Starting phenix.real_space_refine on Thu Jul 25 22:54:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vue_43529/07_2024/8vue_43529.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vue_43529/07_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_43529/07_2024/8vue_43529.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vue_43529/07_2024/8vue_43529.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vue_43529/07_2024/8vue_43529.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vue_43529/07_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-5388/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: 11.52, per 1000 atoms: 0.54 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: 10.73 Conformation dependent library (CDL) restraints added in 4.1 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: 3.62 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: 8.40 Time building geometry restraints manager: 11.37 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 " ideal model delta sigma weight residual 1.236 1.154 0.082 1.19e-02 7.06e+03 4.81e+01 bond pdb=" C VAL K 99 " pdb=" O VAL K 99 " ideal model delta sigma weight residual 1.236 1.154 0.082 1.19e-02 7.06e+03 4.76e+01 ... (remaining 21985 not shown) Histogram of bond angle deviations from ideal: 98.74 - 105.85: 534 105.85 - 112.95: 11920 112.95 - 120.05: 7317 120.05 - 127.15: 9788 127.15 - 134.25: 303 Bond angle restraints: 29862 Sorted by residual: angle pdb=" CA THR L 29 " pdb=" CB THR L 29 " pdb=" OG1 THR L 29 " ideal model delta sigma weight residual 109.60 99.60 10.00 1.50e+00 4.44e-01 4.44e+01 angle pdb=" C SER J 31 " pdb=" N TYR J 32 " pdb=" CA TYR J 32 " ideal model delta sigma weight residual 121.54 134.25 -12.71 1.91e+00 2.74e-01 4.43e+01 angle pdb=" C SER L 31 " pdb=" N TYR L 32 " pdb=" CA TYR L 32 " ideal model delta sigma weight residual 121.54 134.25 -12.71 1.91e+00 2.74e-01 4.43e+01 angle pdb=" CA THR J 29 " pdb=" CB THR J 29 " pdb=" OG1 THR J 29 " ideal model delta sigma weight residual 109.60 99.63 9.97 1.50e+00 4.44e-01 4.42e+01 angle pdb=" C SER H 31 " pdb=" N TYR H 32 " pdb=" CA TYR H 32 " ideal model delta sigma weight residual 121.54 134.22 -12.68 1.91e+00 2.74e-01 4.40e+01 ... (remaining 29857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 11603 18.05 - 36.09: 1285 36.09 - 54.14: 273 54.14 - 72.19: 69 72.19 - 90.24: 24 Dihedral angle restraints: 13254 sinusoidal: 5262 harmonic: 7992 Sorted by residual: dihedral pdb=" CB CYS E 46 " pdb=" SG CYS E 46 " pdb=" SG CYS E 278 " pdb=" CB CYS E 278 " ideal model delta sinusoidal sigma weight residual -86.00 -15.13 -70.87 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CB CYS C 46 " pdb=" SG CYS C 46 " pdb=" SG CYS C 278 " pdb=" CB CYS C 278 " ideal model delta sinusoidal sigma weight residual -86.00 -15.15 -70.85 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CB CYS A 46 " pdb=" SG CYS A 46 " pdb=" SG CYS A 278 " pdb=" CB CYS A 278 " ideal model delta sinusoidal sigma weight residual -86.00 -15.15 -70.85 1 1.00e+01 1.00e-02 6.45e+01 ... (remaining 13251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 3062 0.091 - 0.182: 223 0.182 - 0.273: 13 0.273 - 0.364: 5 0.364 - 0.455: 9 Chirality restraints: 3312 Sorted by residual: chirality pdb=" CA VAL I 100D" pdb=" N VAL I 100D" pdb=" C VAL I 100D" pdb=" CB VAL I 100D" both_signs ideal model delta sigma weight residual False 2.44 2.90 -0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CA VAL K 100D" pdb=" N VAL K 100D" pdb=" C VAL K 100D" pdb=" CB VAL K 100D" both_signs ideal model delta sigma weight residual False 2.44 2.90 -0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CA VAL G 100D" pdb=" N VAL G 100D" pdb=" C VAL G 100D" pdb=" CB VAL G 100D" both_signs ideal model delta sigma weight residual False 2.44 2.89 -0.45 2.00e-01 2.50e+01 5.13e+00 ... (remaining 3309 not shown) Planarity restraints: 3858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA I 95 " -0.055 2.00e-02 2.50e+03 1.04e-01 1.09e+02 pdb=" C ALA I 95 " 0.180 2.00e-02 2.50e+03 pdb=" O ALA I 95 " -0.067 2.00e-02 2.50e+03 pdb=" N GLY I 96 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA K 95 " 0.054 2.00e-02 2.50e+03 1.04e-01 1.08e+02 pdb=" C ALA K 95 " -0.180 2.00e-02 2.50e+03 pdb=" O ALA K 95 " 0.067 2.00e-02 2.50e+03 pdb=" N GLY K 96 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 95 " -0.054 2.00e-02 2.50e+03 1.04e-01 1.08e+02 pdb=" C ALA G 95 " 0.180 2.00e-02 2.50e+03 pdb=" O ALA G 95 " -0.067 2.00e-02 2.50e+03 pdb=" N GLY G 96 " -0.058 2.00e-02 2.50e+03 ... (remaining 3855 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 103 2.44 - 3.06: 14188 3.06 - 3.67: 31717 3.67 - 4.29: 48475 4.29 - 4.90: 81854 Nonbonded interactions: 176337 Sorted by model distance: nonbonded pdb=" CB ALA K 93 " pdb=" CD1 LEU K 100G" model vdw 1.828 3.880 nonbonded pdb=" CB ALA G 93 " pdb=" CD1 LEU G 100G" model vdw 1.828 3.880 nonbonded pdb=" CB ALA I 93 " pdb=" CD1 LEU I 100G" model vdw 1.830 3.880 nonbonded pdb=" ND2 ASN I 100E" pdb=" O SER J 91 " model vdw 1.936 2.520 nonbonded pdb=" ND2 ASN K 100E" pdb=" O SER L 91 " model vdw 2.004 2.520 ... (remaining 176332 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 63.760 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 21990 Z= 0.477 Angle : 0.941 12.709 29862 Z= 0.567 Chirality : 0.055 0.455 3312 Planarity : 0.006 0.104 3855 Dihedral : 15.990 90.236 8028 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.13 % Favored : 93.54 % Rotamer: Outliers : 4.98 % Allowed : 7.22 % Favored : 87.80 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.26 (0.14), residues: 2724 helix: -0.14 (0.24), residues: 384 sheet: -0.96 (0.16), residues: 849 loop : -2.26 (0.14), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 35A HIS 0.005 0.001 HIS E 12 PHE 0.017 0.002 PHE J 118 TYR 0.018 0.002 TYR B 358 ARG 0.004 0.001 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 1 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 532 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 412 time to evaluate : 2.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 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: 0.4000 time to fit residues: 291.5054 Evaluate side-chains 261 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 227 time to evaluate : 2.582 ------------------------------------------------------------------------------- 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: 8.9990 chunk 113 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 211 optimal weight: 0.9990 chunk 81 optimal weight: 0.0970 chunk 128 optimal weight: 0.6980 chunk 157 optimal weight: 3.9990 chunk 245 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 155 ASN G 192 GLN ** G 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN H 55 GLN H 124 GLN H 147 GLN I 192 GLN I 197 ASN ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 ASN ** K 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 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 55 GLN L 147 GLN L 158 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21990 Z= 0.199 Angle : 0.616 6.474 29862 Z= 0.329 Chirality : 0.044 0.145 3312 Planarity : 0.005 0.066 3855 Dihedral : 6.218 45.915 3063 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.74 % Allowed : 12.70 % Favored : 84.56 % 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: -0.97 (0.16), residues: 2724 helix: 1.24 (0.26), residues: 405 sheet: -0.30 (0.17), residues: 840 loop : -1.41 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 148 HIS 0.010 0.001 HIS J 198 PHE 0.024 0.002 PHE H 139 TYR 0.023 0.001 TYR J 140 ARG 0.007 0.001 ARG A 212 *********************** 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 327 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 261 time to evaluate : 2.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8872 (mmt) cc_final: 0.8430 (mmt) REVERT: E 293 MET cc_start: 0.8881 (mmt) cc_final: 0.8438 (mmt) REVERT: G 144 ASP cc_start: 0.6959 (t0) cc_final: 0.6654 (t0) REVERT: G 154 TRP cc_start: 0.7880 (m100) cc_final: 0.6820 (m100) REVERT: G 209 LYS cc_start: 0.8006 (tppt) cc_final: 0.7655 (mmtp) REVERT: H 105 GLU cc_start: 0.7815 (tp30) cc_final: 0.7419 (tp30) REVERT: H 118 PHE cc_start: 0.7468 (m-80) cc_final: 0.6918 (m-80) REVERT: H 138 ASN cc_start: 0.8330 (m-40) cc_final: 0.7729 (t0) REVERT: H 142 ARG cc_start: 0.8845 (ttt-90) cc_final: 0.8614 (mtp-110) REVERT: H 189 HIS cc_start: 0.8538 (m90) cc_final: 0.8294 (m-70) REVERT: I 209 LYS cc_start: 0.8135 (tppt) cc_final: 0.7811 (mmmm) REVERT: K 100 ASN cc_start: 0.8633 (OUTLIER) cc_final: 0.7735 (m-40) REVERT: K 144 ASP cc_start: 0.7098 (t0) cc_final: 0.6869 (t0) REVERT: K 154 TRP cc_start: 0.7903 (m100) cc_final: 0.6292 (m100) REVERT: K 166 PHE cc_start: 0.7633 (m-10) cc_final: 0.7279 (m-10) REVERT: K 176 TYR cc_start: 0.8658 (m-80) cc_final: 0.8297 (m-80) REVERT: K 179 SER cc_start: 0.6926 (OUTLIER) cc_final: 0.6489 (p) REVERT: J 118 PHE cc_start: 0.7202 (m-10) cc_final: 0.6968 (m-10) REVERT: J 142 ARG cc_start: 0.8634 (tpp80) cc_final: 0.8200 (mmm-85) REVERT: J 158 ASN cc_start: 0.6844 (OUTLIER) cc_final: 0.6030 (p0) REVERT: J 189 HIS cc_start: 0.8310 (m90) cc_final: 0.8050 (m90) REVERT: J 190 LYS cc_start: 0.7967 (tptt) cc_final: 0.7588 (tppt) REVERT: L 70 ASP cc_start: 0.7079 (m-30) cc_final: 0.6847 (m-30) REVERT: L 106 ILE cc_start: 0.7856 (mm) cc_final: 0.7557 (mm) REVERT: L 142 ARG cc_start: 0.8537 (tpp80) cc_final: 0.8142 (mmm160) outliers start: 66 outliers final: 34 residues processed: 313 average time/residue: 0.3441 time to fit residues: 165.4334 Evaluate side-chains 254 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 217 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 277 ASN 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 24 MET Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 277 ASN 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 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 100 ASN Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 158 ASN 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: 3.9990 chunk 76 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 chunk 166 optimal weight: 0.0670 chunk 67 optimal weight: 3.9990 chunk 245 optimal weight: 0.4980 chunk 265 optimal weight: 0.9980 chunk 218 optimal weight: 1.9990 chunk 243 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- 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 150 ASN ** B 376 GLN ** 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 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 124 GLN I 197 ASN ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 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: 0.8216 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21990 Z= 0.203 Angle : 0.572 8.552 29862 Z= 0.302 Chirality : 0.044 0.166 3312 Planarity : 0.004 0.056 3855 Dihedral : 5.157 44.520 3016 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.57 % Allowed : 15.11 % Favored : 82.32 % 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: -0.43 (0.16), residues: 2724 helix: 1.72 (0.26), residues: 405 sheet: 0.04 (0.18), residues: 861 loop : -1.07 (0.16), residues: 1458 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 0.020 0.002 PHE H 139 TYR 0.033 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 295 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 233 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8889 (mmt) cc_final: 0.8457 (mmt) REVERT: D 437 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7643 (mm-30) REVERT: E 286 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7561 (ptp) REVERT: E 293 MET cc_start: 0.8921 (mmt) cc_final: 0.8551 (mmt) REVERT: G 144 ASP cc_start: 0.6991 (t0) cc_final: 0.6735 (t0) REVERT: G 154 TRP cc_start: 0.7832 (m100) cc_final: 0.6681 (m100) REVERT: G 176 TYR cc_start: 0.8256 (m-80) cc_final: 0.8051 (m-80) REVERT: G 192 GLN cc_start: 0.5265 (OUTLIER) cc_final: 0.4855 (mm110) REVERT: G 195 ILE cc_start: 0.6456 (tp) cc_final: 0.6103 (tp) REVERT: G 209 LYS cc_start: 0.8161 (tppt) cc_final: 0.7827 (mmtp) REVERT: H 118 PHE cc_start: 0.7447 (m-80) cc_final: 0.6857 (m-10) REVERT: H 138 ASN cc_start: 0.8142 (m-40) cc_final: 0.7518 (t0) REVERT: H 192 TYR cc_start: 0.8396 (m-10) cc_final: 0.8046 (m-10) REVERT: I 176 TYR cc_start: 0.8400 (m-80) cc_final: 0.8120 (m-80) REVERT: I 192 GLN cc_start: 0.5121 (OUTLIER) cc_final: 0.4544 (mm110) REVERT: I 209 LYS cc_start: 0.8065 (tppt) cc_final: 0.7780 (mmmm) REVERT: K 100 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.7835 (m-40) REVERT: K 105 GLN cc_start: 0.8601 (pp30) cc_final: 0.7845 (pp30) REVERT: K 144 ASP cc_start: 0.7096 (t0) cc_final: 0.6802 (t0) REVERT: K 154 TRP cc_start: 0.7925 (m100) cc_final: 0.6422 (m100) REVERT: K 176 TYR cc_start: 0.8671 (m-80) cc_final: 0.8217 (m-80) REVERT: J 118 PHE cc_start: 0.7000 (m-10) cc_final: 0.6783 (m-10) REVERT: J 142 ARG cc_start: 0.8590 (tpp80) cc_final: 0.8013 (mmm-85) REVERT: J 189 HIS cc_start: 0.8306 (m90) cc_final: 0.8092 (m90) REVERT: J 190 LYS cc_start: 0.7890 (tptt) cc_final: 0.7631 (tppt) REVERT: L 170 ASP cc_start: 0.8276 (t0) cc_final: 0.7782 (t0) outliers start: 62 outliers final: 38 residues processed: 282 average time/residue: 0.3386 time to fit residues: 146.3989 Evaluate side-chains 256 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 214 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 277 ASN Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 277 ASN 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 192 GLN Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain G residue 208 ASP Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 114 SER 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 99 VAL Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 192 GLN Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain J residue 117 ILE 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 201 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 10.0000 chunk 184 optimal weight: 20.0000 chunk 127 optimal weight: 3.9990 chunk 27 optimal weight: 0.0970 chunk 117 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 246 optimal weight: 7.9990 chunk 260 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 chunk 233 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- 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 376 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 376 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 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN G 197 ASN ** G 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN I 197 ASN ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 171 GLN J 147 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 21990 Z= 0.430 Angle : 0.674 8.516 29862 Z= 0.354 Chirality : 0.046 0.157 3312 Planarity : 0.005 0.056 3855 Dihedral : 5.506 46.556 3011 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.69 % Allowed : 16.15 % Favored : 80.16 % 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: -0.50 (0.16), residues: 2724 helix: 1.66 (0.25), residues: 402 sheet: 0.02 (0.18), residues: 903 loop : -1.17 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 148 HIS 0.007 0.002 HIS E 184 PHE 0.019 0.002 PHE K 78 TYR 0.023 0.002 TYR J 140 ARG 0.005 0.001 ARG H 24 *********************** 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 312 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 223 time to evaluate : 2.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8799 (mmt) cc_final: 0.8444 (mmt) REVERT: B 377 LYS cc_start: 0.8601 (ttmt) cc_final: 0.8249 (ttmm) REVERT: C 293 MET cc_start: 0.8800 (mmt) cc_final: 0.8581 (mmt) REVERT: D 436 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7845 (mmm) REVERT: E 5 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7856 (m-30) REVERT: E 293 MET cc_start: 0.8852 (mmt) cc_final: 0.8502 (mmt) REVERT: F 377 LYS cc_start: 0.8689 (ttmt) cc_final: 0.8167 (ttmm) REVERT: G 144 ASP cc_start: 0.7150 (t0) cc_final: 0.6818 (t0) REVERT: G 154 TRP cc_start: 0.7862 (m100) cc_final: 0.6723 (m100) REVERT: G 176 TYR cc_start: 0.8401 (m-80) cc_final: 0.8105 (m-80) REVERT: G 195 ILE cc_start: 0.6576 (tp) cc_final: 0.6259 (tp) REVERT: G 209 LYS cc_start: 0.8190 (tppt) cc_final: 0.7816 (mmtp) REVERT: G 212 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6455 (mp0) REVERT: H 106 ILE cc_start: 0.8571 (mm) cc_final: 0.8288 (tt) REVERT: H 118 PHE cc_start: 0.7443 (m-80) cc_final: 0.6917 (m-10) REVERT: H 138 ASN cc_start: 0.8119 (m-40) cc_final: 0.7469 (t0) REVERT: H 161 GLU cc_start: 0.8934 (pp20) cc_final: 0.8551 (pp20) REVERT: H 192 TYR cc_start: 0.8395 (m-10) cc_final: 0.8039 (m-10) REVERT: I 105 GLN cc_start: 0.8738 (pp30) cc_final: 0.8096 (pp30) REVERT: K 43 ARG cc_start: 0.7176 (mpp80) cc_final: 0.6946 (mpp80) REVERT: K 100 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8031 (m-40) REVERT: K 105 GLN cc_start: 0.8685 (pp30) cc_final: 0.8045 (pp30) REVERT: K 154 TRP cc_start: 0.8067 (m100) cc_final: 0.6466 (m100) REVERT: K 166 PHE cc_start: 0.7924 (m-10) cc_final: 0.7676 (m-10) REVERT: K 176 TYR cc_start: 0.8627 (m-80) cc_final: 0.8193 (m-80) REVERT: J 118 PHE cc_start: 0.7095 (m-10) cc_final: 0.6887 (m-10) REVERT: J 189 HIS cc_start: 0.8273 (m90) cc_final: 0.8052 (m90) outliers start: 89 outliers final: 54 residues processed: 298 average time/residue: 0.3300 time to fit residues: 152.6642 Evaluate side-chains 256 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 198 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 277 ASN 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 490 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 277 ASN 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 E residue 5 ASP Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 277 ASN Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain F residue 482 CYS 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 108 LEU 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 198 VAL Chi-restraints excluded: chain G residue 208 ASP Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 115 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 70 ASN Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 111 VAL 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 211 VAL Chi-restraints excluded: chain K residue 65 ASN 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 100 ASN Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 171 GLN Chi-restraints excluded: chain K residue 198 VAL Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 198 HIS Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 115 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 217 optimal weight: 0.8980 chunk 148 optimal weight: 0.0570 chunk 3 optimal weight: 0.6980 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 222 optimal weight: 20.0000 chunk 180 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 234 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 376 GLN ** 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 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 ASN H 3 GLN ** I 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21990 Z= 0.164 Angle : 0.545 7.507 29862 Z= 0.286 Chirality : 0.043 0.156 3312 Planarity : 0.004 0.056 3855 Dihedral : 4.967 45.397 3011 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.57 % Allowed : 17.73 % 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: -0.21 (0.16), residues: 2724 helix: 2.02 (0.25), residues: 408 sheet: 0.18 (0.18), residues: 879 loop : -1.00 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 148 HIS 0.006 0.001 HIS L 198 PHE 0.024 0.001 PHE J 139 TYR 0.033 0.001 TYR J 140 ARG 0.006 0.000 ARG H 24 *********************** 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 295 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 233 time to evaluate : 2.501 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: 0.8792 (mmt) cc_final: 0.8399 (mmt) REVERT: B 446 ASP cc_start: 0.8116 (t70) cc_final: 0.7768 (t0) REVERT: D 392 LYS cc_start: 0.8856 (tppt) cc_final: 0.8620 (ttmm) REVERT: D 446 ASP cc_start: 0.8147 (t70) cc_final: 0.7725 (t0) REVERT: E 286 MET cc_start: 0.7832 (ptm) cc_final: 0.7594 (ptp) REVERT: E 293 MET cc_start: 0.8905 (mmt) cc_final: 0.8569 (mmt) REVERT: G 105 GLN cc_start: 0.8485 (pp30) cc_final: 0.8285 (pp30) REVERT: G 144 ASP cc_start: 0.6972 (t0) cc_final: 0.6708 (t0) REVERT: G 209 LYS cc_start: 0.8062 (tppt) cc_final: 0.7786 (mmtp) REVERT: H 138 ASN cc_start: 0.8018 (m-40) cc_final: 0.7373 (t0) REVERT: H 161 GLU cc_start: 0.8908 (pp20) cc_final: 0.8500 (pp20) REVERT: H 189 HIS cc_start: 0.8007 (m-70) cc_final: 0.7713 (m-70) REVERT: I 105 GLN cc_start: 0.8565 (pp30) cc_final: 0.7871 (pp30) REVERT: I 176 TYR cc_start: 0.8443 (m-80) cc_final: 0.8048 (m-80) REVERT: K 100 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.7905 (m-40) REVERT: K 105 GLN cc_start: 0.8480 (pp30) cc_final: 0.7857 (pp30) REVERT: K 166 PHE cc_start: 0.7865 (m-10) cc_final: 0.7646 (m-10) REVERT: K 176 TYR cc_start: 0.8595 (m-80) cc_final: 0.8176 (m-80) REVERT: J 108 ARG cc_start: 0.7547 (ptm160) cc_final: 0.7283 (ptt90) REVERT: J 116 PHE cc_start: 0.7882 (m-10) cc_final: 0.7681 (m-10) REVERT: J 118 PHE cc_start: 0.7141 (m-10) cc_final: 0.6941 (m-10) REVERT: L 108 ARG cc_start: 0.8214 (ptm160) cc_final: 0.7997 (ptm160) REVERT: L 165 GLU cc_start: 0.8715 (pm20) cc_final: 0.8231 (pm20) outliers start: 62 outliers final: 49 residues processed: 285 average time/residue: 0.3496 time to fit residues: 152.9737 Evaluate side-chains 263 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 213 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 5 ASP 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 E residue 24 MET Chi-restraints excluded: chain E residue 278 CYS Chi-restraints excluded: chain F residue 482 CYS 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 108 LEU Chi-restraints excluded: chain G residue 142 VAL 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 208 ASP Chi-restraints excluded: chain H residue 19 VAL 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 197 THR 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 97 VAL 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 197 ASN 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 100 ASN 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 115 VAL Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 198 HIS 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 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: 4.9990 chunk 51 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 216 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 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 376 GLN ** 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 376 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 39 GLN ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN ** I 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21990 Z= 0.217 Angle : 0.559 8.295 29862 Z= 0.293 Chirality : 0.044 0.153 3312 Planarity : 0.004 0.050 3855 Dihedral : 4.910 44.766 3011 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.91 % Allowed : 18.18 % Favored : 78.91 % 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: -0.10 (0.16), residues: 2724 helix: 2.12 (0.25), residues: 408 sheet: 0.26 (0.18), residues: 861 loop : -0.91 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 154 HIS 0.006 0.001 HIS J 198 PHE 0.019 0.001 PHE L 139 TYR 0.024 0.001 TYR J 140 ARG 0.006 0.000 ARG H 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 286 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 216 time to evaluate : 2.278 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: 0.8838 (mmt) cc_final: 0.8432 (mmt) REVERT: D 392 LYS cc_start: 0.8866 (tppt) cc_final: 0.8631 (ttmm) REVERT: E 286 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7635 (ptp) REVERT: E 293 MET cc_start: 0.8857 (mmt) cc_final: 0.8520 (mmt) REVERT: G 105 GLN cc_start: 0.8487 (pp30) cc_final: 0.8257 (pp30) REVERT: G 144 ASP cc_start: 0.7064 (t0) cc_final: 0.6817 (t0) REVERT: G 154 TRP cc_start: 0.7843 (m100) cc_final: 0.7264 (m100) REVERT: G 212 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.6358 (mp0) REVERT: H 106 ILE cc_start: 0.8674 (mm) cc_final: 0.8389 (tt) REVERT: H 138 ASN cc_start: 0.7944 (m-40) cc_final: 0.7308 (t0) REVERT: H 142 ARG cc_start: 0.8694 (ttt-90) cc_final: 0.8442 (tpp80) REVERT: H 161 GLU cc_start: 0.8905 (pp20) cc_final: 0.8480 (pp20) REVERT: H 189 HIS cc_start: 0.8033 (m-70) cc_final: 0.7738 (m-70) REVERT: I 105 GLN cc_start: 0.8549 (pp30) cc_final: 0.7877 (pp30) REVERT: I 117 LYS cc_start: 0.8150 (mmtt) cc_final: 0.7937 (mmtt) REVERT: I 145 TYR cc_start: 0.7136 (p90) cc_final: 0.6551 (p90) REVERT: K 100 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.7983 (m-40) REVERT: K 105 GLN cc_start: 0.8501 (pp30) cc_final: 0.7898 (pp30) REVERT: K 143 LYS cc_start: 0.7500 (mmmt) cc_final: 0.7158 (mmmt) REVERT: K 176 TYR cc_start: 0.8559 (m-80) cc_final: 0.8134 (m-80) REVERT: J 108 ARG cc_start: 0.7864 (ptm160) cc_final: 0.7283 (ptt90) REVERT: J 161 GLU cc_start: 0.8946 (pp20) cc_final: 0.8389 (pp20) REVERT: J 189 HIS cc_start: 0.8250 (m-70) cc_final: 0.7971 (m-70) REVERT: L 108 ARG cc_start: 0.8304 (ptm160) cc_final: 0.7969 (ptm160) REVERT: L 165 GLU cc_start: 0.8702 (pm20) cc_final: 0.8254 (pm20) REVERT: L 181 LEU cc_start: 0.7528 (pt) cc_final: 0.7189 (mt) REVERT: L 198 HIS cc_start: 0.4899 (OUTLIER) cc_final: 0.4151 (t-90) outliers start: 70 outliers final: 52 residues processed: 275 average time/residue: 0.3322 time to fit residues: 140.9979 Evaluate side-chains 259 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 203 time to evaluate : 2.332 ------------------------------------------------------------------------------- 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 366 SER Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 5 ASP 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 490 THR Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 278 CYS Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain F residue 482 CYS 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 108 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain H residue 19 VAL 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 209 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 70 ASN Chi-restraints excluded: chain I residue 97 VAL 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 70 ASN Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain K residue 198 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 198 HIS 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: 0.2980 chunk 29 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 219 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 260 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 158 optimal weight: 30.0000 chunk 120 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 376 GLN ** 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 376 GLN ** 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 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 155 ASN I 171 GLN I 204 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4093 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= 0.216 Angle : 0.559 8.288 29862 Z= 0.292 Chirality : 0.043 0.153 3312 Planarity : 0.004 0.050 3855 Dihedral : 4.873 44.407 3011 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.45 % Allowed : 18.14 % Favored : 78.41 % 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: -0.07 (0.17), residues: 2724 helix: 2.18 (0.25), residues: 408 sheet: 0.26 (0.18), residues: 879 loop : -0.90 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 148 HIS 0.006 0.001 HIS J 198 PHE 0.027 0.002 PHE H 118 TYR 0.025 0.001 TYR J 140 ARG 0.007 0.000 ARG H 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 297 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 214 time to evaluate : 2.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8817 (mmt) cc_final: 0.8420 (mmt) REVERT: D 392 LYS cc_start: 0.8867 (tppt) cc_final: 0.8625 (ttmm) REVERT: E 5 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7896 (m-30) REVERT: E 293 MET cc_start: 0.8855 (mmt) cc_final: 0.8491 (mmt) REVERT: F 377 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8162 (ttmm) REVERT: G 144 ASP cc_start: 0.7117 (t0) cc_final: 0.6873 (t0) REVERT: G 154 TRP cc_start: 0.7814 (m100) cc_final: 0.7348 (m100) REVERT: H 138 ASN cc_start: 0.7959 (m-40) cc_final: 0.7308 (t0) REVERT: H 143 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7454 (pm20) REVERT: H 161 GLU cc_start: 0.8944 (pp20) cc_final: 0.8517 (pp20) REVERT: H 189 HIS cc_start: 0.7729 (m-70) cc_final: 0.7474 (m-70) REVERT: I 105 GLN cc_start: 0.8555 (pp30) cc_final: 0.7878 (pp30) REVERT: I 145 TYR cc_start: 0.7050 (p90) cc_final: 0.6610 (p90) REVERT: K 100 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8029 (m-40) REVERT: K 105 GLN cc_start: 0.8480 (pp30) cc_final: 0.7861 (pp30) REVERT: K 176 TYR cc_start: 0.8567 (m-80) cc_final: 0.8214 (m-80) REVERT: K 192 GLN cc_start: 0.4232 (OUTLIER) cc_final: 0.3323 (mm110) REVERT: J 108 ARG cc_start: 0.7810 (ptm160) cc_final: 0.7138 (ptt90) REVERT: J 161 GLU cc_start: 0.8983 (pp20) cc_final: 0.8448 (pp20) REVERT: J 189 HIS cc_start: 0.8204 (m-70) cc_final: 0.7973 (m-70) REVERT: L 108 ARG cc_start: 0.8340 (ptm160) cc_final: 0.8009 (ptm160) REVERT: L 165 GLU cc_start: 0.8726 (pm20) cc_final: 0.8444 (pm20) outliers start: 83 outliers final: 64 residues processed: 287 average time/residue: 0.3321 time to fit residues: 147.3873 Evaluate side-chains 270 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 202 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP 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 479 ASP Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 5 ASP 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 277 ASN Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 278 CYS Chi-restraints excluded: chain F residue 478 CYS Chi-restraints excluded: chain F residue 482 CYS 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 108 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 143 GLU 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 70 ASN Chi-restraints excluded: chain I residue 97 VAL 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 70 ASN Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain K residue 140 CYS Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 192 GLN Chi-restraints excluded: chain K residue 198 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 146 VAL 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: 6.9990 chunk 103 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 78 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 165 optimal weight: 8.9990 chunk 177 optimal weight: 0.0970 chunk 128 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 204 optimal weight: 9.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 376 GLN ** 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 376 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 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 GLN K 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21990 Z= 0.161 Angle : 0.544 8.750 29862 Z= 0.283 Chirality : 0.043 0.152 3312 Planarity : 0.004 0.048 3855 Dihedral : 4.723 43.535 3011 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.91 % Allowed : 18.72 % Favored : 78.37 % 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: 0.04 (0.17), residues: 2724 helix: 2.28 (0.25), residues: 408 sheet: 0.31 (0.18), residues: 879 loop : -0.83 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 148 HIS 0.007 0.001 HIS J 198 PHE 0.019 0.001 PHE L 139 TYR 0.026 0.001 TYR J 140 ARG 0.008 0.000 ARG H 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 285 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 215 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8638 (t80) cc_final: 0.8174 (t80) REVERT: A 261 VAL cc_start: 0.9277 (OUTLIER) cc_final: 0.9033 (p) REVERT: A 293 MET cc_start: 0.8828 (mmt) cc_final: 0.8380 (mmt) REVERT: D 392 LYS cc_start: 0.8862 (tppt) cc_final: 0.8622 (ttmm) REVERT: E 5 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7854 (m-30) REVERT: E 293 MET cc_start: 0.8905 (mmt) cc_final: 0.8536 (mmt) REVERT: G 144 ASP cc_start: 0.7180 (t0) cc_final: 0.6957 (t0) REVERT: G 154 TRP cc_start: 0.7819 (m100) cc_final: 0.7363 (m100) REVERT: H 138 ASN cc_start: 0.7997 (m-40) cc_final: 0.7464 (t0) REVERT: H 142 ARG cc_start: 0.8828 (ttt-90) cc_final: 0.8424 (tpp80) REVERT: H 161 GLU cc_start: 0.8974 (pp20) cc_final: 0.8526 (pp20) REVERT: H 189 HIS cc_start: 0.7802 (m-70) cc_final: 0.7411 (m-70) REVERT: I 105 GLN cc_start: 0.8476 (pp30) cc_final: 0.7811 (pp30) REVERT: I 145 TYR cc_start: 0.7013 (p90) cc_final: 0.6550 (p90) REVERT: I 154 TRP cc_start: 0.7794 (m100) cc_final: 0.7327 (m100) REVERT: K 100 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.7953 (m-40) REVERT: K 105 GLN cc_start: 0.8419 (pp30) cc_final: 0.7818 (pp30) REVERT: K 143 LYS cc_start: 0.7671 (mmmt) cc_final: 0.7298 (mmmt) REVERT: K 176 TYR cc_start: 0.8569 (m-80) cc_final: 0.8176 (m-80) REVERT: K 192 GLN cc_start: 0.4966 (OUTLIER) cc_final: 0.4208 (mm110) REVERT: J 108 ARG cc_start: 0.7770 (ptm160) cc_final: 0.7221 (ptt90) REVERT: J 189 HIS cc_start: 0.8093 (m-70) cc_final: 0.7856 (m-70) REVERT: L 108 ARG cc_start: 0.8299 (ptm160) cc_final: 0.8055 (ptm160) REVERT: L 165 GLU cc_start: 0.8700 (pm20) cc_final: 0.8420 (pm20) outliers start: 70 outliers final: 61 residues processed: 274 average time/residue: 0.3227 time to fit residues: 137.3059 Evaluate side-chains 272 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 207 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 261 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 436 MET Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 142 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 479 ASP Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 278 CYS Chi-restraints excluded: chain F residue 482 CYS 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 108 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 70 ASP 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 209 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 70 ASN Chi-restraints excluded: chain I residue 97 VAL 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 70 ASN Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain K residue 140 CYS Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 192 GLN Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 198 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 115 VAL 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 201 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 6.9990 chunk 249 optimal weight: 3.9990 chunk 227 optimal weight: 0.0000 chunk 242 optimal weight: 0.8980 chunk 145 optimal weight: 0.0870 chunk 105 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 chunk 219 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 overall best weight: 0.4762 ------------------------------------------------------------------------------- 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 376 GLN ** 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 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** K 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21990 Z= 0.145 Angle : 0.535 8.718 29862 Z= 0.278 Chirality : 0.043 0.168 3312 Planarity : 0.004 0.047 3855 Dihedral : 4.561 42.031 3011 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.86 % Allowed : 19.05 % Favored : 78.08 % 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: 0.15 (0.17), residues: 2724 helix: 2.38 (0.26), residues: 408 sheet: 0.39 (0.18), residues: 879 loop : -0.76 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 35A HIS 0.008 0.001 HIS J 198 PHE 0.019 0.001 PHE J 139 TYR 0.030 0.001 TYR J 140 ARG 0.009 0.000 ARG H 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 296 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 227 time to evaluate : 2.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8608 (t80) cc_final: 0.8200 (t80) REVERT: A 261 VAL cc_start: 0.9259 (OUTLIER) cc_final: 0.9028 (p) REVERT: A 293 MET cc_start: 0.8792 (mmt) cc_final: 0.8372 (mmt) REVERT: D 353 ASP cc_start: 0.7221 (p0) cc_final: 0.6850 (p0) REVERT: E 293 MET cc_start: 0.8885 (mmt) cc_final: 0.8504 (mmt) REVERT: G 13 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8313 (mmmm) REVERT: G 85 GLU cc_start: 0.7509 (mp0) cc_final: 0.7237 (mp0) REVERT: G 144 ASP cc_start: 0.7131 (t0) cc_final: 0.6900 (t0) REVERT: G 154 TRP cc_start: 0.7843 (m100) cc_final: 0.7450 (m100) REVERT: G 209 LYS cc_start: 0.7507 (tptp) cc_final: 0.6867 (mmtp) REVERT: H 138 ASN cc_start: 0.7949 (m-40) cc_final: 0.7451 (t0) REVERT: H 142 ARG cc_start: 0.8791 (ttt-90) cc_final: 0.8445 (tpp80) REVERT: H 161 GLU cc_start: 0.9035 (pp20) cc_final: 0.8590 (pp20) REVERT: H 170 ASP cc_start: 0.7294 (t0) cc_final: 0.7093 (t0) REVERT: H 189 HIS cc_start: 0.7798 (m-70) cc_final: 0.7384 (m-70) REVERT: I 105 GLN cc_start: 0.8448 (pp30) cc_final: 0.7830 (pp30) REVERT: I 117 LYS cc_start: 0.8091 (mmtt) cc_final: 0.7791 (mmtt) REVERT: I 145 TYR cc_start: 0.6927 (p90) cc_final: 0.6531 (p90) REVERT: I 154 TRP cc_start: 0.7826 (m100) cc_final: 0.7378 (m100) REVERT: K 100 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.7932 (m-40) REVERT: K 105 GLN cc_start: 0.8391 (pp30) cc_final: 0.7845 (pp30) REVERT: K 143 LYS cc_start: 0.7764 (mmmt) cc_final: 0.7430 (mmmt) REVERT: K 176 TYR cc_start: 0.8532 (m-80) cc_final: 0.8172 (m-80) REVERT: J 108 ARG cc_start: 0.7585 (ptm160) cc_final: 0.6936 (ptt90) REVERT: L 108 ARG cc_start: 0.8258 (ptm160) cc_final: 0.8000 (ptm160) REVERT: L 138 ASN cc_start: 0.7919 (m110) cc_final: 0.7149 (t0) REVERT: L 161 GLU cc_start: 0.8851 (pp20) cc_final: 0.8501 (pp20) REVERT: L 165 GLU cc_start: 0.8629 (pm20) cc_final: 0.8209 (pm20) REVERT: L 170 ASP cc_start: 0.7232 (t0) cc_final: 0.6764 (t0) outliers start: 69 outliers final: 60 residues processed: 284 average time/residue: 0.3385 time to fit residues: 148.9086 Evaluate side-chains 273 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 210 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 261 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 436 MET Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 142 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 479 ASP Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 278 CYS Chi-restraints excluded: chain F residue 482 CYS Chi-restraints excluded: chain G residue 13 LYS 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 142 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 70 ASP 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 209 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 70 ASN Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 121 VAL 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 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 100 ASN Chi-restraints excluded: chain K residue 140 CYS 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 J residue 19 VAL Chi-restraints excluded: chain J residue 115 VAL 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 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 3.9990 chunk 256 optimal weight: 7.9990 chunk 156 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 268 optimal weight: 5.9990 chunk 247 optimal weight: 7.9990 chunk 214 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 165 optimal weight: 10.0000 chunk 131 optimal weight: 0.8980 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 ASN ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 GLN H 3 GLN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21990 Z= 0.354 Angle : 0.635 8.717 29862 Z= 0.331 Chirality : 0.045 0.165 3312 Planarity : 0.004 0.045 3855 Dihedral : 5.069 44.870 3011 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.99 % Allowed : 19.43 % Favored : 77.58 % 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: -0.07 (0.17), residues: 2724 helix: 2.14 (0.25), residues: 402 sheet: 0.25 (0.18), residues: 858 loop : -0.86 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 348 HIS 0.014 0.002 HIS E 299 PHE 0.019 0.002 PHE H 139 TYR 0.023 0.002 TYR F 356 ARG 0.006 0.000 ARG L 61 ********************** 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 286 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 214 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8842 (mmt) cc_final: 0.8423 (mmt) REVERT: B 377 LYS cc_start: 0.8563 (ttmt) cc_final: 0.8164 (ttmm) REVERT: E 5 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7895 (m-30) REVERT: E 293 MET cc_start: 0.8860 (mmt) cc_final: 0.8564 (mmt) REVERT: F 377 LYS cc_start: 0.8635 (ttmt) cc_final: 0.8131 (ttmm) REVERT: G 13 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8221 (mtmm) REVERT: G 85 GLU cc_start: 0.7605 (mp0) cc_final: 0.7343 (mp0) REVERT: G 144 ASP cc_start: 0.7233 (t0) cc_final: 0.6984 (t0) REVERT: H 138 ASN cc_start: 0.7982 (m-40) cc_final: 0.7495 (t0) REVERT: H 142 ARG cc_start: 0.8815 (ttt-90) cc_final: 0.8454 (tpp80) REVERT: H 161 GLU cc_start: 0.8988 (pp20) cc_final: 0.8499 (pp20) REVERT: H 170 ASP cc_start: 0.7490 (t0) cc_final: 0.7270 (t0) REVERT: H 189 HIS cc_start: 0.7856 (m-70) cc_final: 0.7401 (m-70) REVERT: I 105 GLN cc_start: 0.8593 (pp30) cc_final: 0.7893 (pp30) REVERT: I 145 TYR cc_start: 0.7028 (p90) cc_final: 0.6688 (p90) REVERT: K 100 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8039 (m-40) REVERT: K 176 TYR cc_start: 0.8545 (m-80) cc_final: 0.8211 (m-80) REVERT: K 192 GLN cc_start: 0.4669 (OUTLIER) cc_final: 0.3801 (mm110) REVERT: J 108 ARG cc_start: 0.7583 (ptm160) cc_final: 0.7080 (ptt90) REVERT: J 161 GLU cc_start: 0.9025 (pp20) cc_final: 0.8460 (pp20) REVERT: L 108 ARG cc_start: 0.8367 (ptm160) cc_final: 0.8132 (ptm160) REVERT: L 138 ASN cc_start: 0.7933 (m110) cc_final: 0.7122 (t0) REVERT: L 161 GLU cc_start: 0.8864 (pp20) cc_final: 0.8464 (pp20) REVERT: L 165 GLU cc_start: 0.8702 (pm20) cc_final: 0.8489 (pm20) REVERT: L 170 ASP cc_start: 0.7295 (t0) cc_final: 0.6874 (t0) outliers start: 72 outliers final: 57 residues processed: 278 average time/residue: 0.3365 time to fit residues: 144.2890 Evaluate side-chains 266 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 205 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 277 ASN 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 490 THR Chi-restraints excluded: chain C residue 5 ASP 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 142 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 490 THR Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 278 CYS 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 142 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 19 VAL 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 209 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 70 ASN Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 121 VAL 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 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 100 ASN Chi-restraints excluded: chain K residue 140 CYS Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 192 GLN Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 198 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 115 VAL 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 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 170 optimal weight: 0.4980 chunk 228 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 197 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 214 optimal weight: 0.0980 chunk 89 optimal weight: 0.9980 chunk 220 optimal weight: 5.9990 chunk 27 optimal weight: 0.0040 chunk 39 optimal weight: 0.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- 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 376 GLN ** 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 376 GLN ** 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** H 3 GLN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN ** K 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.102566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.074092 restraints weight = 51438.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.076592 restraints weight = 23495.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.078171 restraints weight = 14572.029| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21990 Z= 0.144 Angle : 0.555 8.892 29862 Z= 0.289 Chirality : 0.043 0.160 3312 Planarity : 0.004 0.049 3855 Dihedral : 4.664 43.207 3011 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.24 % Allowed : 20.34 % Favored : 77.42 % 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 (0.17), residues: 2724 helix: 2.33 (0.26), residues: 408 sheet: 0.38 (0.18), residues: 879 loop : -0.77 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 35A HIS 0.011 0.001 HIS J 198 PHE 0.020 0.001 PHE H 139 TYR 0.022 0.001 TYR F 356 ARG 0.009 0.000 ARG G 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4168.40 seconds wall clock time: 80 minutes 22.40 seconds (4822.40 seconds total)