm) cc_final: 0.8249 (tmm) REVERT: E 607 GLU cc_start: 0.7334 (mt-10) cc_final: 0.7032 (mp0) REVERT: F 244 TYR cc_start: 0.7802 (p90) cc_final: 0.7535 (p90) REVERT: F 607 GLU cc_start: 0.8058 (mp0) cc_final: 0.7825 (mp0) REVERT: F 740 MET cc_start: 0.8631 (tmm) cc_final: 0.8343 (tmm) outliers start: 43 outliers final: 24 residues processed: 378 average time/residue: 0.4980 time to fit residues: 320.7428 Evaluate side-chains 355 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 326 time to evaluate : 4.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 TYR Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain Y residue 117 ASP Chi-restraints excluded: chain Y residue 169 SER Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 479 optimal weight: 0.9980 chunk 365 optimal weight: 3.9990 chunk 252 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 231 optimal weight: 0.0040 chunk 326 optimal weight: 40.0000 chunk 487 optimal weight: 4.9990 chunk 516 optimal weight: 7.9990 chunk 254 optimal weight: 5.9990 chunk 462 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 GLN ** E 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN F 660 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 43852 Z= 0.282 Angle : 0.659 9.992 59392 Z= 0.319 Chirality : 0.045 0.183 6567 Planarity : 0.005 0.092 7737 Dihedral : 8.893 150.808 6027 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.28 % Favored : 91.33 % Rotamer: Outliers : 1.28 % Allowed : 13.47 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.33 % 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: -0.21 (0.12), residues: 5362 helix: 1.00 (0.11), residues: 2478 sheet: 0.24 (0.20), residues: 660 loop : -1.59 (0.14), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP E 551 HIS 0.011 0.001 HIS E 404 PHE 0.017 0.001 PHE E 131 TYR 0.029 0.001 TYR Z 131 ARG 0.006 0.000 ARG E 753 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 338 time to evaluate : 4.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 78 PHE cc_start: 0.8962 (m-80) cc_final: 0.8734 (m-80) REVERT: W 106 TRP cc_start: 0.7158 (t60) cc_final: 0.6827 (t60) REVERT: X 57 THR cc_start: 0.6585 (p) cc_final: 0.6356 (p) REVERT: X 122 MET cc_start: 0.7895 (tmt) cc_final: 0.7465 (tmm) REVERT: X 192 MET cc_start: 0.8961 (ppp) cc_final: 0.8595 (ppp) REVERT: Z 1 MET cc_start: 0.4552 (ttt) cc_final: 0.3845 (tmm) REVERT: Z 127 MET cc_start: 0.9038 (pmm) cc_final: 0.8439 (ppp) REVERT: Z 173 GLU cc_start: 0.8844 (mp0) cc_final: 0.8298 (mp0) REVERT: Z 192 MET cc_start: 0.7837 (ptt) cc_final: 0.7540 (ptp) REVERT: Z 198 ASN cc_start: 0.8138 (t0) cc_final: 0.7905 (t0) REVERT: B 561 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7643 (tm-30) REVERT: C 173 TYR cc_start: 0.6797 (p90) cc_final: 0.6379 (p90) REVERT: C 611 MET cc_start: 0.7754 (mmm) cc_final: 0.7521 (mmp) REVERT: D 508 MET cc_start: 0.4644 (OUTLIER) cc_final: 0.4371 (ttm) REVERT: D 651 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7463 (tttm) REVERT: D 678 MET cc_start: 0.7990 (tpp) cc_final: 0.7764 (tpp) REVERT: D 720 MET cc_start: 0.0241 (OUTLIER) cc_final: -0.0101 (mtp) REVERT: D 730 GLU cc_start: 0.5339 (OUTLIER) cc_final: 0.4835 (pm20) REVERT: E 84 MET cc_start: 0.6946 (ppp) cc_final: 0.6699 (ppp) REVERT: E 244 TYR cc_start: 0.7647 (p90) cc_final: 0.7299 (p90) REVERT: E 315 LYS cc_start: 0.8616 (tppt) cc_final: 0.8211 (tptt) REVERT: E 332 MET cc_start: 0.8890 (tpp) cc_final: 0.8596 (tpp) REVERT: E 379 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: E 427 MET cc_start: 0.8592 (tmm) cc_final: 0.8261 (tmm) REVERT: E 607 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7107 (mp0) REVERT: E 608 MET cc_start: 0.8786 (tmm) cc_final: 0.8371 (tmm) REVERT: F 607 GLU cc_start: 0.8173 (mp0) cc_final: 0.7922 (mp0) REVERT: F 740 MET cc_start: 0.8786 (tmm) cc_final: 0.8469 (tmm) outliers start: 59 outliers final: 38 residues processed: 374 average time/residue: 0.5364 time to fit residues: 341.3290 Evaluate side-chains 365 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 322 time to evaluate : 5.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain Z residue 188 PHE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 551 TRP Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 429 optimal weight: 10.0000 chunk 293 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 384 optimal weight: 9.9990 chunk 212 optimal weight: 0.7980 chunk 440 optimal weight: 8.9990 chunk 356 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 263 optimal weight: 1.9990 chunk 463 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 172 ASN ** Z 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 735 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 43852 Z= 0.214 Angle : 0.629 12.663 59392 Z= 0.301 Chirality : 0.044 0.198 6567 Planarity : 0.004 0.090 7737 Dihedral : 8.649 154.238 6027 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.93 % Favored : 91.70 % Rotamer: Outliers : 1.37 % Allowed : 14.89 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % 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: -0.13 (0.12), residues: 5362 helix: 1.09 (0.11), residues: 2468 sheet: 0.25 (0.20), residues: 664 loop : -1.58 (0.13), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP E 551 HIS 0.005 0.001 HIS E 404 PHE 0.017 0.001 PHE Z 78 TYR 0.026 0.001 TYR F 244 ARG 0.005 0.000 ARG F 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 345 time to evaluate : 5.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.4822 (ttt) cc_final: 0.3190 (tmm) REVERT: W 78 PHE cc_start: 0.8945 (m-80) cc_final: 0.8716 (m-80) REVERT: W 106 TRP cc_start: 0.7087 (t60) cc_final: 0.6775 (t60) REVERT: X 57 THR cc_start: 0.6586 (p) cc_final: 0.6360 (p) REVERT: X 122 MET cc_start: 0.7996 (tmt) cc_final: 0.7554 (tmm) REVERT: X 192 MET cc_start: 0.8967 (ppp) cc_final: 0.8564 (ppp) REVERT: Y 172 ASN cc_start: 0.8356 (m110) cc_final: 0.7791 (p0) REVERT: Z 1 MET cc_start: 0.4559 (ttt) cc_final: 0.3802 (tmm) REVERT: Z 127 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8472 (ppp) REVERT: Z 173 GLU cc_start: 0.8830 (mp0) cc_final: 0.8021 (mp0) REVERT: Z 192 MET cc_start: 0.7719 (ptt) cc_final: 0.7379 (ptp) REVERT: Z 198 ASN cc_start: 0.8150 (t0) cc_final: 0.7912 (t0) REVERT: B 561 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7637 (tm-30) REVERT: C 173 TYR cc_start: 0.6767 (p90) cc_final: 0.6281 (p90) REVERT: D 651 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7444 (tttm) REVERT: D 720 MET cc_start: 0.0246 (OUTLIER) cc_final: -0.0074 (mtp) REVERT: D 730 GLU cc_start: 0.5290 (OUTLIER) cc_final: 0.4816 (pm20) REVERT: E 46 MET cc_start: 0.6620 (mtp) cc_final: 0.4868 (tpt) REVERT: E 244 TYR cc_start: 0.7686 (p90) cc_final: 0.7347 (p90) REVERT: E 315 LYS cc_start: 0.8612 (tppt) cc_final: 0.8184 (tptt) REVERT: E 379 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: E 427 MET cc_start: 0.8570 (tmm) cc_final: 0.8227 (tmm) REVERT: E 607 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7050 (mp0) REVERT: E 608 MET cc_start: 0.8834 (tmm) cc_final: 0.8595 (tmm) REVERT: F 491 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7896 (mm-30) REVERT: F 740 MET cc_start: 0.8613 (tmm) cc_final: 0.8264 (tmm) outliers start: 63 outliers final: 35 residues processed: 385 average time/residue: 0.4908 time to fit residues: 320.9204 Evaluate side-chains 364 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 324 time to evaluate : 4.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain Z residue 127 MET Chi-restraints excluded: chain Z residue 188 PHE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 551 TRP Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 173 optimal weight: 1.9990 chunk 464 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 303 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 516 optimal weight: 0.7980 chunk 428 optimal weight: 8.9990 chunk 239 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 271 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 81 GLN ** Y 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN D 714 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 43852 Z= 0.195 Angle : 0.631 13.989 59392 Z= 0.299 Chirality : 0.044 0.207 6567 Planarity : 0.004 0.088 7737 Dihedral : 8.400 155.646 6027 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.08 % Favored : 91.53 % Rotamer: Outliers : 1.76 % Allowed : 15.52 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % 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: -0.08 (0.12), residues: 5362 helix: 1.14 (0.11), residues: 2475 sheet: 0.30 (0.20), residues: 664 loop : -1.56 (0.14), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP E 551 HIS 0.003 0.001 HIS B 183 PHE 0.016 0.001 PHE D 552 TYR 0.019 0.001 TYR C 244 ARG 0.004 0.000 ARG C 599 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 339 time to evaluate : 4.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.4877 (ttt) cc_final: 0.3963 (tmm) REVERT: W 38 TYR cc_start: 0.3608 (OUTLIER) cc_final: 0.2625 (t80) REVERT: W 78 PHE cc_start: 0.8967 (m-80) cc_final: 0.8706 (m-80) REVERT: W 106 TRP cc_start: 0.7057 (t60) cc_final: 0.6733 (t60) REVERT: W 155 LEU cc_start: 0.9412 (mm) cc_final: 0.9153 (mt) REVERT: X 57 THR cc_start: 0.6626 (p) cc_final: 0.6394 (p) REVERT: X 122 MET cc_start: 0.8050 (tmt) cc_final: 0.7600 (tmm) REVERT: X 192 MET cc_start: 0.8985 (ppp) cc_final: 0.8553 (ppp) REVERT: Y 172 ASN cc_start: 0.8335 (m110) cc_final: 0.7818 (p0) REVERT: Z 1 MET cc_start: 0.4586 (ttt) cc_final: 0.3717 (tmm) REVERT: Z 127 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8429 (ppp) REVERT: Z 173 GLU cc_start: 0.8830 (mp0) cc_final: 0.8022 (mp0) REVERT: Z 192 MET cc_start: 0.7528 (ptt) cc_final: 0.7198 (ptp) REVERT: Z 198 ASN cc_start: 0.8123 (t0) cc_final: 0.7859 (t0) REVERT: B 561 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7687 (tm-30) REVERT: B 601 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8335 (tp) REVERT: C 173 TYR cc_start: 0.6793 (p90) cc_final: 0.6274 (p90) REVERT: C 670 VAL cc_start: 0.4439 (OUTLIER) cc_final: 0.3842 (p) REVERT: C 702 SER cc_start: 0.8889 (t) cc_final: 0.8371 (p) REVERT: D 602 ASN cc_start: 0.8313 (m-40) cc_final: 0.8080 (m-40) REVERT: D 651 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7432 (tttm) REVERT: D 678 MET cc_start: 0.8126 (tpp) cc_final: 0.7753 (tpp) REVERT: D 720 MET cc_start: 0.0484 (OUTLIER) cc_final: 0.0214 (mtp) REVERT: D 730 GLU cc_start: 0.5419 (OUTLIER) cc_final: 0.5002 (pm20) REVERT: E 244 TYR cc_start: 0.7687 (p90) cc_final: 0.7331 (p90) REVERT: E 315 LYS cc_start: 0.8580 (tppt) cc_final: 0.8166 (tptt) REVERT: E 379 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.7036 (mp0) REVERT: E 427 MET cc_start: 0.8543 (tmm) cc_final: 0.8236 (tmm) REVERT: E 607 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6942 (mp0) REVERT: E 608 MET cc_start: 0.8829 (tmm) cc_final: 0.8547 (tmm) REVERT: F 491 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7879 (mm-30) REVERT: F 740 MET cc_start: 0.8599 (tmm) cc_final: 0.8256 (tmm) outliers start: 81 outliers final: 50 residues processed: 394 average time/residue: 0.4898 time to fit residues: 329.1741 Evaluate side-chains 382 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 324 time to evaluate : 4.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 TYR Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain Z residue 127 MET Chi-restraints excluded: chain Z residue 139 ASP Chi-restraints excluded: chain Z residue 188 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 551 TRP Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 498 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 294 optimal weight: 7.9990 chunk 377 optimal weight: 8.9990 chunk 292 optimal weight: 7.9990 chunk 434 optimal weight: 8.9990 chunk 288 optimal weight: 0.9980 chunk 514 optimal weight: 1.9990 chunk 322 optimal weight: 0.9980 chunk 313 optimal weight: 30.0000 chunk 237 optimal weight: 40.0000 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN A 340 HIS ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 43852 Z= 0.332 Angle : 0.715 13.679 59392 Z= 0.344 Chirality : 0.046 0.184 6567 Planarity : 0.005 0.091 7737 Dihedral : 8.508 157.885 6027 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.05 % Favored : 90.60 % Rotamer: Outliers : 2.11 % Allowed : 16.28 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % 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: -0.37 (0.12), residues: 5362 helix: 0.92 (0.11), residues: 2461 sheet: 0.02 (0.20), residues: 674 loop : -1.68 (0.13), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP E 551 HIS 0.005 0.001 HIS B 183 PHE 0.030 0.002 PHE B 575 TYR 0.022 0.002 TYR F 244 ARG 0.006 0.000 ARG X 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 333 time to evaluate : 5.084 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: W 1 MET cc_start: 0.5329 (ttt) cc_final: 0.3948 (tmm) REVERT: W 78 PHE cc_start: 0.9011 (m-80) cc_final: 0.8746 (m-80) REVERT: W 106 TRP cc_start: 0.7196 (t60) cc_final: 0.6840 (t60) REVERT: X 57 THR cc_start: 0.6571 (p) cc_final: 0.6298 (p) REVERT: X 102 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7678 (mt) REVERT: X 122 MET cc_start: 0.8342 (tmt) cc_final: 0.7725 (tmm) REVERT: X 192 MET cc_start: 0.9006 (ppp) cc_final: 0.8560 (ppp) REVERT: Y 172 ASN cc_start: 0.8264 (m110) cc_final: 0.7745 (p0) REVERT: Z 127 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8469 (ppp) REVERT: Z 173 GLU cc_start: 0.8902 (mp0) cc_final: 0.8031 (mp0) REVERT: Z 192 MET cc_start: 0.7470 (ptt) cc_final: 0.7119 (ptp) REVERT: Z 198 ASN cc_start: 0.8131 (t0) cc_final: 0.7872 (t0) REVERT: B 489 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9129 (mm) REVERT: B 561 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7697 (tm-30) REVERT: B 601 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8256 (tp) REVERT: C 173 TYR cc_start: 0.6935 (p90) cc_final: 0.6391 (p90) REVERT: D 508 MET cc_start: 0.4244 (ttm) cc_final: 0.3937 (ttm) REVERT: D 651 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7570 (tttm) REVERT: D 661 LEU cc_start: 0.8292 (tp) cc_final: 0.7700 (tt) REVERT: D 720 MET cc_start: 0.0685 (OUTLIER) cc_final: 0.0432 (mtp) REVERT: E 244 TYR cc_start: 0.7826 (p90) cc_final: 0.7423 (p90) REVERT: E 315 LYS cc_start: 0.8593 (tppt) cc_final: 0.8173 (tptt) REVERT: E 379 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: E 427 MET cc_start: 0.8597 (tmm) cc_final: 0.8279 (tmm) REVERT: E 607 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7078 (mp0) REVERT: E 608 MET cc_start: 0.8871 (tmm) cc_final: 0.8573 (tmm) REVERT: F 607 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: F 608 MET cc_start: 0.7924 (mtm) cc_final: 0.7683 (mtm) REVERT: F 740 MET cc_start: 0.8635 (tmm) cc_final: 0.8267 (tmm) outliers start: 97 outliers final: 66 residues processed: 401 average time/residue: 0.5132 time to fit residues: 347.0310 Evaluate side-chains 393 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 319 time to evaluate : 4.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain W residue 84 THR Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain X residue 42 TRP Chi-restraints excluded: chain X residue 64 VAL Chi-restraints excluded: chain X residue 101 MET Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 110 VAL Chi-restraints excluded: chain X residue 173 GLU Chi-restraints excluded: chain Y residue 117 ASP Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain Z residue 127 MET Chi-restraints excluded: chain Z residue 139 ASP Chi-restraints excluded: chain Z residue 188 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 551 TRP Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 713 ARG Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 425 LYS Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 607 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 318 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 307 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 327 optimal weight: 9.9990 chunk 350 optimal weight: 0.0470 chunk 254 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 404 optimal weight: 3.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 43852 Z= 0.162 Angle : 0.637 14.485 59392 Z= 0.302 Chirality : 0.043 0.239 6567 Planarity : 0.004 0.085 7737 Dihedral : 8.209 154.846 6027 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.03 % Favored : 92.61 % Rotamer: Outliers : 1.52 % Allowed : 17.02 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % 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: -0.10 (0.12), residues: 5362 helix: 1.15 (0.11), residues: 2462 sheet: 0.28 (0.20), residues: 671 loop : -1.61 (0.13), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP Z 106 HIS 0.004 0.001 HIS F 340 PHE 0.029 0.001 PHE B 575 TYR 0.018 0.001 TYR B 244 ARG 0.005 0.000 ARG E 113 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 340 time to evaluate : 4.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.5164 (ttt) cc_final: 0.3909 (tmm) REVERT: W 78 PHE cc_start: 0.8981 (m-80) cc_final: 0.8709 (m-80) REVERT: W 106 TRP cc_start: 0.7100 (t60) cc_final: 0.6735 (t60) REVERT: X 102 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7620 (mt) REVERT: X 122 MET cc_start: 0.8091 (tmt) cc_final: 0.7580 (tmm) REVERT: X 192 MET cc_start: 0.9000 (ppp) cc_final: 0.8549 (ppp) REVERT: Y 172 ASN cc_start: 0.8214 (m110) cc_final: 0.7738 (p0) REVERT: Y 174 LEU cc_start: 0.9140 (mt) cc_final: 0.8924 (mt) REVERT: Z 127 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8484 (ppp) REVERT: Z 157 TRP cc_start: 0.8587 (m100) cc_final: 0.8155 (m100) REVERT: Z 173 GLU cc_start: 0.8826 (mp0) cc_final: 0.8015 (mp0) REVERT: Z 192 MET cc_start: 0.7533 (ptt) cc_final: 0.7225 (ptp) REVERT: Z 198 ASN cc_start: 0.8106 (t0) cc_final: 0.7835 (t0) REVERT: B 433 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6578 (pp20) REVERT: B 561 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7690 (tm-30) REVERT: C 702 SER cc_start: 0.8898 (t) cc_final: 0.8369 (p) REVERT: D 508 MET cc_start: 0.4099 (ttm) cc_final: 0.3861 (ttm) REVERT: D 651 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7513 (tttm) REVERT: D 661 LEU cc_start: 0.8133 (tp) cc_final: 0.7721 (tt) REVERT: D 730 GLU cc_start: 0.5387 (OUTLIER) cc_final: 0.5004 (pm20) REVERT: E 244 TYR cc_start: 0.7760 (p90) cc_final: 0.7369 (p90) REVERT: E 315 LYS cc_start: 0.8547 (tppt) cc_final: 0.8161 (tptt) REVERT: E 379 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: E 427 MET cc_start: 0.8529 (tmm) cc_final: 0.8214 (tmm) REVERT: E 607 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6979 (mp0) REVERT: E 608 MET cc_start: 0.8834 (tmm) cc_final: 0.8522 (tmm) REVERT: F 315 LYS cc_start: 0.8982 (mptt) cc_final: 0.8738 (mmmt) REVERT: F 491 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7621 (mm-30) REVERT: F 740 MET cc_start: 0.8596 (tmm) cc_final: 0.8232 (tmm) outliers start: 70 outliers final: 43 residues processed: 389 average time/residue: 0.5049 time to fit residues: 334.3403 Evaluate side-chains 370 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 321 time to evaluate : 4.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 TYR Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain X residue 42 TRP Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 110 VAL Chi-restraints excluded: chain X residue 173 GLU Chi-restraints excluded: chain Y residue 98 TYR Chi-restraints excluded: chain Y residue 121 LEU Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain Z residue 127 MET Chi-restraints excluded: chain Z residue 139 ASP Chi-restraints excluded: chain Z residue 188 PHE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 686 ASP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 607 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 468 optimal weight: 6.9990 chunk 493 optimal weight: 1.9990 chunk 449 optimal weight: 0.0170 chunk 479 optimal weight: 0.3980 chunk 492 optimal weight: 0.8980 chunk 288 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 376 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 433 optimal weight: 4.9990 chunk 453 optimal weight: 0.9980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 43852 Z= 0.162 Angle : 0.645 15.106 59392 Z= 0.305 Chirality : 0.044 0.318 6567 Planarity : 0.004 0.081 7737 Dihedral : 8.075 153.230 6027 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.40 % Favored : 92.22 % Rotamer: Outliers : 1.33 % Allowed : 17.37 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % 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: -0.03 (0.12), residues: 5362 helix: 1.19 (0.11), residues: 2460 sheet: 0.38 (0.20), residues: 663 loop : -1.56 (0.13), residues: 2239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP E 551 HIS 0.004 0.000 HIS F 340 PHE 0.036 0.001 PHE Y 78 TYR 0.024 0.001 TYR Y 48 ARG 0.007 0.000 ARG A 560 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 350 time to evaluate : 4.782 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: W 1 MET cc_start: 0.5181 (ttt) cc_final: 0.3964 (tmm) REVERT: W 78 PHE cc_start: 0.8967 (m-80) cc_final: 0.8703 (m-80) REVERT: W 106 TRP cc_start: 0.7054 (t60) cc_final: 0.6693 (t60) REVERT: W 182 LEU cc_start: 0.9288 (mm) cc_final: 0.8936 (pp) REVERT: X 57 THR cc_start: 0.6486 (p) cc_final: 0.6269 (p) REVERT: X 102 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7583 (mt) REVERT: X 122 MET cc_start: 0.8185 (tmt) cc_final: 0.7670 (tmm) REVERT: X 192 MET cc_start: 0.9011 (ppp) cc_final: 0.8553 (ppp) REVERT: Y 172 ASN cc_start: 0.8183 (m110) cc_final: 0.7702 (p0) REVERT: Z 1 MET cc_start: 0.5766 (tmm) cc_final: 0.5354 (tmm) REVERT: Z 127 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8452 (ppp) REVERT: Z 157 TRP cc_start: 0.8572 (m100) cc_final: 0.8145 (m100) REVERT: Z 173 GLU cc_start: 0.8819 (mp0) cc_final: 0.7994 (mp0) REVERT: Z 192 MET cc_start: 0.7511 (ptt) cc_final: 0.6766 (tpt) REVERT: Z 198 ASN cc_start: 0.8102 (t0) cc_final: 0.7832 (t0) REVERT: B 433 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6626 (pp20) REVERT: B 561 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7687 (tm-30) REVERT: D 417 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8036 (mm-30) REVERT: D 651 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7490 (tttm) REVERT: D 730 GLU cc_start: 0.5366 (OUTLIER) cc_final: 0.4966 (pm20) REVERT: E 244 TYR cc_start: 0.7677 (p90) cc_final: 0.7304 (p90) REVERT: E 315 LYS cc_start: 0.8526 (tppt) cc_final: 0.8120 (tptt) REVERT: E 379 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.7028 (mp0) REVERT: E 427 MET cc_start: 0.8535 (tmm) cc_final: 0.8241 (tmm) REVERT: E 607 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6962 (mp0) REVERT: E 608 MET cc_start: 0.8794 (tmm) cc_final: 0.8467 (tmm) REVERT: F 315 LYS cc_start: 0.8980 (mptt) cc_final: 0.8734 (mmmt) REVERT: F 491 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7593 (mm-30) REVERT: F 740 MET cc_start: 0.8582 (tmm) cc_final: 0.8212 (tmm) outliers start: 61 outliers final: 49 residues processed: 392 average time/residue: 0.4964 time to fit residues: 331.6602 Evaluate side-chains 390 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 335 time to evaluate : 4.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 TYR Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 110 VAL Chi-restraints excluded: chain X residue 173 GLU Chi-restraints excluded: chain Y residue 98 TYR Chi-restraints excluded: chain Y residue 121 LEU Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain Z residue 127 MET Chi-restraints excluded: chain Z residue 139 ASP Chi-restraints excluded: chain Z residue 188 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 714 GLN Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 607 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 477 optimal weight: 1.9990 chunk 314 optimal weight: 20.0000 chunk 507 optimal weight: 2.9990 chunk 309 optimal weight: 6.9990 chunk 240 optimal weight: 7.9990 chunk 352 optimal weight: 0.8980 chunk 532 optimal weight: 4.9990 chunk 489 optimal weight: 0.7980 chunk 423 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 327 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS B 115 HIS ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 43852 Z= 0.251 Angle : 0.688 14.490 59392 Z= 0.326 Chirality : 0.045 0.275 6567 Planarity : 0.005 0.082 7737 Dihedral : 8.176 153.325 6027 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.11 % Favored : 91.50 % Rotamer: Outliers : 1.37 % Allowed : 17.58 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % 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: -0.11 (0.12), residues: 5362 helix: 1.13 (0.11), residues: 2464 sheet: 0.32 (0.21), residues: 642 loop : -1.60 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP Y 42 HIS 0.004 0.001 HIS F 340 PHE 0.041 0.001 PHE Y 78 TYR 0.018 0.001 TYR B 244 ARG 0.005 0.000 ARG X 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 323 time to evaluate : 4.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.5304 (ttt) cc_final: 0.4036 (tmm) REVERT: W 78 PHE cc_start: 0.8995 (m-80) cc_final: 0.8719 (m-80) REVERT: W 106 TRP cc_start: 0.7166 (t60) cc_final: 0.6785 (t60) REVERT: W 182 LEU cc_start: 0.9308 (mm) cc_final: 0.8944 (pp) REVERT: X 57 THR cc_start: 0.6551 (p) cc_final: 0.6322 (p) REVERT: X 102 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7624 (mt) REVERT: X 122 MET cc_start: 0.8301 (tmt) cc_final: 0.7728 (tmm) REVERT: Y 44 GLU cc_start: 0.4918 (mp0) cc_final: 0.4150 (tm-30) REVERT: Y 192 MET cc_start: 0.6472 (ptt) cc_final: 0.6127 (ptt) REVERT: Z 127 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8467 (ppp) REVERT: Z 173 GLU cc_start: 0.8848 (mp0) cc_final: 0.8034 (mp0) REVERT: Z 192 MET cc_start: 0.7581 (ptt) cc_final: 0.7300 (ptp) REVERT: Z 198 ASN cc_start: 0.8128 (t0) cc_final: 0.7879 (t0) REVERT: A 292 GLU cc_start: 0.8341 (tp30) cc_final: 0.8066 (tp30) REVERT: A 508 MET cc_start: 0.6007 (tpp) cc_final: 0.4321 (mtp) REVERT: B 433 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6385 (pp20) REVERT: B 561 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7709 (tm-30) REVERT: C 607 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8411 (mm-30) REVERT: D 651 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7620 (tttm) REVERT: D 730 GLU cc_start: 0.5501 (OUTLIER) cc_final: 0.5047 (pm20) REVERT: E 244 TYR cc_start: 0.7822 (p90) cc_final: 0.7412 (p90) REVERT: E 315 LYS cc_start: 0.8507 (tppt) cc_final: 0.8098 (tptt) REVERT: E 379 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: E 427 MET cc_start: 0.8583 (tmm) cc_final: 0.8265 (tmm) REVERT: E 607 GLU cc_start: 0.7256 (mt-10) cc_final: 0.7011 (mp0) REVERT: E 608 MET cc_start: 0.8850 (tmm) cc_final: 0.8527 (tmm) REVERT: F 102 ILE cc_start: 0.8602 (mt) cc_final: 0.8361 (mp) REVERT: F 315 LYS cc_start: 0.9035 (mptt) cc_final: 0.8815 (mmmt) REVERT: F 491 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7659 (mm-30) REVERT: F 740 MET cc_start: 0.8596 (tmm) cc_final: 0.8219 (tmm) outliers start: 63 outliers final: 49 residues processed: 369 average time/residue: 0.5056 time to fit residues: 318.4310 Evaluate side-chains 372 residues out of total 4595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 316 time to evaluate : 4.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain X residue 64 VAL Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 110 VAL Chi-restraints excluded: chain X residue 173 GLU Chi-restraints excluded: chain Y residue 98 TYR Chi-restraints excluded: chain Y residue 121 LEU Chi-restraints excluded: chain Z residue 127 MET Chi-restraints excluded: chain Z residue 139 ASP Chi-restraints excluded: chain Z residue 188 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 714 GLN Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 607 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 259 optimal weight: 0.9980 chunk 336 optimal weight: 1.9990 chunk 451 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 chunk 390 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 424 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 435 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 172 ASN ** Z 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS D 602 ASN ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.123519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.086180 restraints weight = 111103.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.088940 restraints weight = 67242.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.089755 restraints weight = 47368.912| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 43852 Z= 0.209 Angle : 0.668 13.752 59392 Z= 0.316 Chirality : 0.044 0.290 6567 Planarity : 0.005 0.080 7737 Dihedral : 8.154 152.246 6027 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.83 % Favored : 91.78 % Rotamer: Outliers : 1.33 % Allowed : 17.74 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % 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: -0.09 (0.12), residues: 5362 helix: 1.16 (0.11), residues: 2454 sheet: 0.33 (0.21), residues: 642 loop : -1.59 (0.13), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP E 551 HIS 0.006 0.001 HIS C 115 PHE 0.042 0.001 PHE Y 78 TYR 0.017 0.001 TYR B 244 ARG 0.004 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7783.25 seconds wall clock time: 141 minutes 2.44 seconds (8462.44 seconds total)