Starting phenix.real_space_refine on Sun Mar 17 07:03:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8goo_34178/03_2024/8goo_34178_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8goo_34178/03_2024/8goo_34178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8goo_34178/03_2024/8goo_34178.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8goo_34178/03_2024/8goo_34178.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8goo_34178/03_2024/8goo_34178_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8goo_34178/03_2024/8goo_34178_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 36 5.16 5 C 10741 2.51 5 N 2894 2.21 5 O 3280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16966 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2725 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 316} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2725 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 316} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2717 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 316} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1479 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1359 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "G" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 95 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'TPO:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1479 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1359 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "M" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1479 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "N" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1359 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "U" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 95 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'TPO:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "V" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 95 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'TPO:plan-1': 3} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 9.28, per 1000 atoms: 0.55 Number of scatterers: 16966 At special positions: 0 Unit cell: (188.554, 188.554, 98.6473, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 15 15.00 O 3280 8.00 N 2894 7.00 C 10741 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 206 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 25 " - pdb=" SG CYS M 99 " distance=2.03 Simple disulfide: pdb=" SG CYS M 150 " - pdb=" SG CYS M 206 " distance=2.03 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 89 " 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=0, symmetry=0 Time building additional restraints: 5.98 Conformation dependent library (CDL) restraints added in 2.5 seconds 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4182 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 42 sheets defined 4.2% alpha, 37.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 100 through 109 Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'E' and resid 123 through 128 Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'L' and resid 123 through 128 Processing helix chain 'L' and resid 184 through 189 Processing helix chain 'M' and resid 65 through 67 No H-bonds generated for 'chain 'M' and resid 65 through 67' Processing helix chain 'M' and resid 91 through 93 No H-bonds generated for 'chain 'M' and resid 91 through 93' Processing helix chain 'N' and resid 123 through 128 Processing helix chain 'N' and resid 184 through 189 Processing sheet with id= A, first strand: chain 'A' and resid 10 through 13 removed outlier: 3.520A pdb=" N VAL A 38 " --> pdb=" O PHE A 118 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 27 through 30 removed outlier: 6.734A pdb=" N ARG A 170 " --> pdb=" O PHE A 28 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ASP A 30 " --> pdb=" O ARG A 170 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL A 172 " --> pdb=" O ASP A 30 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 165 through 167 removed outlier: 6.604A pdb=" N VAL A 56 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLN A 86 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU A 58 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASN A 84 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL A 60 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ILE A 82 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 128 through 130 Processing sheet with id= E, first strand: chain 'A' and resid 184 through 190 Processing sheet with id= F, first strand: chain 'A' and resid 336 through 342 removed outlier: 3.722A pdb=" N VAL A 336 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR A 322 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 232 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 255 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLN A 238 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ALA A 240 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LYS A 251 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE A 242 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLN A 249 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.520A pdb=" N VAL B 38 " --> pdb=" O PHE B 118 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 27 through 30 removed outlier: 6.733A pdb=" N ARG B 170 " --> pdb=" O PHE B 28 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ASP B 30 " --> pdb=" O ARG B 170 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL B 172 " --> pdb=" O ASP B 30 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 165 through 167 removed outlier: 6.605A pdb=" N VAL B 56 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N GLN B 86 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU B 58 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ASN B 84 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL B 60 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE B 82 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 128 through 130 Processing sheet with id= K, first strand: chain 'B' and resid 184 through 190 Processing sheet with id= L, first strand: chain 'B' and resid 336 through 342 removed outlier: 3.722A pdb=" N VAL B 336 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR B 322 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 232 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA B 255 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLN B 238 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ALA B 240 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LYS B 251 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 242 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLN B 249 " --> pdb=" O ILE B 242 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.520A pdb=" N VAL C 38 " --> pdb=" O PHE C 118 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 27 through 30 removed outlier: 6.733A pdb=" N ARG C 170 " --> pdb=" O PHE C 28 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N ASP C 30 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL C 172 " --> pdb=" O ASP C 30 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 165 through 167 removed outlier: 6.605A pdb=" N VAL C 56 " --> pdb=" O GLN C 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLN C 86 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU C 58 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASN C 84 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL C 60 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE C 82 " --> pdb=" O VAL C 60 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 128 through 130 Processing sheet with id= Q, first strand: chain 'C' and resid 184 through 190 Processing sheet with id= R, first strand: chain 'C' and resid 336 through 342 removed outlier: 3.721A pdb=" N VAL C 336 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR C 322 " --> pdb=" O PHE C 342 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE C 232 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA C 255 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLN C 238 " --> pdb=" O PRO C 253 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ALA C 240 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LYS C 251 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE C 242 " --> pdb=" O GLN C 249 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLN C 249 " --> pdb=" O ILE C 242 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 6 through 10 removed outlier: 3.528A pdb=" N GLN D 6 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER D 28 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 8 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET D 86 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR D 81 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 13 through 15 removed outlier: 4.237A pdb=" N GLY D 13 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR D 120 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE D 37 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA D 52 " --> pdb=" O TRP D 39 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 130 through 134 removed outlier: 6.078A pdb=" N TYR D 186 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER D 189 " --> pdb=" O PHE D 176 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 161 through 163 Processing sheet with id= W, first strand: chain 'E' and resid 5 through 8 removed outlier: 4.622A pdb=" N VAL E 20 " --> pdb=" O ILE E 76 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE E 76 " --> pdb=" O VAL E 20 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 12 through 14 removed outlier: 3.787A pdb=" N GLU E 106 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 86 through 91 removed outlier: 3.709A pdb=" N THR E 86 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 115 through 119 removed outlier: 3.733A pdb=" N ASN E 138 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR E 174 " --> pdb=" O ASN E 139 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.528A pdb=" N GLN H 6 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER H 28 " --> pdb=" O GLN H 6 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL H 8 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET H 86 " --> pdb=" O LEU H 21 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'H' and resid 13 through 15 removed outlier: 4.238A pdb=" N GLY H 13 " --> pdb=" O LEU H 118 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR H 120 " --> pdb=" O GLY H 13 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE H 37 " --> pdb=" O ILE H 54 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.078A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER H 189 " --> pdb=" O PHE H 176 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 161 through 163 Processing sheet with id= AE, first strand: chain 'L' and resid 5 through 8 removed outlier: 4.621A pdb=" N VAL L 20 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE L 76 " --> pdb=" O VAL L 20 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'L' and resid 12 through 14 removed outlier: 3.787A pdb=" N GLU L 106 " --> pdb=" O LEU L 12 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'L' and resid 86 through 91 removed outlier: 3.710A pdb=" N THR L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.734A pdb=" N ASN L 138 " --> pdb=" O SER L 115 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'M' and resid 6 through 10 removed outlier: 3.527A pdb=" N GLN M 6 " --> pdb=" O SER M 28 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER M 28 " --> pdb=" O GLN M 6 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL M 8 " --> pdb=" O ALA M 26 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET M 86 " --> pdb=" O LEU M 21 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR M 81 " --> pdb=" O ASP M 76 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'M' and resid 13 through 15 removed outlier: 4.237A pdb=" N GLY M 13 " --> pdb=" O LEU M 118 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR M 120 " --> pdb=" O GLY M 13 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE M 37 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA M 52 " --> pdb=" O TRP M 39 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ARG M 41 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N TRP M 50 " --> pdb=" O ARG M 41 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'M' and resid 130 through 134 removed outlier: 6.078A pdb=" N TYR M 186 " --> pdb=" O ASP M 154 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER M 189 " --> pdb=" O PHE M 176 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'M' and resid 161 through 163 Processing sheet with id= AM, first strand: chain 'N' and resid 5 through 8 removed outlier: 4.623A pdb=" N VAL N 20 " --> pdb=" O ILE N 76 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE N 76 " --> pdb=" O VAL N 20 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'N' and resid 12 through 14 removed outlier: 3.788A pdb=" N GLU N 106 " --> pdb=" O LEU N 12 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'N' and resid 86 through 91 removed outlier: 3.709A pdb=" N THR N 86 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLN N 38 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU N 47 " --> pdb=" O GLN N 38 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'N' and resid 115 through 119 removed outlier: 3.734A pdb=" N ASN N 138 " --> pdb=" O SER N 115 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR N 174 " --> pdb=" O ASN N 139 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1503 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.58 Time building geometry restraints manager: 6.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5463 1.35 - 1.46: 4075 1.46 - 1.58: 7742 1.58 - 1.70: 37 1.70 - 1.81: 48 Bond restraints: 17365 Sorted by residual: bond pdb=" OG1 TPO U 339 " pdb=" P TPO U 339 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" OG1 TPO U 342 " pdb=" P TPO U 342 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" OG1 TPO G 342 " pdb=" P TPO G 342 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" OG1 TPO V 342 " pdb=" P TPO V 342 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" OG1 TPO G 339 " pdb=" P TPO G 339 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.80e+01 ... (remaining 17360 not shown) Histogram of bond angle deviations from ideal: 99.85 - 106.68: 637 106.68 - 113.51: 9569 113.51 - 120.34: 5637 120.34 - 127.17: 7637 127.17 - 134.00: 193 Bond angle restraints: 23673 Sorted by residual: angle pdb=" N GLU B 339 " pdb=" CA GLU B 339 " pdb=" C GLU B 339 " ideal model delta sigma weight residual 109.85 117.22 -7.37 1.58e+00 4.01e-01 2.18e+01 angle pdb=" CA GLU B 339 " pdb=" C GLU B 339 " pdb=" O GLU B 339 " ideal model delta sigma weight residual 121.46 116.63 4.83 1.17e+00 7.31e-01 1.70e+01 angle pdb=" N GLU B 339 " pdb=" CA GLU B 339 " pdb=" CB GLU B 339 " ideal model delta sigma weight residual 111.20 104.69 6.51 1.62e+00 3.81e-01 1.62e+01 angle pdb=" CB TPO G 339 " pdb=" OG1 TPO G 339 " pdb=" P TPO G 339 " ideal model delta sigma weight residual 119.31 107.78 11.53 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C LEU A 49 " pdb=" N LYS A 50 " pdb=" CA LYS A 50 " ideal model delta sigma weight residual 121.54 128.81 -7.27 1.91e+00 2.74e-01 1.45e+01 ... (remaining 23668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 9490 17.54 - 35.07: 799 35.07 - 52.61: 90 52.61 - 70.14: 12 70.14 - 87.68: 12 Dihedral angle restraints: 10403 sinusoidal: 3920 harmonic: 6483 Sorted by residual: dihedral pdb=" CA PRO A 95 " pdb=" C PRO A 95 " pdb=" N ARG A 96 " pdb=" CA ARG A 96 " ideal model delta harmonic sigma weight residual 0.00 -33.16 33.16 0 5.00e+00 4.00e-02 4.40e+01 dihedral pdb=" CA PRO B 95 " pdb=" C PRO B 95 " pdb=" N ARG B 96 " pdb=" CA ARG B 96 " ideal model delta harmonic sigma weight residual 0.00 -33.16 33.16 0 5.00e+00 4.00e-02 4.40e+01 dihedral pdb=" CA PRO C 95 " pdb=" C PRO C 95 " pdb=" N ARG C 96 " pdb=" CA ARG C 96 " ideal model delta harmonic sigma weight residual 0.00 -33.10 33.10 0 5.00e+00 4.00e-02 4.38e+01 ... (remaining 10400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1963 0.040 - 0.079: 434 0.079 - 0.119: 265 0.119 - 0.159: 22 0.159 - 0.199: 7 Chirality restraints: 2691 Sorted by residual: chirality pdb=" CB TPO V 342 " pdb=" CA TPO V 342 " pdb=" OG1 TPO V 342 " pdb=" CG2 TPO V 342 " both_signs ideal model delta sigma weight residual False 2.48 2.68 -0.20 2.00e-01 2.50e+01 9.85e-01 chirality pdb=" CA VAL V 340 " pdb=" N VAL V 340 " pdb=" C VAL V 340 " pdb=" CB VAL V 340 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.58e-01 chirality pdb=" CB TPO U 342 " pdb=" CA TPO U 342 " pdb=" OG1 TPO U 342 " pdb=" CG2 TPO U 342 " both_signs ideal model delta sigma weight residual False 2.48 2.67 -0.19 2.00e-01 2.50e+01 8.58e-01 ... (remaining 2688 not shown) Planarity restraints: 3032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 91 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO B 92 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 92 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 92 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 91 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO A 92 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 92 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 92 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 91 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO C 92 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 92 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 92 " -0.026 5.00e-02 4.00e+02 ... (remaining 3029 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1810 2.76 - 3.29: 16355 3.29 - 3.83: 27334 3.83 - 4.36: 29863 4.36 - 4.90: 52898 Nonbonded interactions: 128260 Sorted by model distance: nonbonded pdb=" OG SER L 64 " pdb=" OG1 THR L 75 " model vdw 2.221 2.440 nonbonded pdb=" OG SER E 64 " pdb=" OG1 THR E 75 " model vdw 2.221 2.440 nonbonded pdb=" OG SER N 64 " pdb=" OG1 THR N 75 " model vdw 2.221 2.440 nonbonded pdb=" O GLY B 212 " pdb=" ND2 ASN H 31 " model vdw 2.240 2.520 nonbonded pdb=" OG SER N 8 " pdb=" OG1 THR N 23 " model vdw 2.255 2.440 ... (remaining 128255 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 307 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 313 or (resid 314 and (name N or \ name CA or name C or name O or name CB )) or resid 315 through 350)) selection = (chain 'B' and (resid 7 through 307 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 313 or (resid 314 and (name N or \ name CA or name C or name O or name CB )) or resid 315 through 350)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'U' selection = chain 'V' } 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=0.00 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: 2.730 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: 10.620 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 45.950 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.130 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 0.111 17365 Z= 0.314 Angle : 0.660 11.533 23673 Z= 0.308 Chirality : 0.044 0.199 2691 Planarity : 0.004 0.047 3032 Dihedral : 12.857 87.676 6194 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.96 % Favored : 94.90 % Rotamer: Outliers : 0.49 % Allowed : 0.66 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.19), residues: 2157 helix: 2.06 (0.61), residues: 78 sheet: 1.28 (0.17), residues: 996 loop : -0.63 (0.20), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 36 HIS 0.002 0.000 HIS A 346 PHE 0.009 0.001 PHE M 30 TYR 0.007 0.001 TYR N 174 ARG 0.004 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 ASN cc_start: 0.8558 (t0) cc_final: 0.8194 (t0) REVERT: H 31 ASN cc_start: 0.8440 (t0) cc_final: 0.7957 (t0) REVERT: M 31 ASN cc_start: 0.8513 (t0) cc_final: 0.7925 (t0) REVERT: N 94 TYR cc_start: 0.8285 (m-80) cc_final: 0.7894 (m-10) REVERT: N 137 LEU cc_start: 0.8941 (mm) cc_final: 0.8708 (mm) outliers start: 9 outliers final: 3 residues processed: 109 average time/residue: 0.2914 time to fit residues: 49.0311 Evaluate side-chains 78 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 184 optimal weight: 1.9990 chunk 165 optimal weight: 0.1980 chunk 92 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 171 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 198 optimal weight: 8.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17365 Z= 0.176 Angle : 0.551 6.321 23673 Z= 0.278 Chirality : 0.043 0.142 2691 Planarity : 0.004 0.044 3032 Dihedral : 4.464 47.660 2427 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.45 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.19), residues: 2157 helix: 1.87 (0.60), residues: 78 sheet: 1.19 (0.17), residues: 969 loop : -0.66 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 36 HIS 0.003 0.001 HIS C 199 PHE 0.011 0.001 PHE B 145 TYR 0.011 0.001 TYR M 98 ARG 0.005 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.9034 (mm) cc_final: 0.8723 (mm) REVERT: D 31 ASN cc_start: 0.8715 (t0) cc_final: 0.8312 (t0) REVERT: D 214 ASN cc_start: 0.8986 (m-40) cc_final: 0.8785 (m-40) REVERT: E 55 LEU cc_start: 0.8856 (tp) cc_final: 0.8642 (tt) REVERT: H 31 ASN cc_start: 0.8783 (t0) cc_final: 0.8423 (t0) REVERT: H 73 ILE cc_start: 0.8907 (tp) cc_final: 0.8585 (pt) REVERT: L 55 LEU cc_start: 0.8928 (tp) cc_final: 0.8683 (tt) REVERT: M 31 ASN cc_start: 0.8701 (t0) cc_final: 0.8226 (t0) REVERT: M 214 ASN cc_start: 0.8858 (m-40) cc_final: 0.8645 (m-40) REVERT: N 94 TYR cc_start: 0.8376 (m-80) cc_final: 0.7923 (m-10) REVERT: N 137 LEU cc_start: 0.9034 (mm) cc_final: 0.8791 (mm) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.2315 time to fit residues: 36.9267 Evaluate side-chains 67 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 135 optimal weight: 20.0000 chunk 54 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 215 optimal weight: 0.0030 chunk 177 optimal weight: 0.0770 chunk 197 optimal weight: 30.0000 chunk 67 optimal weight: 0.9980 chunk 159 optimal weight: 7.9990 overall best weight: 0.8152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17365 Z= 0.155 Angle : 0.547 7.278 23673 Z= 0.270 Chirality : 0.043 0.158 2691 Planarity : 0.004 0.047 3032 Dihedral : 4.387 44.820 2427 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.45 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.18), residues: 2157 helix: 1.65 (0.58), residues: 78 sheet: 1.08 (0.16), residues: 987 loop : -0.64 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 36 HIS 0.002 0.001 HIS C 199 PHE 0.007 0.001 PHE B 117 TYR 0.009 0.001 TYR M 98 ARG 0.007 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 2.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.9034 (mm) cc_final: 0.8642 (mm) REVERT: B 58 LEU cc_start: 0.9197 (mm) cc_final: 0.8761 (mm) REVERT: B 209 TYR cc_start: 0.6128 (m-10) cc_final: 0.5924 (m-10) REVERT: C 58 LEU cc_start: 0.9120 (mm) cc_final: 0.8694 (mm) REVERT: D 31 ASN cc_start: 0.8737 (t0) cc_final: 0.8342 (t0) REVERT: D 214 ASN cc_start: 0.8757 (m-40) cc_final: 0.8512 (m-40) REVERT: E 55 LEU cc_start: 0.8892 (tp) cc_final: 0.8634 (tt) REVERT: H 31 ASN cc_start: 0.8768 (t0) cc_final: 0.8385 (t0) REVERT: H 73 ILE cc_start: 0.8884 (tp) cc_final: 0.8648 (pt) REVERT: M 31 ASN cc_start: 0.8638 (t0) cc_final: 0.8154 (t0) REVERT: M 214 ASN cc_start: 0.8865 (m-40) cc_final: 0.8663 (m-40) REVERT: N 55 LEU cc_start: 0.8756 (tp) cc_final: 0.8448 (tt) REVERT: N 94 TYR cc_start: 0.8264 (m-80) cc_final: 0.7843 (m-10) REVERT: N 137 LEU cc_start: 0.9008 (mm) cc_final: 0.8562 (mm) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2486 time to fit residues: 40.3284 Evaluate side-chains 66 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 196 optimal weight: 7.9990 chunk 149 optimal weight: 0.0470 chunk 103 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 95 optimal weight: 0.0980 chunk 133 optimal weight: 10.0000 chunk 199 optimal weight: 0.4980 chunk 211 optimal weight: 0.7980 chunk 104 optimal weight: 0.3980 chunk 189 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 125 GLN ** N 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17365 Z= 0.131 Angle : 0.541 8.045 23673 Z= 0.261 Chirality : 0.043 0.148 2691 Planarity : 0.004 0.044 3032 Dihedral : 4.270 39.122 2427 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.45 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.18), residues: 2157 helix: 1.61 (0.59), residues: 78 sheet: 1.00 (0.16), residues: 1014 loop : -0.61 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 36 HIS 0.002 0.000 HIS A 199 PHE 0.008 0.001 PHE C 191 TYR 0.009 0.001 TYR M 98 ARG 0.002 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.8996 (mm) cc_final: 0.8701 (mm) REVERT: B 209 TYR cc_start: 0.6151 (m-10) cc_final: 0.5895 (m-10) REVERT: D 31 ASN cc_start: 0.8661 (t0) cc_final: 0.8220 (t0) REVERT: D 214 ASN cc_start: 0.8818 (m-40) cc_final: 0.8580 (m-40) REVERT: E 55 LEU cc_start: 0.8876 (tp) cc_final: 0.8638 (tt) REVERT: E 137 LEU cc_start: 0.8872 (tt) cc_final: 0.8399 (mm) REVERT: H 31 ASN cc_start: 0.8734 (t0) cc_final: 0.8336 (t0) REVERT: H 73 ILE cc_start: 0.8859 (tp) cc_final: 0.8537 (mm) REVERT: H 214 ASN cc_start: 0.8786 (m-40) cc_final: 0.8555 (m-40) REVERT: M 31 ASN cc_start: 0.8571 (t0) cc_final: 0.8067 (t0) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2281 time to fit residues: 39.4718 Evaluate side-chains 70 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 176 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 157 optimal weight: 20.0000 chunk 87 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 190 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN B 86 GLN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 125 GLN ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 17365 Z= 0.361 Angle : 0.724 8.396 23673 Z= 0.371 Chirality : 0.047 0.234 2691 Planarity : 0.005 0.046 3032 Dihedral : 5.663 41.203 2427 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.46 % Favored : 92.40 % Rotamer: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.18), residues: 2157 helix: 1.32 (0.61), residues: 78 sheet: 0.33 (0.16), residues: 1023 loop : -0.88 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 39 HIS 0.006 0.001 HIS A 114 PHE 0.023 0.003 PHE L 99 TYR 0.024 0.002 TYR L 56 ARG 0.008 0.001 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 2.067 Fit side-chains REVERT: A 58 LEU cc_start: 0.9081 (mm) cc_final: 0.8669 (mm) REVERT: A 345 MET cc_start: 0.8393 (ppp) cc_final: 0.8144 (ppp) REVERT: C 345 MET cc_start: 0.8510 (ppp) cc_final: 0.8261 (ppp) REVERT: E 137 LEU cc_start: 0.8938 (tt) cc_final: 0.8401 (mm) REVERT: L 137 LEU cc_start: 0.9070 (tt) cc_final: 0.8659 (mm) REVERT: M 31 ASN cc_start: 0.8686 (t0) cc_final: 0.8451 (t0) REVERT: N 137 LEU cc_start: 0.8978 (tt) cc_final: 0.8441 (mm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2229 time to fit residues: 26.6414 Evaluate side-chains 45 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 71 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 211 optimal weight: 6.9990 chunk 175 optimal weight: 0.0970 chunk 98 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 0.0170 chunk 111 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17365 Z= 0.149 Angle : 0.581 7.805 23673 Z= 0.284 Chirality : 0.044 0.136 2691 Planarity : 0.004 0.047 3032 Dihedral : 4.732 40.255 2427 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.50 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.18), residues: 2157 helix: 1.09 (0.61), residues: 78 sheet: 0.72 (0.16), residues: 990 loop : -0.84 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 36 HIS 0.002 0.001 HIS M 210 PHE 0.009 0.001 PHE B 117 TYR 0.020 0.001 TYR N 94 ARG 0.003 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 2.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.9031 (mm) cc_final: 0.8793 (mm) REVERT: A 345 MET cc_start: 0.8442 (ppp) cc_final: 0.8222 (ppp) REVERT: B 345 MET cc_start: 0.8547 (ppp) cc_final: 0.8148 (ppp) REVERT: D 214 ASN cc_start: 0.8844 (m-40) cc_final: 0.8623 (m-40) REVERT: E 55 LEU cc_start: 0.9011 (tp) cc_final: 0.8734 (tt) REVERT: E 137 LEU cc_start: 0.8899 (tt) cc_final: 0.8371 (mm) REVERT: H 214 ASN cc_start: 0.8878 (m-40) cc_final: 0.8629 (m-40) REVERT: L 55 LEU cc_start: 0.8940 (tp) cc_final: 0.8655 (tt) REVERT: L 137 LEU cc_start: 0.9014 (tt) cc_final: 0.8593 (mm) REVERT: M 31 ASN cc_start: 0.8597 (t0) cc_final: 0.8387 (t0) REVERT: M 214 ASN cc_start: 0.8621 (m-40) cc_final: 0.8287 (m-40) REVERT: N 137 LEU cc_start: 0.8921 (tt) cc_final: 0.8337 (mm) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2334 time to fit residues: 34.2034 Evaluate side-chains 58 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 204 optimal weight: 0.4980 chunk 23 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 211 optimal weight: 0.0980 chunk 132 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN C 86 GLN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17365 Z= 0.354 Angle : 0.699 7.463 23673 Z= 0.356 Chirality : 0.046 0.245 2691 Planarity : 0.005 0.047 3032 Dihedral : 5.454 42.658 2427 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.70 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.18), residues: 2157 helix: 0.71 (0.60), residues: 78 sheet: 0.10 (0.16), residues: 1041 loop : -1.02 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 106 HIS 0.005 0.001 HIS C 220 PHE 0.017 0.002 PHE A 55 TYR 0.025 0.002 TYR D 107 ARG 0.007 0.001 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 2.117 Fit side-chains REVERT: A 345 MET cc_start: 0.8680 (ppp) cc_final: 0.8478 (ppp) REVERT: B 54 VAL cc_start: 0.9602 (t) cc_final: 0.9399 (p) REVERT: B 345 MET cc_start: 0.8831 (ppp) cc_final: 0.8416 (ppp) REVERT: E 137 LEU cc_start: 0.8980 (tt) cc_final: 0.8487 (mm) REVERT: L 137 LEU cc_start: 0.9120 (tt) cc_final: 0.8673 (mm) REVERT: N 137 LEU cc_start: 0.9029 (tt) cc_final: 0.8454 (mm) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2077 time to fit residues: 24.6365 Evaluate side-chains 43 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 130 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 165 optimal weight: 9.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17365 Z= 0.163 Angle : 0.582 8.540 23673 Z= 0.286 Chirality : 0.044 0.147 2691 Planarity : 0.004 0.046 3032 Dihedral : 4.821 43.410 2427 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.91 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.18), residues: 2157 helix: 0.68 (0.59), residues: 78 sheet: 0.41 (0.16), residues: 981 loop : -0.99 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 36 HIS 0.002 0.001 HIS A 220 PHE 0.021 0.001 PHE M 71 TYR 0.010 0.001 TYR M 98 ARG 0.004 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 2.205 Fit side-chains revert: symmetry clash REVERT: A 345 MET cc_start: 0.8609 (ppp) cc_final: 0.8263 (ppp) REVERT: B 345 MET cc_start: 0.8798 (ppp) cc_final: 0.8399 (ppp) REVERT: E 137 LEU cc_start: 0.8956 (tt) cc_final: 0.8432 (mp) REVERT: H 73 ILE cc_start: 0.9155 (tp) cc_final: 0.8844 (mm) REVERT: L 137 LEU cc_start: 0.9093 (tt) cc_final: 0.8690 (mp) REVERT: M 214 ASN cc_start: 0.8643 (m-40) cc_final: 0.8443 (m110) REVERT: N 137 LEU cc_start: 0.8994 (tt) cc_final: 0.8429 (mm) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.2161 time to fit residues: 29.3882 Evaluate side-chains 53 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 192 optimal weight: 0.9980 chunk 202 optimal weight: 0.9980 chunk 184 optimal weight: 0.0980 chunk 196 optimal weight: 6.9990 chunk 118 optimal weight: 40.0000 chunk 85 optimal weight: 0.4980 chunk 154 optimal weight: 0.0270 chunk 60 optimal weight: 9.9990 chunk 177 optimal weight: 0.0370 chunk 186 optimal weight: 5.9990 chunk 129 optimal weight: 0.0980 overall best weight: 0.1516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 159 ASN ** N 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17365 Z= 0.136 Angle : 0.567 8.446 23673 Z= 0.273 Chirality : 0.044 0.141 2691 Planarity : 0.004 0.044 3032 Dihedral : 4.391 43.293 2427 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.78 % Favored : 95.13 % Rotamer: Outliers : 0.05 % Allowed : 0.55 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.18), residues: 2157 helix: 0.89 (0.60), residues: 78 sheet: 0.54 (0.16), residues: 1005 loop : -0.79 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 36 HIS 0.003 0.000 HIS H 210 PHE 0.013 0.001 PHE H 71 TYR 0.009 0.001 TYR N 94 ARG 0.003 0.000 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 345 MET cc_start: 0.8621 (ppp) cc_final: 0.8280 (ppp) REVERT: D 31 ASN cc_start: 0.8709 (t0) cc_final: 0.8469 (t0) REVERT: D 214 ASN cc_start: 0.8812 (m-40) cc_final: 0.8578 (m-40) REVERT: E 5 MET cc_start: 0.7777 (tpp) cc_final: 0.7323 (tpp) REVERT: E 55 LEU cc_start: 0.8861 (tp) cc_final: 0.8637 (tt) REVERT: E 137 LEU cc_start: 0.8929 (tt) cc_final: 0.8382 (mp) REVERT: L 137 LEU cc_start: 0.9069 (tt) cc_final: 0.8649 (mp) REVERT: M 73 ILE cc_start: 0.9149 (tp) cc_final: 0.8870 (mm) REVERT: M 214 ASN cc_start: 0.8592 (m-40) cc_final: 0.8214 (m-40) REVERT: N 137 LEU cc_start: 0.8955 (tt) cc_final: 0.8393 (mm) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.2351 time to fit residues: 32.8522 Evaluate side-chains 61 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 207 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 chunk 218 optimal weight: 8.9990 chunk 200 optimal weight: 5.9990 chunk 173 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 134 optimal weight: 20.0000 chunk 106 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17365 Z= 0.154 Angle : 0.559 8.290 23673 Z= 0.271 Chirality : 0.044 0.157 2691 Planarity : 0.004 0.043 3032 Dihedral : 4.445 43.686 2427 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.18), residues: 2157 helix: 0.94 (0.61), residues: 78 sheet: 0.73 (0.16), residues: 996 loop : -0.89 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 50 HIS 0.002 0.001 HIS D 38 PHE 0.014 0.001 PHE H 71 TYR 0.010 0.001 TYR M 98 ARG 0.007 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 2.071 Fit side-chains REVERT: B 54 VAL cc_start: 0.9464 (t) cc_final: 0.9246 (p) REVERT: B 209 TYR cc_start: 0.6447 (m-10) cc_final: 0.6188 (m-10) REVERT: B 345 MET cc_start: 0.8730 (ppp) cc_final: 0.8373 (ppp) REVERT: C 96 ARG cc_start: 0.8207 (tpm170) cc_final: 0.7998 (tpm170) REVERT: D 31 ASN cc_start: 0.8735 (t0) cc_final: 0.8507 (t0) REVERT: D 214 ASN cc_start: 0.8696 (m-40) cc_final: 0.8442 (m-40) REVERT: E 5 MET cc_start: 0.7693 (tpp) cc_final: 0.7273 (tpp) REVERT: E 137 LEU cc_start: 0.8968 (tt) cc_final: 0.8473 (mp) REVERT: H 90 ARG cc_start: 0.8227 (mpp80) cc_final: 0.7713 (mpp80) REVERT: H 214 ASN cc_start: 0.8823 (m-40) cc_final: 0.8599 (m-40) REVERT: L 137 LEU cc_start: 0.9083 (tt) cc_final: 0.8631 (mp) REVERT: M 214 ASN cc_start: 0.8603 (m-40) cc_final: 0.8235 (m-40) REVERT: N 137 LEU cc_start: 0.8980 (tt) cc_final: 0.8411 (mm) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.2531 time to fit residues: 30.5018 Evaluate side-chains 58 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 185 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 174 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 ASN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.059868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.041608 restraints weight = 121522.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.042919 restraints weight = 86492.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.043225 restraints weight = 60956.630| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 17365 Z= 0.492 Angle : 0.802 9.793 23673 Z= 0.413 Chirality : 0.049 0.247 2691 Planarity : 0.006 0.061 3032 Dihedral : 5.901 45.671 2427 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 25.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.18), residues: 2157 helix: 0.01 (0.57), residues: 78 sheet: -0.07 (0.16), residues: 1026 loop : -1.28 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP D 39 HIS 0.008 0.002 HIS B 220 PHE 0.027 0.003 PHE N 99 TYR 0.031 0.003 TYR M 107 ARG 0.012 0.001 ARG M 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2656.75 seconds wall clock time: 49 minutes 49.76 seconds (2989.76 seconds total)