Starting phenix.real_space_refine on Sun Aug 11 02:24:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vue_43529/08_2024/8vue_43529.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vue_43529/08_2024/8vue_43529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vue_43529/08_2024/8vue_43529.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vue_43529/08_2024/8vue_43529.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vue_43529/08_2024/8vue_43529.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vue_43529/08_2024/8vue_43529.cif" } resolution = 3.59 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= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11436 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 13512 2.51 5 N 3666 2.21 5 O 4227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 25": "OE1" <-> "OE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "B PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B GLU 363": "OE1" <-> "OE2" Residue "B GLU 373": "OE1" <-> "OE2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B GLU 439": "OE1" <-> "OE2" Residue "B GLU 481": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "C GLU 25": "OE1" <-> "OE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "D PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 345": "OE1" <-> "OE2" Residue "D GLU 363": "OE1" <-> "OE2" Residue "D GLU 373": "OE1" <-> "OE2" Residue "D GLU 403": "OE1" <-> "OE2" Residue "D GLU 439": "OE1" <-> "OE2" Residue "D GLU 481": "OE1" <-> "OE2" Residue "D GLU 484": "OE1" <-> "OE2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 231": "OE1" <-> "OE2" Residue "E GLU 246": "OE1" <-> "OE2" Residue "E GLU 305": "OE1" <-> "OE2" Residue "F PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 345": "OE1" <-> "OE2" Residue "F GLU 363": "OE1" <-> "OE2" Residue "F GLU 373": "OE1" <-> "OE2" Residue "F GLU 403": "OE1" <-> "OE2" Residue "F GLU 439": "OE1" <-> "OE2" Residue "F GLU 481": "OE1" <-> "OE2" Residue "F GLU 484": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 85": "OE1" <-> "OE2" Residue "G GLU 212": "OE1" <-> "OE2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H GLU 123": "OE1" <-> "OE2" Residue "H GLU 143": "OE1" <-> "OE2" Residue "H GLU 161": "OE1" <-> "OE2" Residue "H GLU 195": "OE1" <-> "OE2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "I GLU 85": "OE1" <-> "OE2" Residue "I GLU 212": "OE1" <-> "OE2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "K GLU 85": "OE1" <-> "OE2" Residue "K GLU 212": "OE1" <-> "OE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J GLU 123": "OE1" <-> "OE2" Residue "J GLU 143": "OE1" <-> "OE2" Residue "J GLU 161": "OE1" <-> "OE2" Residue "J GLU 195": "OE1" <-> "OE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L GLU 123": "OE1" <-> "OE2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "L GLU 161": "OE1" <-> "OE2" Residue "L GLU 195": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 21501 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2541 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 18, 'TRANS': 302} Chain: "B" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1328 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 1, 'TRANS': 162} Chain: "C" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2541 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 18, 'TRANS': 302} Chain: "D" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1328 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 1, 'TRANS': 162} Chain: "E" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2541 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 18, 'TRANS': 302} Chain: "F" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1328 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 1, 'TRANS': 162} Chain: "G" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1694 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1590 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 197} Chain: "I" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1694 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1694 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1590 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 197} Chain: "L" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1590 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 197} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.00, per 1000 atoms: 0.51 Number of scatterers: 21501 At special positions: 0 Unit cell: (167.865, 185.193, 146.205, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 4227 8.00 N 3666 7.00 C 13512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS B 471 " distance=2.08 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.02 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 482 " distance=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS D 471 " distance=1.99 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS D 478 " - pdb=" SG CYS D 482 " distance=2.03 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS F 471 " distance=2.02 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 278 " distance=2.03 Simple disulfide: pdb=" SG CYS E 59 " - pdb=" SG CYS E 71 " distance=2.03 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 306 " distance=2.02 Simple disulfide: pdb=" SG CYS F 478 " - pdb=" SG CYS F 482 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 140 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 140 " - pdb=" SG CYS I 196 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 140 " - pdb=" SG CYS K 196 " distance=2.02 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 134 " - pdb=" SG CYS J 194 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 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=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 169 " " NAG C 601 " - " ASN C 169 " " NAG E 601 " - " ASN E 169 " Time building additional restraints: 8.91 Conformation dependent library (CDL) restraints added in 3.8 seconds 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5136 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 60 sheets defined 16.9% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 68 through 75 removed outlier: 3.807A pdb=" N ASP A 72 " --> pdb=" O PRO A 69 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLU A 73 " --> pdb=" O MET A 70 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 75 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.554A pdb=" N TRP A 126 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 371 through 393 removed outlier: 3.927A pdb=" N MET B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 460 Processing helix chain 'B' and resid 479 through 489 Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 68 through 75 removed outlier: 3.807A pdb=" N ASP C 72 " --> pdb=" O PRO C 69 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLU C 73 " --> pdb=" O MET C 70 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 75 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 110 Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.554A pdb=" N TRP C 126 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'D' and resid 371 through 393 removed outlier: 3.927A pdb=" N MET D 393 " --> pdb=" O ILE D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 460 Processing helix chain 'D' and resid 479 through 489 Processing helix chain 'E' and resid 60 through 67 Processing helix chain 'E' and resid 68 through 75 removed outlier: 3.808A pdb=" N ASP E 72 " --> pdb=" O PRO E 69 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N GLU E 73 " --> pdb=" O MET E 70 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE E 75 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 110 Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.558A pdb=" N TRP E 126 " --> pdb=" O LYS E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 195 Processing helix chain 'F' and resid 371 through 393 removed outlier: 3.927A pdb=" N MET F 393 " --> pdb=" O ILE F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 460 Processing helix chain 'F' and resid 479 through 489 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.638A pdb=" N THR G 87 " --> pdb=" O PRO G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 158 No H-bonds generated for 'chain 'G' and resid 156 through 158' Processing helix chain 'G' and resid 185 through 190 removed outlier: 4.466A pdb=" N GLY G 190 " --> pdb=" O SER G 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'H' and resid 183 through 188 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.639A pdb=" N THR I 87 " --> pdb=" O PRO I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 158 No H-bonds generated for 'chain 'I' and resid 156 through 158' Processing helix chain 'I' and resid 185 through 190 removed outlier: 4.467A pdb=" N GLY I 190 " --> pdb=" O SER I 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.639A pdb=" N THR K 87 " --> pdb=" O PRO K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 158 No H-bonds generated for 'chain 'K' and resid 156 through 158' Processing helix chain 'K' and resid 185 through 190 removed outlier: 4.467A pdb=" N GLY K 190 " --> pdb=" O SER K 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 128 Processing helix chain 'J' and resid 183 through 188 Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'B' and resid 365 through 370 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA4, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.598A pdb=" N LEU A 54 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE A 83 " --> pdb=" O MET A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.783A pdb=" N SER A 98 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N TRP A 234 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASP A 175 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS A 114 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS A 263 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE A 112 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.783A pdb=" N SER A 98 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N TRP A 234 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.484A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 146 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB1, first strand: chain 'A' and resid 287 through 288 Processing sheet with id=AB2, first strand: chain 'D' and resid 365 through 370 Processing sheet with id=AB3, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AB4, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AB5, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AB6, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.599A pdb=" N LEU C 54 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE C 83 " --> pdb=" O MET C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 97 through 99 removed outlier: 6.784A pdb=" N SER C 98 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N TRP C 234 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP C 175 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N HIS C 114 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS C 263 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE C 112 " --> pdb=" O LYS C 263 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 97 through 99 removed outlier: 6.784A pdb=" N SER C 98 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N TRP C 234 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.484A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 146 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC2, first strand: chain 'C' and resid 287 through 288 Processing sheet with id=AC3, first strand: chain 'F' and resid 365 through 370 Processing sheet with id=AC4, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AC5, first strand: chain 'E' and resid 33 through 35 Processing sheet with id=AC6, first strand: chain 'E' and resid 37 through 38 Processing sheet with id=AC7, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.598A pdb=" N LEU E 54 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE E 83 " --> pdb=" O MET E 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 97 through 99 removed outlier: 6.783A pdb=" N SER E 98 " --> pdb=" O PHE E 232 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N TRP E 234 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASP E 175 " --> pdb=" O ILE E 260 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS E 114 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS E 263 " --> pdb=" O ILE E 112 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE E 112 " --> pdb=" O LYS E 263 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 97 through 99 removed outlier: 6.783A pdb=" N SER E 98 " --> pdb=" O PHE E 232 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N TRP E 234 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 136 through 141 removed outlier: 4.484A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER E 146 " --> pdb=" O CYS E 139 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD3, first strand: chain 'E' and resid 287 through 288 Processing sheet with id=AD4, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.517A pdb=" N VAL G 12 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP G 35A" --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.517A pdb=" N VAL G 12 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS G 92 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TRP G 103 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY G 96 " --> pdb=" O SER G 100F" (cutoff:3.500A) removed outlier: 8.081A pdb=" N SER G 100F" --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ARG G 98 " --> pdb=" O VAL G 100D" (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL G 100D" --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 120 through 124 removed outlier: 6.110A pdb=" N TYR G 176 " --> pdb=" O ASP G 144 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 120 through 124 removed outlier: 6.110A pdb=" N TYR G 176 " --> pdb=" O ASP G 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 151 through 154 Processing sheet with id=AE1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.581A pdb=" N GLU H 105 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 114 through 118 removed outlier: 5.256A pdb=" N SER H 131 " --> pdb=" O LEU H 181 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU H 181 " --> pdb=" O SER H 131 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL H 133 " --> pdb=" O LEU H 179 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU H 179 " --> pdb=" O VAL H 133 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU H 135 " --> pdb=" O SER H 177 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N SER H 177 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASN H 137 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU H 175 " --> pdb=" O ASN H 137 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 153 through 154 Processing sheet with id=AE5, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.517A pdb=" N VAL I 12 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP I 35A" --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG I 50 " --> pdb=" O TRP I 35A" (cutoff:3.500A) removed outlier: 6.440A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.517A pdb=" N VAL I 12 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS I 92 " --> pdb=" O TRP I 103 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TRP I 103 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG I 94 " --> pdb=" O ASP I 101 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY I 96 " --> pdb=" O SER I 100F" (cutoff:3.500A) removed outlier: 8.083A pdb=" N SER I 100F" --> pdb=" O GLY I 96 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ARG I 98 " --> pdb=" O VAL I 100D" (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL I 100D" --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 120 through 124 removed outlier: 6.108A pdb=" N TYR I 176 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 120 through 124 removed outlier: 6.108A pdb=" N TYR I 176 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 151 through 154 Processing sheet with id=AF2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.517A pdb=" N VAL K 12 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TRP K 35A" --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG K 50 " --> pdb=" O TRP K 35A" (cutoff:3.500A) removed outlier: 6.443A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.517A pdb=" N VAL K 12 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS K 92 " --> pdb=" O TRP K 103 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TRP K 103 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG K 94 " --> pdb=" O ASP K 101 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY K 96 " --> pdb=" O SER K 100F" (cutoff:3.500A) removed outlier: 8.082A pdb=" N SER K 100F" --> pdb=" O GLY K 96 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ARG K 98 " --> pdb=" O VAL K 100D" (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL K 100D" --> pdb=" O ARG K 98 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 120 through 124 removed outlier: 6.110A pdb=" N TYR K 176 " --> pdb=" O ASP K 144 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 120 through 124 removed outlier: 6.110A pdb=" N TYR K 176 " --> pdb=" O ASP K 144 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 151 through 154 Processing sheet with id=AF8, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AF9, first strand: chain 'J' and resid 11 through 13 removed outlier: 3.583A pdb=" N GLU J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 114 through 118 removed outlier: 5.255A pdb=" N SER J 131 " --> pdb=" O LEU J 181 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU J 181 " --> pdb=" O SER J 131 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL J 133 " --> pdb=" O LEU J 179 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU J 179 " --> pdb=" O VAL J 133 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU J 135 " --> pdb=" O SER J 177 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N SER J 177 " --> pdb=" O LEU J 135 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASN J 137 " --> pdb=" O LEU J 175 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU J 175 " --> pdb=" O ASN J 137 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 153 through 154 Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG4, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.581A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.254A pdb=" N SER L 131 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU L 181 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL L 133 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU L 179 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 153 through 154 966 hydrogen bonds defined for protein. 2493 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: 9.52 Time building geometry restraints manager: 9.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 3597 1.29 - 1.43: 5799 1.43 - 1.56: 12465 1.56 - 1.70: 0 1.70 - 1.83: 129 Bond restraints: 21990 Sorted by residual: bond pdb=" CA SER G 100F" pdb=" CB SER G 100F" ideal model delta sigma weight residual 1.526 1.437 0.088 1.25e-02 6.40e+03 5.00e+01 bond pdb=" CA SER I 100F" pdb=" CB SER I 100F" ideal model delta sigma weight residual 1.526 1.438 0.088 1.25e-02 6.40e+03 4.94e+01 bond pdb=" CA SER K 100F" pdb=" CB SER K 100F" ideal model delta sigma weight residual 1.526 1.438 0.087 1.25e-02 6.40e+03 4.87e+01 bond pdb=" C VAL I 99 " pdb=" O VAL I 99 " ideaFit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.7154 (mtm) cc_final: 0.6860 (mtm) REVERT: A 293 MET cc_start: 0.8890 (mmt) cc_final: 0.8410 (mmt) REVERT: B 446 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7875 (t0) REVERT: D 395 THR cc_start: 0.7184 (t) cc_final: 0.6845 (p) REVERT: D 446 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7701 (t0) REVERT: E 293 MET cc_start: 0.8898 (mmt) cc_final: 0.8471 (mmt) REVERT: F 497 SER cc_start: 0.7624 (OUTLIER) cc_final: 0.7346 (t) REVERT: G 54 ARG cc_start: 0.7495 (ptt90) cc_final: 0.6847 (ptm-80) REVERT: G 209 LYS cc_start: 0.7865 (tppt) cc_final: 0.7492 (mmtp) REVERT: H 36 TYR cc_start: 0.8616 (m-80) cc_final: 0.8307 (m-10) REVERT: H 106 ILE cc_start: 0.7812 (mm) cc_final: 0.7336 (mm) REVERT: H 116 PHE cc_start: 0.7647 (m-80) cc_final: 0.7274 (m-10) REVERT: H 135 LEU cc_start: 0.9005 (mt) cc_final: 0.8689 (mp) REVERT: H 171 SER cc_start: 0.8817 (OUTLIER) cc_final: 0.8552 (p) REVERT: H 188 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8245 (mttm) REVERT: H 189 HIS cc_start: 0.8646 (m90) cc_final: 0.8133 (m-70) REVERT: I 154 TRP cc_start: 0.7978 (m100) cc_final: 0.6276 (m100) REVERT: I 179 SER cc_start: 0.7097 (OUTLIER) cc_final: 0.6835 (p) REVERT: I 209 LYS cc_start: 0.8310 (tppt) cc_final: 0.7863 (mmtp) REVERT: K 122 PHE cc_start: 0.7540 (m-10) cc_final: 0.6975 (m-10) REVERT: K 154 TRP cc_start: 0.7956 (m100) cc_final: 0.7524 (m100) REVERT: K 176 TYR cc_start: 0.8797 (m-10) cc_final: 0.8266 (m-80) REVERT: K 179 SER cc_start: 0.6844 (OUTLIER) cc_final: 0.6635 (p) REVERT: K 209 LYS cc_start: 0.8564 (tppt) cc_final: 0.8273 (mmtp) REVERT: J 70 ASP cc_start: 0.7056 (m-30) cc_final: 0.6541 (m-30) REVERT: J 106 ILE cc_start: 0.7657 (mm) cc_final: 0.7088 (mm) REVERT: J 189 HIS cc_start: 0.8513 (m90) cc_final: 0.8188 (m90) REVERT: J 190 LYS cc_start: 0.8041 (tptt) cc_final: 0.7405 (tppt) REVERT: J 210 ASN cc_start: 0.8568 (m-40) cc_final: 0.8207 (t0) REVERT: L 106 ILE cc_start: 0.7788 (mm) cc_final: 0.7312 (mm) REVERT: L 190 LYS cc_start: 0.8194 (tptt) cc_final: 0.7751 (tppt) outliers start: 120 outliers final: 27 residues processed: 499 average time/residue: 0.3669 time to fit residues: 266.3074 Evaluate side-chains 261 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 227 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 446 ASP Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 458 LEU Chi-restraints excluded: chain F residue 497 SER Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 188 LYS Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 171 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 20.0000 chunk 204 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 211 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 128 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 245 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 ASN A 119 GLN A 183 HIS C 4 GLN ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 119 GLN ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 ASN E 119 GLN G 6 GLN G 155 ASN G 192 GLN G 204 ASN H 27 GLN H 55 GLN H 124 GLN ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 192 GLN I 197 ASN I 204 ASN K 6 GLN K 155 ASN K 204 ASN J 27 GLN J 38 GLN J 55 GLN J 124 GLN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 158 ASN J 199 GLN L 27 GLN L 38 GLN L 55 GLN L 147 GLN L 158 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21990 Z= 0.215 Angle : 0.635 7.474 29862 Z= 0.339 Chirality : 0.045 0.144 3312 Planarity : 0.005 0.076 3855 Dihedral : 6.088 44.908 3063 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.57 % Allowed : 11.83 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.16), residues: 2724 helix: 1.28 (0.25), residues: 402 sheet: -0.26 (0.17), residues: 870 loop : -1.48 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 148 HIS 0.010 0.002 HIS L 198 PHE 0.026 0.002 PHE I 122 TYR 0.029 0.001 TYR J 140 ARG 0.007 0.001 ARG G 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 278 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8817 (mmt) cc_final: 0.8321 (mmt) REVERT: B 437 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7881 (mm-30) REVERT: E 286 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7708 (ptp) REVERT: E 293 MET cc_start: 0.8898 (mmt) cc_final: 0.8463 (mmt) REVERT: F 437 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7739 (mm-30) REVERT: G 144 ASP cc_start: 0.6977 (t0) cc_final: 0.6663 (t0) REVERT: G 154 TRP cc_start: 0.7905 (m100) cc_final: 0.6797 (m100) REVERT: G 194 TYR cc_start: 0.6366 (m-80) cc_final: 0.6158 (m-80) REVERT: G 195 ILE cc_start: 0.6473 (tp) cc_final: 0.6032 (tp) REVERT: G 209 LYS cc_start: 0.8112 (tppt) cc_final: 0.7773 (mmtp) REVERT: H 24 ARG cc_start: 0.8073 (ttm110) cc_final: 0.7865 (ttm110) REVERT: H 36 TYR cc_start: 0.8869 (m-80) cc_final: 0.8587 (m-10) REVERT: H 118 PHE cc_start: 0.7365 (m-80) cc_final: 0.7070 (m-80) REVERT: H 138 ASN cc_start: 0.8287 (m-40) cc_final: 0.7669 (t0) REVERT: H 142 ARG cc_start: 0.8838 (ttt-90) cc_final: 0.8239 (mmm-85) REVERT: H 190 LYS cc_start: 0.7989 (tptt) cc_final: 0.7465 (tppt) REVERT: I 209 LYS cc_start: 0.8145 (tppt) cc_final: 0.7835 (mmmm) REVERT: K 144 ASP cc_start: 0.7080 (t0) cc_final: 0.6833 (t0) REVERT: K 166 PHE cc_start: 0.7582 (m-10) cc_final: 0.7159 (m-10) REVERT: J 142 ARG cc_start: 0.8682 (tpp80) cc_final: 0.8095 (mmm-85) REVERT: J 189 HIS cc_start: 0.8268 (m90) cc_final: 0.7983 (m90) REVERT: J 190 LYS cc_start: 0.8163 (tptt) cc_final: 0.7655 (tppt) REVERT: L 142 ARG cc_start: 0.8697 (tpp80) cc_final: 0.8108 (mmm160) REVERT: L 190 LYS cc_start: 0.8090 (tptt) cc_final: 0.7848 (tppt) outliers start: 62 outliers final: 29 residues processed: 327 average time/residue: 0.3472 time to fit residues: 171.8612 Evaluate side-chains 242 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 212 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 115 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 166 optimal weight: 0.0000 chunk 67 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 chunk 265 optimal weight: 0.6980 chunk 218 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 ASN ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 HIS ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100EASN G 197 ASN H 38 GLN H 124 GLN H 147 GLN I 197 ASN K 6 GLN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21990 Z= 0.272 Angle : 0.617 8.396 29862 Z= 0.327 Chirality : 0.045 0.164 3312 Planarity : 0.005 0.071 3855 Dihedral : 5.247 39.173 3015 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.49 % Allowed : 14.82 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.16), residues: 2724 helix: 1.65 (0.25), residues: 402 sheet: 0.07 (0.18), residues: 870 loop : -1.23 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 154 HIS 0.007 0.001 HIS A 32 PHE 0.020 0.002 PHE H 139 TYR 0.013 0.001 TYR J 140 ARG 0.004 0.000 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 234 time to evaluate : 2.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8847 (mmt) cc_final: 0.8389 (mmt) REVERT: E 293 MET cc_start: 0.8901 (mmt) cc_final: 0.8551 (mmt) REVERT: G 144 ASP cc_start: 0.6862 (t0) cc_final: 0.6582 (t0) REVERT: G 154 TRP cc_start: 0.7935 (m100) cc_final: 0.6807 (m100) REVERT: G 194 TYR cc_start: 0.6661 (m-80) cc_final: 0.6407 (m-80) REVERT: G 195 ILE cc_start: 0.6441 (tp) cc_final: 0.6094 (tp) REVERT: G 209 LYS cc_start: 0.8185 (tppt) cc_final: 0.7832 (mmtp) REVERT: H 118 PHE cc_start: 0.7532 (m-80) cc_final: 0.6701 (m-10) REVERT: H 138 ASN cc_start: 0.8235 (m-40) cc_final: 0.7574 (t0) REVERT: H 187 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8377 (mm-30) REVERT: H 192 TYR cc_start: 0.8562 (m-10) cc_final: 0.8234 (m-10) REVERT: I 13 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8189 (mtmm) REVERT: I 209 LYS cc_start: 0.8042 (tppt) cc_final: 0.7712 (mmmm) REVERT: K 105 GLN cc_start: 0.8550 (pp30) cc_final: 0.7758 (pp30) REVERT: K 144 ASP cc_start: 0.7114 (t0) cc_final: 0.6818 (t0) REVERT: K 166 PHE cc_start: 0.7770 (m-80) cc_final: 0.7377 (m-10) REVERT: J 142 ARG cc_start: 0.8627 (tpp80) cc_final: 0.7768 (mmm-85) REVERT: J 143 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7467 (pm20) REVERT: J 190 LYS cc_start: 0.7968 (tptt) cc_final: 0.7521 (tppt) REVERT: L 108 ARG cc_start: 0.8265 (ptm160) cc_final: 0.7992 (ptm160) REVERT: L 142 ARG cc_start: 0.8828 (tpp80) cc_final: 0.8480 (tpp80) outliers start: 60 outliers final: 34 residues processed: 280 average time/residue: 0.3637 time to fit residues: 153.5721 Evaluate side-chains 244 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 208 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 209 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 198 VAL Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 115 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 chunk 164 optimal weight: 20.0000 chunk 246 optimal weight: 2.9990 chunk 260 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 HIS ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN G 171 GLN G 197 ASN I 197 ASN J 147 GLN J 189 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21990 Z= 0.356 Angle : 0.637 8.851 29862 Z= 0.336 Chirality : 0.045 0.156 3312 Planarity : 0.005 0.074 3855 Dihedral : 5.222 40.174 3009 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.24 % Allowed : 15.40 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.16), residues: 2724 helix: 1.61 (0.24), residues: 408 sheet: 0.22 (0.18), residues: 864 loop : -1.19 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 148 HIS 0.007 0.002 HIS C 184 PHE 0.018 0.002 PHE G 78 TYR 0.021 0.001 TYR A 141 ARG 0.005 0.001 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 231 time to evaluate : 2.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8800 (mmt) cc_final: 0.8396 (mmt) REVERT: C 293 MET cc_start: 0.8796 (mmt) cc_final: 0.8570 (mmt) REVERT: E 293 MET cc_start: 0.8838 (mmt) cc_final: 0.8509 (mmt) REVERT: F 377 LYS cc_start: 0.8673 (ttmt) cc_final: 0.8167 (ttmm) REVERT: G 144 ASP cc_start: 0.7076 (t0) cc_final: 0.6760 (t0) REVERT: G 154 TRP cc_start: 0.7944 (m100) cc_final: 0.6815 (m100) REVERT: G 171 GLN cc_start: 0.7968 (tm130) cc_final: 0.7123 (mt0) REVERT: G 195 ILE cc_start: 0.6605 (tp) cc_final: 0.6284 (tp) REVERT: G 209 LYS cc_start: 0.8160 (tppt) cc_final: 0.7850 (mmtp) REVERT: G 212 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6490 (mp0) REVERT: H 118 PHE cc_start: 0.7314 (m-80) cc_final: 0.6805 (m-10) REVERT: H 138 ASN cc_start: 0.8124 (m-40) cc_final: 0.7484 (t0) REVERT: H 161 GLU cc_start: 0.8909 (pp20) cc_final: 0.8505 (pp20) REVERT: H 189 HIS cc_start: 0.7658 (m-70) cc_final: 0.7380 (m-70) REVERT: H 192 TYR cc_start: 0.8418 (m-10) cc_final: 0.8124 (m-10) REVERT: I 13 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8329 (mtmm) REVERT: I 105 GLN cc_start: 0.8608 (pp30) cc_final: 0.7935 (pp30) REVERT: K 105 GLN cc_start: 0.8567 (pp30) cc_final: 0.7890 (pp30) REVERT: K 154 TRP cc_start: 0.8154 (m100) cc_final: 0.7119 (m100) REVERT: K 166 PHE cc_start: 0.7884 (m-80) cc_final: 0.7543 (m-10) REVERT: K 176 TYR cc_start: 0.8516 (m-80) cc_final: 0.8234 (m-80) REVERT: K 209 LYS cc_start: 0.8285 (mmtp) cc_final: 0.8071 (mmtp) REVERT: J 143 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7335 (pm20) REVERT: J 190 LYS cc_start: 0.8091 (tptt) cc_final: 0.7745 (tppt) REVERT: L 108 ARG cc_start: 0.8456 (ptm160) cc_final: 0.8188 (ptm160) outliers start: 78 outliers final: 48 residues processed: 293 average time/residue: 0.3368 time to fit residues: 151.9238 Evaluate side-chains 257 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 206 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 209 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 140 CYS Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 171 SER Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 201 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 217 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 222 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 234 optimal weight: 0.0050 chunk 65 optimal weight: 1.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 HIS ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21990 Z= 0.270 Angle : 0.598 8.633 29862 Z= 0.314 Chirality : 0.044 0.149 3312 Planarity : 0.004 0.073 3855 Dihedral : 5.036 39.414 3009 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.49 % Allowed : 15.57 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.16), residues: 2724 helix: 1.84 (0.24), residues: 408 sheet: 0.31 (0.18), residues: 864 loop : -1.13 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 154 HIS 0.006 0.001 HIS E 299 PHE 0.018 0.002 PHE L 139 TYR 0.020 0.001 TYR E 141 ARG 0.005 0.000 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 234 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8786 (mmt) cc_final: 0.8358 (mmt) REVERT: A 305 GLU cc_start: 0.6718 (tm-30) cc_final: 0.6445 (pp20) REVERT: C 293 MET cc_start: 0.8760 (mmt) cc_final: 0.8515 (mmt) REVERT: E 57 ARG cc_start: 0.7556 (ttm110) cc_final: 0.7349 (ttm110) REVERT: E 293 MET cc_start: 0.8843 (mmt) cc_final: 0.8506 (mmt) REVERT: G 143 LYS cc_start: 0.7863 (tppt) cc_final: 0.7581 (mmmt) REVERT: G 144 ASP cc_start: 0.6968 (t0) cc_final: 0.6648 (t0) REVERT: G 145 TYR cc_start: 0.6583 (p90) cc_final: 0.6268 (p90) REVERT: G 192 GLN cc_start: 0.5115 (OUTLIER) cc_final: 0.4553 (mm110) REVERT: G 209 LYS cc_start: 0.8078 (tppt) cc_final: 0.7866 (mmtp) REVERT: H 138 ASN cc_start: 0.8161 (m-40) cc_final: 0.7503 (t0) REVERT: H 161 GLU cc_start: 0.8960 (pp20) cc_final: 0.8523 (pp20) REVERT: H 189 HIS cc_start: 0.7610 (m-70) cc_final: 0.7228 (m-70) REVERT: H 192 TYR cc_start: 0.8395 (m-10) cc_final: 0.7988 (m-10) REVERT: I 13 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8337 (mtmm) REVERT: I 105 GLN cc_start: 0.8550 (pp30) cc_final: 0.7895 (pp30) REVERT: I 176 TYR cc_start: 0.8413 (m-80) cc_final: 0.8093 (m-80) REVERT: K 105 GLN cc_start: 0.8523 (pp30) cc_final: 0.7855 (pp30) REVERT: K 154 TRP cc_start: 0.8139 (m100) cc_final: 0.6626 (m100) REVERT: K 209 LYS cc_start: 0.8333 (mmtp) cc_final: 0.8106 (mmtp) REVERT: J 143 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7272 (pm20) REVERT: J 189 HIS cc_start: 0.7800 (m90) cc_final: 0.7227 (m90) REVERT: J 190 LYS cc_start: 0.8175 (tptt) cc_final: 0.7844 (tppt) REVERT: L 108 ARG cc_start: 0.8450 (ptm160) cc_final: 0.8137 (ptm160) outliers start: 84 outliers final: 59 residues processed: 310 average time/residue: 0.3273 time to fit residues: 156.6641 Evaluate side-chains 271 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 209 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 278 CYS Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 192 GLN Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 209 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 140 CYS Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 198 VAL Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 201 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 87 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 216 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 86 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 HIS ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 GLN I 100EASN I 197 ASN K 192 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21990 Z= 0.222 Angle : 0.579 8.116 29862 Z= 0.304 Chirality : 0.044 0.145 3312 Planarity : 0.004 0.070 3855 Dihedral : 4.903 38.828 3009 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.24 % Allowed : 16.19 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.16), residues: 2724 helix: 2.02 (0.25), residues: 408 sheet: 0.41 (0.18), residues: 864 loop : -1.05 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 154 HIS 0.008 0.001 HIS J 198 PHE 0.019 0.002 PHE L 139 TYR 0.012 0.001 TYR E 141 ARG 0.006 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 228 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 293 MET cc_start: 0.8745 (mmt) cc_final: 0.8491 (mmt) REVERT: E 293 MET cc_start: 0.8852 (mmt) cc_final: 0.8488 (mmt) REVERT: G 143 LYS cc_start: 0.7866 (tppt) cc_final: 0.7629 (mmmt) REVERT: G 144 ASP cc_start: 0.7116 (t0) cc_final: 0.6841 (t0) REVERT: G 154 TRP cc_start: 0.7948 (m100) cc_final: 0.7334 (m100) REVERT: G 209 LYS cc_start: 0.8056 (tppt) cc_final: 0.7841 (mmtp) REVERT: H 138 ASN cc_start: 0.8069 (m-40) cc_final: 0.7468 (t0) REVERT: H 189 HIS cc_start: 0.7737 (m-70) cc_final: 0.7387 (m-70) REVERT: H 192 TYR cc_start: 0.8257 (m-10) cc_final: 0.7915 (m-10) REVERT: I 13 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8308 (mtmm) REVERT: I 100 ASN cc_start: 0.8307 (m-40) cc_final: 0.8101 (m-40) REVERT: I 105 GLN cc_start: 0.8505 (pp30) cc_final: 0.7820 (pp30) REVERT: I 192 GLN cc_start: 0.4557 (OUTLIER) cc_final: 0.3965 (mm110) REVERT: K 105 GLN cc_start: 0.8457 (pp30) cc_final: 0.7796 (pp30) REVERT: K 209 LYS cc_start: 0.8336 (mmtp) cc_final: 0.8048 (mmtp) REVERT: J 105 GLU cc_start: 0.8235 (tp30) cc_final: 0.7582 (tp30) REVERT: J 143 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7335 (pm20) REVERT: J 161 GLU cc_start: 0.8962 (pp20) cc_final: 0.8390 (pp20) REVERT: J 189 HIS cc_start: 0.7829 (m90) cc_final: 0.7245 (m90) REVERT: J 190 LYS cc_start: 0.8250 (tptt) cc_final: 0.7960 (tppt) REVERT: L 108 ARG cc_start: 0.8446 (ptm160) cc_final: 0.8182 (ptm160) REVERT: L 181 LEU cc_start: 0.7254 (pt) cc_final: 0.6825 (mt) outliers start: 78 outliers final: 58 residues processed: 297 average time/residue: 0.3319 time to fit residues: 152.6664 Evaluate side-chains 265 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 204 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 278 CYS Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 482 CYS Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 209 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 140 CYS Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 192 GLN Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain K residue 70 ASN Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 198 VAL Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 201 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 251 optimal weight: 0.0070 chunk 29 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 219 optimal weight: 0.5980 chunk 145 optimal weight: 0.1980 chunk 260 optimal weight: 3.9990 chunk 162 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 ASN ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 HIS E 32 HIS ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 476 HIS ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21990 Z= 0.157 Angle : 0.561 8.187 29862 Z= 0.293 Chirality : 0.043 0.145 3312 Planarity : 0.004 0.069 3855 Dihedral : 4.671 37.760 3009 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.49 % Allowed : 17.19 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2724 helix: 2.18 (0.25), residues: 408 sheet: 0.47 (0.18), residues: 870 loop : -0.89 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 154 HIS 0.009 0.001 HIS J 198 PHE 0.026 0.001 PHE H 118 TYR 0.010 0.001 TYR L 36 ARG 0.007 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 242 time to evaluate : 2.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8630 (t80) cc_final: 0.8154 (t80) REVERT: E 293 MET cc_start: 0.8832 (mmt) cc_final: 0.8501 (mmt) REVERT: G 145 TYR cc_start: 0.6492 (p90) cc_final: 0.6159 (p90) REVERT: G 154 TRP cc_start: 0.7995 (m100) cc_final: 0.7451 (m100) REVERT: H 138 ASN cc_start: 0.8008 (m-40) cc_final: 0.7392 (t0) REVERT: H 161 GLU cc_start: 0.9000 (pp20) cc_final: 0.8557 (pp20) REVERT: H 167 ASP cc_start: 0.8316 (t70) cc_final: 0.7967 (t0) REVERT: H 189 HIS cc_start: 0.7585 (m-70) cc_final: 0.7118 (m-70) REVERT: H 190 LYS cc_start: 0.8199 (tptt) cc_final: 0.7901 (tppt) REVERT: H 192 TYR cc_start: 0.8199 (m-10) cc_final: 0.7863 (m-10) REVERT: I 13 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8322 (mtmm) REVERT: I 105 GLN cc_start: 0.8413 (pp30) cc_final: 0.7707 (pp30) REVERT: I 145 TYR cc_start: 0.6981 (p90) cc_final: 0.6490 (p90) REVERT: I 154 TRP cc_start: 0.7798 (m100) cc_final: 0.7453 (m100) REVERT: I 192 GLN cc_start: 0.5453 (OUTLIER) cc_final: 0.5152 (mm110) REVERT: K 100 ASN cc_start: 0.8338 (m-40) cc_final: 0.8044 (m-40) REVERT: K 105 GLN cc_start: 0.8399 (pp30) cc_final: 0.7661 (pp30) REVERT: K 209 LYS cc_start: 0.8238 (mmtp) cc_final: 0.8034 (mmtp) REVERT: J 105 GLU cc_start: 0.8137 (tp30) cc_final: 0.7493 (tp30) REVERT: J 143 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7314 (pm20) REVERT: J 161 GLU cc_start: 0.9028 (pp20) cc_final: 0.8474 (pp20) REVERT: J 167 ASP cc_start: 0.8327 (t70) cc_final: 0.8068 (t0) REVERT: L 105 GLU cc_start: 0.8058 (tp30) cc_final: 0.7602 (tp30) REVERT: L 106 ILE cc_start: 0.8058 (mt) cc_final: 0.7740 (mm) REVERT: L 108 ARG cc_start: 0.8306 (ptm160) cc_final: 0.8069 (ptm160) REVERT: L 167 ASP cc_start: 0.8388 (t70) cc_final: 0.8124 (t0) REVERT: L 170 ASP cc_start: 0.7070 (t0) cc_final: 0.6787 (t0) outliers start: 60 outliers final: 51 residues processed: 295 average time/residue: 0.3414 time to fit residues: 153.5071 Evaluate side-chains 265 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 211 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 278 CYS Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 482 CYS Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 209 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 70 ASN Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 140 CYS Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 192 GLN Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 198 VAL Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 201 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 78 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 204 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21990 Z= 0.221 Angle : 0.588 8.685 29862 Z= 0.307 Chirality : 0.044 0.147 3312 Planarity : 0.004 0.065 3855 Dihedral : 4.722 38.073 3009 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.11 % Allowed : 17.06 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2724 helix: 2.16 (0.25), residues: 408 sheet: 0.46 (0.18), residues: 870 loop : -0.86 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 426 HIS 0.010 0.001 HIS J 198 PHE 0.019 0.002 PHE L 139 TYR 0.018 0.001 TYR F 496 ARG 0.006 0.000 ARG J 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 221 time to evaluate : 2.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 293 MET cc_start: 0.8851 (mmt) cc_final: 0.8488 (mmt) REVERT: F 377 LYS cc_start: 0.8648 (ttmt) cc_final: 0.8155 (ttmm) REVERT: G 13 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8311 (mmmm) REVERT: G 145 TYR cc_start: 0.6576 (p90) cc_final: 0.6285 (p90) REVERT: G 154 TRP cc_start: 0.7988 (m100) cc_final: 0.7782 (m100) REVERT: G 209 LYS cc_start: 0.7974 (mmtp) cc_final: 0.7632 (tptp) REVERT: H 105 GLU cc_start: 0.8373 (tp30) cc_final: 0.8169 (tp30) REVERT: H 138 ASN cc_start: 0.8040 (m-40) cc_final: 0.7464 (t0) REVERT: H 142 ARG cc_start: 0.8646 (ttt-90) cc_final: 0.8118 (mtt-85) REVERT: H 148 TRP cc_start: 0.5911 (m100) cc_final: 0.5689 (m100) REVERT: H 161 GLU cc_start: 0.9034 (pp20) cc_final: 0.8572 (pp20) REVERT: H 167 ASP cc_start: 0.8348 (t70) cc_final: 0.7975 (t0) REVERT: H 189 HIS cc_start: 0.7709 (m-70) cc_final: 0.7321 (m-70) REVERT: H 190 LYS cc_start: 0.8215 (tptt) cc_final: 0.7906 (tppt) REVERT: H 192 TYR cc_start: 0.8230 (m-10) cc_final: 0.8014 (m-10) REVERT: I 13 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8294 (mtmm) REVERT: I 105 GLN cc_start: 0.8443 (pp30) cc_final: 0.7703 (pp30) REVERT: I 145 TYR cc_start: 0.6954 (p90) cc_final: 0.6591 (p90) REVERT: I 192 GLN cc_start: 0.5112 (OUTLIER) cc_final: 0.4818 (mm-40) REVERT: K 105 GLN cc_start: 0.8413 (pp30) cc_final: 0.7777 (pp30) REVERT: K 154 TRP cc_start: 0.8155 (m100) cc_final: 0.7491 (m100) REVERT: K 209 LYS cc_start: 0.8063 (mmtp) cc_final: 0.7856 (mmtp) REVERT: J 105 GLU cc_start: 0.8173 (tp30) cc_final: 0.7494 (tp30) REVERT: J 143 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7254 (pm20) REVERT: J 161 GLU cc_start: 0.9029 (pp20) cc_final: 0.8463 (pp20) REVERT: J 167 ASP cc_start: 0.8308 (t70) cc_final: 0.8052 (t0) REVERT: J 190 LYS cc_start: 0.8156 (tptt) cc_final: 0.7837 (tppt) REVERT: L 108 ARG cc_start: 0.8335 (ptm160) cc_final: 0.8109 (ptm160) REVERT: L 138 ASN cc_start: 0.8009 (m110) cc_final: 0.7176 (t0) REVERT: L 167 ASP cc_start: 0.8498 (t70) cc_final: 0.8211 (t0) outliers start: 75 outliers final: 65 residues processed: 286 average time/residue: 0.3521 time to fit residues: 155.1598 Evaluate side-chains 274 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 205 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 478 CYS Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 278 CYS Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 482 CYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 209 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 140 CYS Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 192 GLN Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 198 VAL Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 201 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 5.9990 chunk 249 optimal weight: 5.9990 chunk 227 optimal weight: 8.9990 chunk 242 optimal weight: 20.0000 chunk 145 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 190 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 229 optimal weight: 9.9990 chunk 241 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21990 Z= 0.329 Angle : 0.636 8.785 29862 Z= 0.333 Chirality : 0.045 0.147 3312 Planarity : 0.004 0.067 3855 Dihedral : 5.048 39.969 3009 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.20 % Allowed : 17.02 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.16), residues: 2724 helix: 2.06 (0.24), residues: 402 sheet: 0.41 (0.18), residues: 894 loop : -0.89 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 426 HIS 0.011 0.001 HIS J 198 PHE 0.019 0.002 PHE L 118 TYR 0.014 0.001 TYR L 36 ARG 0.006 0.001 ARG J 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 209 time to evaluate : 2.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 293 MET cc_start: 0.8846 (mmt) cc_final: 0.8513 (mmt) REVERT: F 377 LYS cc_start: 0.8650 (ttmt) cc_final: 0.8140 (ttmm) REVERT: G 13 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8262 (mtmm) REVERT: H 105 GLU cc_start: 0.8418 (tp30) cc_final: 0.8158 (tp30) REVERT: H 138 ASN cc_start: 0.8033 (m-40) cc_final: 0.7459 (t0) REVERT: H 142 ARG cc_start: 0.8674 (ttt-90) cc_final: 0.8104 (mtt-85) REVERT: H 161 GLU cc_start: 0.9015 (pp20) cc_final: 0.8526 (pp20) REVERT: H 189 HIS cc_start: 0.7718 (m-70) cc_final: 0.7307 (m-70) REVERT: H 192 TYR cc_start: 0.8229 (m-10) cc_final: 0.7991 (m-10) REVERT: I 13 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8361 (mtmm) REVERT: I 105 GLN cc_start: 0.8528 (pp30) cc_final: 0.7756 (pp30) REVERT: I 145 TYR cc_start: 0.6814 (p90) cc_final: 0.6602 (p90) REVERT: I 154 TRP cc_start: 0.7782 (m100) cc_final: 0.7521 (m100) REVERT: I 192 GLN cc_start: 0.5093 (OUTLIER) cc_final: 0.4873 (mm110) REVERT: K 209 LYS cc_start: 0.8038 (mmtp) cc_final: 0.7832 (mmtp) REVERT: J 105 GLU cc_start: 0.8109 (tp30) cc_final: 0.7556 (tp30) REVERT: J 143 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7223 (pm20) REVERT: J 161 GLU cc_start: 0.8974 (pp20) cc_final: 0.8383 (pp20) REVERT: J 167 ASP cc_start: 0.8367 (t70) cc_final: 0.8102 (t0) REVERT: J 189 HIS cc_start: 0.7807 (m90) cc_final: 0.7556 (m-70) REVERT: L 108 ARG cc_start: 0.8454 (ptm160) cc_final: 0.8236 (ptm160) REVERT: L 138 ASN cc_start: 0.7962 (m110) cc_final: 0.7132 (t0) REVERT: L 161 GLU cc_start: 0.8806 (pp20) cc_final: 0.8400 (pp20) REVERT: L 167 ASP cc_start: 0.8286 (t70) cc_final: 0.8021 (t0) outliers start: 77 outliers final: 65 residues processed: 276 average time/residue: 0.3345 time to fit residues: 142.1145 Evaluate side-chains 271 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 202 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 478 CYS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 278 CYS Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 482 CYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 209 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 140 CYS Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 192 GLN Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain K residue 70 ASN Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 198 VAL Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 6.9990 chunk 256 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 121 optimal weight: 0.0370 chunk 178 optimal weight: 0.9990 chunk 268 optimal weight: 9.9990 chunk 247 optimal weight: 0.9990 chunk 214 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 165 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN K 171 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21990 Z= 0.190 Angle : 0.592 8.871 29862 Z= 0.310 Chirality : 0.044 0.147 3312 Planarity : 0.004 0.068 3855 Dihedral : 4.805 39.065 3009 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.57 % Allowed : 17.77 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2724 helix: 2.17 (0.25), residues: 405 sheet: 0.45 (0.18), residues: 870 loop : -0.85 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 148 HIS 0.011 0.001 HIS J 198 PHE 0.018 0.001 PHE L 139 TYR 0.013 0.001 TYR C 141 ARG 0.009 0.000 ARG L 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 213 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 293 MET cc_start: 0.8827 (mmt) cc_final: 0.8483 (mmt) REVERT: G 13 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8252 (mtmm) REVERT: H 138 ASN cc_start: 0.7973 (m-40) cc_final: 0.7406 (t0) REVERT: H 142 ARG cc_start: 0.8710 (ttt-90) cc_final: 0.8141 (mtt-85) REVERT: H 161 GLU cc_start: 0.8976 (pp20) cc_final: 0.8479 (pp20) REVERT: H 167 ASP cc_start: 0.8384 (t70) cc_final: 0.7984 (t0) REVERT: H 189 HIS cc_start: 0.7458 (m-70) cc_final: 0.6953 (m-70) REVERT: I 13 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8322 (mtmm) REVERT: I 105 GLN cc_start: 0.8462 (pp30) cc_final: 0.7711 (pp30) REVERT: I 145 TYR cc_start: 0.6978 (p90) cc_final: 0.6626 (p90) REVERT: I 154 TRP cc_start: 0.7739 (m100) cc_final: 0.7538 (m100) REVERT: I 192 GLN cc_start: 0.5038 (OUTLIER) cc_final: 0.4706 (mm-40) REVERT: K 100 ASN cc_start: 0.8329 (m-40) cc_final: 0.7990 (m-40) REVERT: K 105 GLN cc_start: 0.8433 (pp30) cc_final: 0.7799 (pp30) REVERT: K 154 TRP cc_start: 0.8147 (m100) cc_final: 0.7675 (m100) REVERT: K 209 LYS cc_start: 0.8009 (mmtp) cc_final: 0.7795 (mmtp) REVERT: J 143 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7179 (pm20) REVERT: J 161 GLU cc_start: 0.8992 (pp20) cc_final: 0.8416 (pp20) REVERT: J 167 ASP cc_start: 0.8375 (t70) cc_final: 0.8137 (t0) REVERT: J 189 HIS cc_start: 0.7813 (m90) cc_final: 0.7588 (m-70) REVERT: L 108 ARG cc_start: 0.8378 (ptm160) cc_final: 0.8134 (ptm160) REVERT: L 138 ASN cc_start: 0.7723 (m110) cc_final: 0.6907 (t0) REVERT: L 161 GLU cc_start: 0.8841 (pp20) cc_final: 0.8459 (pp20) REVERT: L 167 ASP cc_start: 0.8438 (t70) cc_final: 0.8158 (t0) outliers start: 62 outliers final: 56 residues processed: 268 average time/residue: 0.3389 time to fit residues: 139.2558 Evaluate side-chains 260 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 200 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 478 CYS Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 278 CYS Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 482 CYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 209 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 140 CYS Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 192 GLN Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 198 VAL Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 170 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 214 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 GLN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.099850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.071096 restraints weight = 51664.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.073520 restraints weight = 23608.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.075062 restraints weight = 14702.154| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21990 Z= 0.235 Angle : 0.602 8.437 29862 Z= 0.316 Chirality : 0.044 0.148 3312 Planarity : 0.004 0.066 3855 Dihedral : 4.833 38.603 3009 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.86 % Allowed : 17.43 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2724 helix: 2.21 (0.25), residues: 402 sheet: 0.41 (0.18), residues: 876 loop : -0.84 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 426 HIS 0.015 0.001 HIS J 198 PHE 0.019 0.002 PHE L 139 TYR 0.017 0.001 TYR F 496 ARG 0.007 0.000 ARG H 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4167.30 seconds wall clock time: 270 minutes 50.99 seconds (16250.99 seconds total)