Starting phenix.real_space_refine on Fri Feb 16 21:36:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usy_26743/02_2024/7usy_26743_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usy_26743/02_2024/7usy_26743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usy_26743/02_2024/7usy_26743.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usy_26743/02_2024/7usy_26743.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usy_26743/02_2024/7usy_26743_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usy_26743/02_2024/7usy_26743_updated.pdb" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 P 4 5.49 5 S 95 5.16 5 C 10812 2.51 5 N 2770 2.21 5 O 2893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 130": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "A GLU 722": "OE1" <-> "OE2" Residue "A GLU 777": "OE1" <-> "OE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B GLU 669": "OE1" <-> "OE2" Residue "B GLU 722": "OE1" <-> "OE2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "J GLU 180": "OE1" <-> "OE2" Residue "J GLU 256": "OE1" <-> "OE2" Residue "J GLU 317": "OE1" <-> "OE2" Residue "J ARG 337": "NH1" <-> "NH2" Residue "J GLU 383": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16582 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4864 Classifications: {'peptide': 602} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 18, 'TRANS': 583} Chain breaks: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 4864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4864 Classifications: {'peptide': 602} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 18, 'TRANS': 583} Chain breaks: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1536 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "D" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 343 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1536 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "F" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 343 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2878 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 93 Unusual residues: {' CA': 2, '3PE': 1, 'NAG': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 93 Unusual residues: {' CA': 2, '3PE': 1, 'NAG': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 9.29, per 1000 atoms: 0.56 Number of scatterers: 16582 At special positions: 0 Unit cell: (143.469, 119.138, 156.893, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 95 16.00 P 4 15.00 O 2893 8.00 N 2770 7.00 C 10812 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 667 " - pdb=" SG CYS A 816 " distance=2.03 Simple disulfide: pdb=" SG CYS B 667 " - pdb=" SG CYS B 816 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.27 Conformation dependent library (CDL) restraints added in 3.0 seconds 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3868 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 75 helices and 10 sheets defined 56.2% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 76 through 95 removed outlier: 4.642A pdb=" N ARG A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N CYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 120 removed outlier: 4.330A pdb=" N SER A 119 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYS A 120 " --> pdb=" O GLN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 148 removed outlier: 3.539A pdb=" N TYR A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 Processing helix chain 'A' and resid 168 through 190 Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 205 through 215 removed outlier: 5.126A pdb=" N THR A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ARG A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 removed outlier: 3.996A pdb=" N VAL A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 219 through 224' Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 262 through 289 removed outlier: 3.608A pdb=" N PHE A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 Processing helix chain 'A' and resid 319 through 342 Processing helix chain 'A' and resid 350 through 380 removed outlier: 3.625A pdb=" N CYS A 364 " --> pdb=" O ASN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 416 removed outlier: 3.536A pdb=" N VAL A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Proline residue: A 407 - end of helix removed outlier: 3.688A pdb=" N LYS A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 458 Processing helix chain 'A' and resid 668 through 694 Processing helix chain 'A' and resid 696 through 705 Processing helix chain 'A' and resid 725 through 743 Processing helix chain 'A' and resid 749 through 771 removed outlier: 3.791A pdb=" N ILE A 755 " --> pdb=" O ALA A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 809 Proline residue: A 802 - end of helix Processing helix chain 'A' and resid 825 through 836 removed outlier: 3.853A pdb=" N VAL A 828 " --> pdb=" O PHE A 825 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ARG A 831 " --> pdb=" O VAL A 828 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU A 834 " --> pdb=" O ARG A 831 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A 835 " --> pdb=" O GLU A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 849 removed outlier: 3.693A pdb=" N HIS A 847 " --> pdb=" O SER A 843 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE A 848 " --> pdb=" O TYR A 844 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 879 Proline residue: A 856 - end of helix Processing helix chain 'B' and resid 76 through 93 Processing helix chain 'B' and resid 100 through 120 removed outlier: 4.490A pdb=" N SER B 119 " --> pdb=" O GLU B 115 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LYS B 120 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 148 Processing helix chain 'B' and resid 153 through 163 Processing helix chain 'B' and resid 167 through 190 removed outlier: 3.821A pdb=" N PHE B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 205 through 215 removed outlier: 5.116A pdb=" N THR B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ARG B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 removed outlier: 4.093A pdb=" N VAL B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N HIS B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 224' Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 262 through 289 removed outlier: 3.760A pdb=" N PHE B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 308 Processing helix chain 'B' and resid 319 through 342 Processing helix chain 'B' and resid 350 through 380 Processing helix chain 'B' and resid 392 through 416 removed outlier: 4.444A pdb=" N VAL B 395 " --> pdb=" O LYS B 392 " (cutoff:3.500A) Proline residue: B 396 - end of helix removed outlier: 4.057A pdb=" N VAL B 399 " --> pdb=" O PRO B 396 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 400 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N PHE B 406 " --> pdb=" O THR B 403 " (cutoff:3.500A) Proline residue: B 407 - end of helix Processing helix chain 'B' and resid 421 through 458 Processing helix chain 'B' and resid 668 through 694 Processing helix chain 'B' and resid 696 through 705 Processing helix chain 'B' and resid 713 through 715 No H-bonds generated for 'chain 'B' and resid 713 through 715' Processing helix chain 'B' and resid 725 through 742 Processing helix chain 'B' and resid 749 through 770 removed outlier: 3.783A pdb=" N ILE B 755 " --> pdb=" O ALA B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 809 Proline residue: B 802 - end of helix Processing helix chain 'B' and resid 826 through 833 removed outlier: 4.109A pdb=" N ARG B 831 " --> pdb=" O VAL B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 849 removed outlier: 3.578A pdb=" N HIS B 847 " --> pdb=" O SER B 843 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE B 848 " --> pdb=" O TYR B 844 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA B 849 " --> pdb=" O ILE B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 879 Proline residue: B 856 - end of helix Processing helix chain 'C' and resid 22 through 31 Processing helix chain 'C' and resid 36 through 49 Processing helix chain 'C' and resid 62 through 65 No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 118 through 129 Processing helix chain 'C' and resid 139 through 149 Processing helix chain 'C' and resid 156 through 169 Processing helix chain 'C' and resid 180 through 189 removed outlier: 3.676A pdb=" N SER C 188 " --> pdb=" O GLU C 184 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ARG C 189 " --> pdb=" O HIS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 196 No H-bonds generated for 'chain 'C' and resid 193 through 196' Processing helix chain 'D' and resid 24 through 45 Processing helix chain 'D' and resid 54 through 62 Processing helix chain 'E' and resid 22 through 31 Processing helix chain 'E' and resid 36 through 49 Processing helix chain 'E' and resid 62 through 65 No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 102 through 111 Processing helix chain 'E' and resid 118 through 129 Processing helix chain 'E' and resid 139 through 150 Processing helix chain 'E' and resid 156 through 169 Processing helix chain 'E' and resid 180 through 189 removed outlier: 4.905A pdb=" N ARG E 189 " --> pdb=" O HIS E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 196 No H-bonds generated for 'chain 'E' and resid 193 through 196' Processing helix chain 'F' and resid 24 through 45 removed outlier: 3.704A pdb=" N PHE F 45 " --> pdb=" O ILE F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 62 Processing helix chain 'J' and resid 180 through 183 No H-bonds generated for 'chain 'J' and resid 180 through 183' Processing helix chain 'J' and resid 363 through 365 No H-bonds generated for 'chain 'J' and resid 363 through 365' Processing sheet with id= A, first strand: chain 'C' and resid 67 through 69 Processing sheet with id= B, first strand: chain 'E' and resid 67 through 69 Processing sheet with id= C, first strand: chain 'J' and resid 120 through 129 Processing sheet with id= D, first strand: chain 'J' and resid 85 through 94 removed outlier: 3.658A pdb=" N GLY J 65 " --> pdb=" O ASP J 155 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR J 148 " --> pdb=" O PHE J 168 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'J' and resid 186 through 193 Processing sheet with id= F, first strand: chain 'J' and resid 214 through 216 removed outlier: 6.365A pdb=" N THR J 330 " --> pdb=" O TYR J 215 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'J' and resid 256 through 258 removed outlier: 3.710A pdb=" N GLU J 256 " --> pdb=" O VAL J 249 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR J 308 " --> pdb=" O LEU J 329 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 347 through 350 Processing sheet with id= I, first strand: chain 'J' and resid 65 through 72 removed outlier: 6.401A pdb=" N VAL J 68 " --> pdb=" O LEU J 101 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU J 101 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU J 70 " --> pdb=" O LYS J 99 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LYS J 99 " --> pdb=" O LEU J 70 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N GLY J 72 " --> pdb=" O ASP J 97 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP J 97 " --> pdb=" O GLY J 72 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 238 through 244 removed outlier: 3.622A pdb=" N PHE J 265 " --> pdb=" O LEU J 241 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN J 243 " --> pdb=" O VAL J 263 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL J 263 " --> pdb=" O GLN J 243 " (cutoff:3.500A) 876 hydrogen bonds defined for protein. 2547 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: 4.56 Time building geometry restraints manager: 7.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2562 1.31 - 1.44: 4665 1.44 - 1.56: 9560 1.56 - 1.69: 9 1.69 - 1.82: 152 Bond restraints: 16948 Sorted by residual: bond pdb=" C21 3PE B1304 " pdb=" O21 3PE B1304 " ideal model delta sigma weight residual 1.316 1.399 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C21 3PE A1304 " pdb=" O21 3PE A1304 " ideal model delta sigma weight residual 1.316 1.398 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C30 PEE B1303 " pdb=" O3 PEE B1303 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C30 PEE A1303 " pdb=" O3 PEE A1303 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C31 3PE A1304 " pdb=" O31 3PE A1304 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 16943 not shown) Histogram of bond angle deviations from ideal: 92.55 - 100.92: 42 100.92 - 109.30: 1072 109.30 - 117.67: 11461 117.67 - 126.05: 10085 126.05 - 134.42: 245 Bond angle restraints: 22905 Sorted by residual: angle pdb=" C ASN J 340 " pdb=" N ALA J 341 " pdb=" CA ALA J 341 " ideal model delta sigma weight residual 120.68 133.70 -13.02 1.52e+00 4.33e-01 7.34e+01 angle pdb=" N SER A 870 " pdb=" CA SER A 870 " pdb=" C SER A 870 " ideal model delta sigma weight residual 111.14 102.17 8.97 1.08e+00 8.57e-01 6.90e+01 angle pdb=" C MET A 810 " pdb=" N SER A 811 " pdb=" CA SER A 811 " ideal model delta sigma weight residual 121.61 132.79 -11.18 1.39e+00 5.18e-01 6.47e+01 angle pdb=" C GLN B 301 " pdb=" CA GLN B 301 " pdb=" CB GLN B 301 " ideal model delta sigma weight residual 116.54 109.86 6.68 1.15e+00 7.56e-01 3.37e+01 angle pdb=" O3P PEE A1303 " pdb=" P PEE A1303 " pdb=" O4P PEE A1303 " ideal model delta sigma weight residual 92.91 109.74 -16.83 3.00e+00 1.11e-01 3.15e+01 ... (remaining 22900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.29: 9853 34.29 - 68.59: 340 68.59 - 102.88: 16 102.88 - 137.17: 1 137.17 - 171.47: 4 Dihedral angle restraints: 10214 sinusoidal: 4247 harmonic: 5967 Sorted by residual: dihedral pdb=" CA PRO J 344 " pdb=" C PRO J 344 " pdb=" N PRO J 345 " pdb=" CA PRO J 345 " ideal model delta harmonic sigma weight residual 180.00 -155.36 -24.64 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" C4 PEE A1303 " pdb=" O4P PEE A1303 " pdb=" P PEE A1303 " pdb=" O1P PEE A1303 " ideal model delta sinusoidal sigma weight residual 57.28 -131.25 -171.47 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C4 PEE B1303 " pdb=" O4P PEE B1303 " pdb=" P PEE B1303 " pdb=" O1P PEE B1303 " ideal model delta sinusoidal sigma weight residual 57.28 -141.02 -161.70 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 10211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1798 0.038 - 0.076: 609 0.076 - 0.115: 149 0.115 - 0.153: 21 0.153 - 0.191: 3 Chirality restraints: 2580 Sorted by residual: chirality pdb=" C2 PEE A1303 " pdb=" C1 PEE A1303 " pdb=" C3 PEE A1303 " pdb=" O2 PEE A1303 " both_signs ideal model delta sigma weight residual False -2.33 -2.52 0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" CG LEU F 30 " pdb=" CB LEU F 30 " pdb=" CD1 LEU F 30 " pdb=" CD2 LEU F 30 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CA ILE J 338 " pdb=" N ILE J 338 " pdb=" C ILE J 338 " pdb=" CB ILE J 338 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.79e-01 ... (remaining 2577 not shown) Planarity restraints: 2843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1305 " 0.202 2.00e-02 2.50e+03 1.67e-01 3.49e+02 pdb=" C7 NAG B1305 " -0.055 2.00e-02 2.50e+03 pdb=" C8 NAG B1305 " 0.146 2.00e-02 2.50e+03 pdb=" N2 NAG B1305 " -0.272 2.00e-02 2.50e+03 pdb=" O7 NAG B1305 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1305 " 0.115 2.00e-02 2.50e+03 9.50e-02 1.13e+02 pdb=" C7 NAG A1305 " -0.032 2.00e-02 2.50e+03 pdb=" C8 NAG A1305 " 0.087 2.00e-02 2.50e+03 pdb=" N2 NAG A1305 " -0.151 2.00e-02 2.50e+03 pdb=" O7 NAG A1305 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 395 " 0.087 5.00e-02 4.00e+02 1.28e-01 2.62e+01 pdb=" N PRO A 396 " -0.221 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " 0.070 5.00e-02 4.00e+02 ... (remaining 2840 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 4 2.11 - 2.81: 4507 2.81 - 3.51: 23201 3.51 - 4.20: 35105 4.20 - 4.90: 64811 Nonbonded interactions: 127628 Sorted by model distance: nonbonded pdb=" OD1 ASP C 171 " pdb="CA CA C 302 " model vdw 1.415 2.510 nonbonded pdb=" ND2 ASN A 209 " pdb=" C3 NAG A1305 " model vdw 1.424 3.550 nonbonded pdb=" ND2 ASN B 209 " pdb=" C3 NAG B1305 " model vdw 1.467 3.550 nonbonded pdb=" OE1 GLU C 182 " pdb="CA CA C 302 " model vdw 1.981 2.510 nonbonded pdb=" OE2 GLU C 182 " pdb="CA CA C 302 " model vdw 2.124 2.510 ... (remaining 127623 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 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.000 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 46.080 Find NCS groups from input model: 0.790 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: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 16948 Z= 0.253 Angle : 0.778 16.825 22905 Z= 0.402 Chirality : 0.041 0.191 2580 Planarity : 0.006 0.167 2843 Dihedral : 17.183 171.469 6340 Min Nonbonded Distance : 1.415 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.28 % Allowed : 23.12 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.19), residues: 2005 helix: 2.08 (0.15), residues: 1157 sheet: 0.95 (0.38), residues: 169 loop : -0.83 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 668 HIS 0.002 0.001 HIS A 731 PHE 0.025 0.001 PHE A 376 TYR 0.032 0.001 TYR B 245 ARG 0.008 0.000 ARG J 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 175 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 426 ARG cc_start: 0.6409 (mmm-85) cc_final: 0.5115 (mmt180) REVERT: A 451 MET cc_start: 0.4165 (tpt) cc_final: 0.3650 (tmm) REVERT: A 783 ARG cc_start: 0.6486 (mtt90) cc_final: 0.4233 (ptt-90) REVERT: A 826 TYR cc_start: 0.7461 (p90) cc_final: 0.6969 (p90) REVERT: A 836 ARG cc_start: 0.5039 (mtt90) cc_final: 0.3789 (mtm-85) REVERT: B 831 ARG cc_start: 0.6385 (mtm180) cc_final: 0.6039 (ttp-170) REVERT: F 30 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6347 (mm) REVERT: J 314 MET cc_start: 0.1849 (mpp) cc_final: 0.1542 (mtt) outliers start: 5 outliers final: 2 residues processed: 180 average time/residue: 0.3020 time to fit residues: 81.1109 Evaluate side-chains 164 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 161 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain J residue 129 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 20.0000 chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 0.0030 chunk 51 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 60 optimal weight: 30.0000 chunk 95 optimal weight: 0.4980 chunk 116 optimal weight: 0.5980 chunk 181 optimal weight: 6.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS B 879 ASN C 57 ASN J 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.0557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16948 Z= 0.151 Angle : 0.499 7.711 22905 Z= 0.254 Chirality : 0.039 0.164 2580 Planarity : 0.004 0.062 2843 Dihedral : 10.399 179.935 2442 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.43 % Allowed : 21.99 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.19), residues: 2005 helix: 2.24 (0.15), residues: 1163 sheet: 1.15 (0.39), residues: 169 loop : -0.72 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 668 HIS 0.002 0.000 HIS E 139 PHE 0.018 0.001 PHE E 105 TYR 0.022 0.001 TYR B 245 ARG 0.005 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 167 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.5306 (tptt) cc_final: 0.4939 (tppt) REVERT: A 245 TYR cc_start: 0.5149 (OUTLIER) cc_final: 0.3864 (t80) REVERT: A 451 MET cc_start: 0.4119 (tpt) cc_final: 0.3578 (tmm) REVERT: A 689 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.6902 (tt) REVERT: A 735 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7801 (t0) REVERT: A 783 ARG cc_start: 0.6446 (mtt90) cc_final: 0.4247 (ptt-90) REVERT: A 826 TYR cc_start: 0.7573 (p90) cc_final: 0.7096 (p90) REVERT: A 873 ARG cc_start: 0.3081 (ttt180) cc_final: 0.2866 (mmm160) REVERT: B 181 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7505 (m-40) REVERT: J 44 TYR cc_start: 0.4031 (OUTLIER) cc_final: 0.3518 (m-10) REVERT: J 314 MET cc_start: 0.1771 (mpp) cc_final: 0.1394 (mtt) outliers start: 43 outliers final: 20 residues processed: 202 average time/residue: 0.2730 time to fit residues: 84.9217 Evaluate side-chains 182 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 157 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain J residue 44 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 50 optimal weight: 0.1980 chunk 181 optimal weight: 40.0000 chunk 196 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 731 HIS B 420 HIS B 735 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16948 Z= 0.233 Angle : 0.529 7.547 22905 Z= 0.271 Chirality : 0.041 0.170 2580 Planarity : 0.004 0.059 2843 Dihedral : 9.816 174.649 2440 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.01 % Allowed : 22.33 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.19), residues: 2005 helix: 2.12 (0.15), residues: 1146 sheet: 1.26 (0.39), residues: 169 loop : -0.78 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 152 HIS 0.006 0.001 HIS E 198 PHE 0.020 0.002 PHE E 105 TYR 0.022 0.001 TYR B 245 ARG 0.005 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 166 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 TYR cc_start: 0.5588 (OUTLIER) cc_final: 0.4207 (t80) REVERT: A 268 MET cc_start: 0.6338 (tpp) cc_final: 0.6110 (tpp) REVERT: A 689 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7157 (tt) REVERT: A 722 GLU cc_start: 0.6099 (mp0) cc_final: 0.5831 (mp0) REVERT: A 735 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7869 (t0) REVERT: A 783 ARG cc_start: 0.6453 (mtt90) cc_final: 0.4257 (ptt-90) REVERT: B 181 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.7670 (m-40) REVERT: B 702 ILE cc_start: 0.5258 (OUTLIER) cc_final: 0.4866 (mt) REVERT: J 44 TYR cc_start: 0.4105 (OUTLIER) cc_final: 0.3556 (m-10) REVERT: J 314 MET cc_start: 0.1990 (mpp) cc_final: 0.1553 (mtt) outliers start: 71 outliers final: 43 residues processed: 223 average time/residue: 0.2523 time to fit residues: 87.8569 Evaluate side-chains 206 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 157 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 223 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 0.0870 chunk 136 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 20 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 182 optimal weight: 8.9990 chunk 193 optimal weight: 0.0000 chunk 95 optimal weight: 2.9990 chunk 173 optimal weight: 50.0000 chunk 52 optimal weight: 0.9990 overall best weight: 0.9766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS B 420 HIS B 735 ASN C 59 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16948 Z= 0.174 Angle : 0.480 7.755 22905 Z= 0.247 Chirality : 0.040 0.138 2580 Planarity : 0.004 0.051 2843 Dihedral : 9.680 175.299 2440 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.50 % Allowed : 23.69 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.19), residues: 2005 helix: 2.21 (0.15), residues: 1150 sheet: 1.30 (0.39), residues: 169 loop : -0.77 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 668 HIS 0.003 0.001 HIS E 198 PHE 0.019 0.001 PHE E 105 TYR 0.024 0.001 TYR B 245 ARG 0.005 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 168 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 TYR cc_start: 0.5301 (OUTLIER) cc_final: 0.4020 (t80) REVERT: A 419 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.7200 (p90) REVERT: A 451 MET cc_start: 0.4433 (tpt) cc_final: 0.3532 (tmm) REVERT: A 689 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7147 (tt) REVERT: A 735 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7833 (t0) REVERT: A 783 ARG cc_start: 0.6509 (mtt90) cc_final: 0.4255 (ptt-90) REVERT: B 181 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.7637 (m-40) REVERT: B 408 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6307 (mpt) REVERT: E 144 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.6977 (mtpt) REVERT: J 44 TYR cc_start: 0.4064 (OUTLIER) cc_final: 0.3511 (m-10) REVERT: J 155 ASP cc_start: 0.6717 (p0) cc_final: 0.6214 (t70) outliers start: 62 outliers final: 40 residues processed: 222 average time/residue: 0.2612 time to fit residues: 89.8535 Evaluate side-chains 204 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 156 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 338 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 143 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 164 optimal weight: 0.0980 chunk 133 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 98 optimal weight: 5.9990 chunk 173 optimal weight: 50.0000 chunk 48 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS B 420 HIS B 735 ASN B 879 ASN C 59 GLN J 267 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16948 Z= 0.158 Angle : 0.468 9.843 22905 Z= 0.241 Chirality : 0.039 0.141 2580 Planarity : 0.004 0.052 2843 Dihedral : 9.531 177.486 2440 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.84 % Allowed : 23.46 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.19), residues: 2005 helix: 2.30 (0.15), residues: 1149 sheet: 1.34 (0.39), residues: 169 loop : -0.75 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 740 HIS 0.003 0.000 HIS E 198 PHE 0.018 0.001 PHE E 105 TYR 0.025 0.001 TYR B 245 ARG 0.006 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 170 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 TYR cc_start: 0.5359 (OUTLIER) cc_final: 0.4041 (t80) REVERT: A 689 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7152 (tt) REVERT: A 735 ASN cc_start: 0.8045 (OUTLIER) cc_final: 0.7803 (t0) REVERT: A 783 ARG cc_start: 0.6493 (mtt90) cc_final: 0.4236 (ptt-90) REVERT: A 836 ARG cc_start: 0.5409 (mtt90) cc_final: 0.4342 (mtm110) REVERT: B 408 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6349 (mpt) REVERT: B 740 TRP cc_start: 0.7171 (m-10) cc_final: 0.6758 (m-10) REVERT: B 795 TRP cc_start: 0.7512 (OUTLIER) cc_final: 0.6359 (t-100) REVERT: B 831 ARG cc_start: 0.6386 (mtm180) cc_final: 0.6166 (ttp-170) REVERT: J 155 ASP cc_start: 0.6831 (p0) cc_final: 0.6186 (t70) outliers start: 68 outliers final: 51 residues processed: 224 average time/residue: 0.2695 time to fit residues: 93.6502 Evaluate side-chains 219 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 163 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 795 TRP Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 169 GLU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 75 HIS Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 338 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 193 optimal weight: 0.0980 chunk 160 optimal weight: 0.0980 chunk 89 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS B 420 HIS C 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16948 Z= 0.137 Angle : 0.458 9.092 22905 Z= 0.234 Chirality : 0.039 0.143 2580 Planarity : 0.004 0.052 2843 Dihedral : 9.416 179.161 2440 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.50 % Allowed : 23.74 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.19), residues: 2005 helix: 2.34 (0.15), residues: 1155 sheet: 1.33 (0.39), residues: 169 loop : -0.73 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 668 HIS 0.002 0.000 HIS C 139 PHE 0.018 0.001 PHE A 369 TYR 0.025 0.001 TYR B 245 ARG 0.008 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 175 time to evaluate : 2.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 TYR cc_start: 0.5271 (OUTLIER) cc_final: 0.3984 (t80) REVERT: A 369 PHE cc_start: 0.6966 (t80) cc_final: 0.6595 (t80) REVERT: A 451 MET cc_start: 0.4299 (tpt) cc_final: 0.3573 (tmm) REVERT: A 689 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7134 (tt) REVERT: A 735 ASN cc_start: 0.8012 (OUTLIER) cc_final: 0.7805 (t0) REVERT: A 779 PHE cc_start: 0.5550 (m-80) cc_final: 0.4633 (m-80) REVERT: A 780 ARG cc_start: 0.5008 (mtm-85) cc_final: 0.4658 (mmm160) REVERT: A 783 ARG cc_start: 0.6523 (mtt90) cc_final: 0.4189 (ptt-90) REVERT: A 826 TYR cc_start: 0.7890 (p90) cc_final: 0.7388 (p90) REVERT: A 836 ARG cc_start: 0.5423 (mtt90) cc_final: 0.4330 (mtm110) REVERT: B 408 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6351 (mpt) REVERT: B 795 TRP cc_start: 0.7558 (OUTLIER) cc_final: 0.6425 (t-100) REVERT: E 144 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.6931 (mtpt) REVERT: J 155 ASP cc_start: 0.6812 (p0) cc_final: 0.6216 (t70) outliers start: 62 outliers final: 41 residues processed: 224 average time/residue: 0.2714 time to fit residues: 92.9265 Evaluate side-chains 210 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 163 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 795 TRP Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 75 HIS Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 338 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 110 optimal weight: 0.3980 chunk 141 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 192 optimal weight: 9.9990 chunk 120 optimal weight: 0.1980 chunk 117 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 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 96 GLN A 731 HIS B 420 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16948 Z= 0.182 Angle : 0.495 14.341 22905 Z= 0.251 Chirality : 0.040 0.144 2580 Planarity : 0.004 0.052 2843 Dihedral : 9.323 173.661 2440 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.13 % Allowed : 23.63 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.19), residues: 2005 helix: 2.22 (0.15), residues: 1150 sheet: 1.41 (0.40), residues: 169 loop : -0.74 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 152 HIS 0.003 0.001 HIS E 198 PHE 0.018 0.001 PHE E 105 TYR 0.025 0.001 TYR B 245 ARG 0.007 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 172 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 TYR cc_start: 0.5473 (OUTLIER) cc_final: 0.4158 (t80) REVERT: A 369 PHE cc_start: 0.7003 (t80) cc_final: 0.6647 (t80) REVERT: A 419 TYR cc_start: 0.7604 (OUTLIER) cc_final: 0.7139 (p90) REVERT: A 451 MET cc_start: 0.4387 (tpt) cc_final: 0.3564 (tmm) REVERT: A 689 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7182 (tt) REVERT: A 735 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7848 (t0) REVERT: A 779 PHE cc_start: 0.5473 (m-80) cc_final: 0.4533 (m-80) REVERT: A 783 ARG cc_start: 0.6479 (mtt90) cc_final: 0.4133 (ptt-90) REVERT: A 826 TYR cc_start: 0.7984 (p90) cc_final: 0.7546 (p90) REVERT: A 836 ARG cc_start: 0.5414 (mtt90) cc_final: 0.4313 (mtm110) REVERT: B 189 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8292 (tt) REVERT: B 408 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6384 (mpt) REVERT: B 795 TRP cc_start: 0.7582 (OUTLIER) cc_final: 0.6404 (t-100) REVERT: E 144 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6960 (mtpt) REVERT: J 155 ASP cc_start: 0.6832 (p0) cc_final: 0.6186 (t70) outliers start: 73 outliers final: 51 residues processed: 230 average time/residue: 0.2430 time to fit residues: 88.0260 Evaluate side-chains 222 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 163 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 795 TRP Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 169 GLU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 75 HIS Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 338 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 131 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 151 optimal weight: 3.9990 chunk 175 optimal weight: 40.0000 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS B 420 HIS B 735 ASN B 786 ASN C 59 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16948 Z= 0.155 Angle : 0.476 12.856 22905 Z= 0.242 Chirality : 0.039 0.145 2580 Planarity : 0.004 0.052 2843 Dihedral : 9.220 171.093 2440 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.56 % Allowed : 24.31 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.19), residues: 2005 helix: 2.28 (0.15), residues: 1154 sheet: 1.45 (0.40), residues: 169 loop : -0.71 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 740 HIS 0.002 0.000 HIS E 198 PHE 0.020 0.001 PHE B 369 TYR 0.026 0.001 TYR B 245 ARG 0.008 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 173 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 TYR cc_start: 0.5373 (OUTLIER) cc_final: 0.4082 (t80) REVERT: A 369 PHE cc_start: 0.6958 (t80) cc_final: 0.6624 (t80) REVERT: A 419 TYR cc_start: 0.7553 (OUTLIER) cc_final: 0.7051 (p90) REVERT: A 451 MET cc_start: 0.4264 (tpt) cc_final: 0.3513 (tmm) REVERT: A 689 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7159 (tt) REVERT: A 722 GLU cc_start: 0.6105 (mp0) cc_final: 0.5702 (mp0) REVERT: A 735 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7805 (t0) REVERT: A 783 ARG cc_start: 0.6338 (mtt90) cc_final: 0.4059 (ptt-90) REVERT: A 826 TYR cc_start: 0.7953 (p90) cc_final: 0.7499 (p90) REVERT: B 181 ASN cc_start: 0.8265 (OUTLIER) cc_final: 0.7588 (m-40) REVERT: B 408 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6338 (mpt) REVERT: B 740 TRP cc_start: 0.7149 (m-10) cc_final: 0.6906 (m-10) REVERT: B 795 TRP cc_start: 0.7554 (OUTLIER) cc_final: 0.6357 (t-100) REVERT: E 144 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.6955 (mtpt) outliers start: 63 outliers final: 48 residues processed: 224 average time/residue: 0.2501 time to fit residues: 89.8536 Evaluate side-chains 215 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 159 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 795 TRP Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 169 GLU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 75 HIS Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 338 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 20.0000 chunk 168 optimal weight: 7.9990 chunk 179 optimal weight: 0.2980 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 141 optimal weight: 0.0060 chunk 55 optimal weight: 0.4980 chunk 162 optimal weight: 3.9990 chunk 169 optimal weight: 20.0000 chunk 117 optimal weight: 0.9990 chunk 189 optimal weight: 8.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS B 420 HIS B 735 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16948 Z= 0.155 Angle : 0.479 12.365 22905 Z= 0.243 Chirality : 0.039 0.146 2580 Planarity : 0.004 0.052 2843 Dihedral : 9.087 168.306 2438 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.39 % Allowed : 24.76 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.19), residues: 2005 helix: 2.30 (0.15), residues: 1153 sheet: 1.46 (0.40), residues: 169 loop : -0.72 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 152 HIS 0.002 0.000 HIS E 198 PHE 0.021 0.001 PHE A 779 TYR 0.028 0.001 TYR B 245 ARG 0.009 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 167 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 TYR cc_start: 0.5381 (OUTLIER) cc_final: 0.4050 (t80) REVERT: A 291 MET cc_start: 0.4790 (mpp) cc_final: 0.4523 (tmm) REVERT: A 419 TYR cc_start: 0.7506 (OUTLIER) cc_final: 0.7005 (p90) REVERT: A 689 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7151 (tt) REVERT: A 735 ASN cc_start: 0.8034 (OUTLIER) cc_final: 0.7792 (t0) REVERT: A 783 ARG cc_start: 0.6321 (mtt90) cc_final: 0.4060 (ptt-90) REVERT: A 826 TYR cc_start: 0.7961 (p90) cc_final: 0.7515 (p90) REVERT: B 408 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6329 (mpt) REVERT: B 740 TRP cc_start: 0.7189 (m-10) cc_final: 0.6870 (m-10) REVERT: B 795 TRP cc_start: 0.7564 (OUTLIER) cc_final: 0.6384 (t-100) REVERT: E 144 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.6957 (mtpt) REVERT: J 155 ASP cc_start: 0.6858 (p0) cc_final: 0.5975 (t70) outliers start: 60 outliers final: 52 residues processed: 218 average time/residue: 0.2504 time to fit residues: 86.3291 Evaluate side-chains 222 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 163 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 795 TRP Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 169 GLU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 75 HIS Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 338 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 chunk 132 optimal weight: 5.9990 chunk 199 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 16 optimal weight: 0.3980 chunk 122 optimal weight: 0.2980 chunk 97 optimal weight: 0.6980 chunk 126 optimal weight: 0.0470 chunk 169 optimal weight: 4.9990 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 731 HIS ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 420 HIS B 735 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16948 Z= 0.131 Angle : 0.470 12.222 22905 Z= 0.237 Chirality : 0.039 0.142 2580 Planarity : 0.004 0.052 2843 Dihedral : 8.938 168.460 2438 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.32 % Allowed : 25.72 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 2.02 (0.19), residues: 2005 helix: 2.45 (0.15), residues: 1156 sheet: 1.52 (0.41), residues: 169 loop : -0.73 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 152 HIS 0.001 0.000 HIS A 233 PHE 0.020 0.001 PHE C 161 TYR 0.029 0.001 TYR B 245 ARG 0.009 0.000 ARG B 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 172 time to evaluate : 2.069 Fit side-chains revert: symmetry clash REVERT: A 96 GLN cc_start: 0.6733 (mm-40) cc_final: 0.6348 (mm110) REVERT: A 291 MET cc_start: 0.4798 (mpp) cc_final: 0.4505 (tmm) REVERT: A 451 MET cc_start: 0.3973 (tpt) cc_final: 0.3424 (tmm) REVERT: A 689 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7112 (tt) REVERT: A 783 ARG cc_start: 0.6254 (mtt90) cc_final: 0.4047 (ptt-90) REVERT: A 826 TYR cc_start: 0.7838 (p90) cc_final: 0.7399 (p90) REVERT: B 740 TRP cc_start: 0.7096 (m-10) cc_final: 0.6846 (m-10) REVERT: B 795 TRP cc_start: 0.7516 (OUTLIER) cc_final: 0.6385 (t-100) REVERT: E 144 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6943 (mtpt) REVERT: J 155 ASP cc_start: 0.6839 (p0) cc_final: 0.5940 (t70) outliers start: 41 outliers final: 31 residues processed: 204 average time/residue: 0.2620 time to fit residues: 83.9662 Evaluate side-chains 200 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 166 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 795 TRP Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 75 HIS Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 338 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 163 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS B 420 HIS B 735 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5191 r_free = 0.5191 target = 0.263452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5157 r_free = 0.5157 target = 0.259469 restraints weight = 19988.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.241947 restraints weight = 45408.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.239697 restraints weight = 46669.476| |-----------------------------------------------------------------------------| r_work (final): 0.4923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16948 Z= 0.218 Angle : 0.526 12.092 22905 Z= 0.267 Chirality : 0.041 0.142 2580 Planarity : 0.004 0.052 2843 Dihedral : 8.998 162.021 2438 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.71 % Allowed : 25.55 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.19), residues: 2005 helix: 2.17 (0.15), residues: 1153 sheet: 1.51 (0.41), residues: 169 loop : -0.72 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 152 HIS 0.005 0.001 HIS E 198 PHE 0.027 0.001 PHE A 369 TYR 0.028 0.001 TYR B 245 ARG 0.010 0.000 ARG B 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2998.00 seconds wall clock time: 55 minutes 41.61 seconds (3341.61 seconds total)