Starting phenix.real_space_refine on Thu Feb 15 10:11:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9b_10735/02_2024/6y9b_10735_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9b_10735/02_2024/6y9b_10735.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9b_10735/02_2024/6y9b_10735_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9b_10735/02_2024/6y9b_10735_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9b_10735/02_2024/6y9b_10735_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9b_10735/02_2024/6y9b_10735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9b_10735/02_2024/6y9b_10735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9b_10735/02_2024/6y9b_10735_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9b_10735/02_2024/6y9b_10735_updated.pdb" } resolution = 2.97 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= 0.002 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 Fe 3 7.16 5 P 3 5.49 5 S 42 5.16 5 C 7851 2.51 5 N 1887 2.21 5 O 2103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 92": "NH1" <-> "NH2" Residue "C ARG 248": "NH1" <-> "NH2" Residue "L ARG 32": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 67": "NH1" <-> "NH2" Residue "H ARG 39": "NH1" <-> "NH2" Residue "H ARG 67": "NH1" <-> "NH2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H ARG 100": "NH1" <-> "NH2" Residue "I ARG 39": "NH1" <-> "NH2" Residue "I ARG 67": "NH1" <-> "NH2" Residue "I ARG 72": "NH1" <-> "NH2" Residue "I ARG 98": "NH1" <-> "NH2" Residue "I ARG 100": "NH1" <-> "NH2" Residue "J ARG 39": "NH1" <-> "NH2" Residue "J ARG 67": "NH1" <-> "NH2" Residue "J ARG 72": "NH1" <-> "NH2" Residue "J ARG 98": "NH1" <-> "NH2" Residue "J ARG 100": "NH1" <-> "NH2" Residue "M ARG 32": "NH1" <-> "NH2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M ARG 67": "NH1" <-> "NH2" Residue "N ARG 32": "NH1" <-> "NH2" Residue "N ARG 60": "NH1" <-> "NH2" Residue "N ARG 67": "NH1" <-> "NH2" Residue "A ARG 92": "NH1" <-> "NH2" Residue "A ARG 248": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 248": "NH1" <-> "NH2" 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: 11889 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 2019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2019 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 13, 'TRANS': 230} Chain breaks: 1 Chain: "L" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 884 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107} Chain: "H" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 977 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "I" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 977 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "J" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 977 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "M" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 884 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107} Chain: "N" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 884 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107} Chain: "A" Number of atoms: 2019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2019 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 13, 'TRANS': 230} Chain breaks: 1 Chain: "B" Number of atoms: 2019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2019 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 13, 'TRANS': 230} Chain breaks: 1 Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'HEM': 1, 'XP4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'HEM': 1, 'XP4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'HEM': 1, 'XP4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.92, per 1000 atoms: 0.58 Number of scatterers: 11889 At special positions: 0 Unit cell: (104.907, 101.821, 114.163, 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) Fe 3 26.01 S 42 16.00 P 3 15.00 O 2103 8.00 N 1887 7.00 C 7851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 94 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 94 " 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.07 Conformation dependent library (CDL) restraints added in 2.3 seconds 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 15 sheets defined 41.2% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'C' and resid 69 through 93 removed outlier: 3.819A pdb=" N HIS C 72 " --> pdb=" O PRO C 69 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU C 73 " --> pdb=" O GLN C 70 " (cutoff:3.500A) Proline residue: C 74 - end of helix removed outlier: 3.597A pdb=" N ILE C 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 83 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 84 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C 87 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 90 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU C 93 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 114 through 143 Proline residue: C 119 - end of helix removed outlier: 4.064A pdb=" N TYR C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Proline residue: C 132 - end of helix removed outlier: 3.653A pdb=" N ALA C 137 " --> pdb=" O GLY C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 180 removed outlier: 3.802A pdb=" N THR C 160 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG C 161 " --> pdb=" O TRP C 157 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS C 162 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLN C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 174 " --> pdb=" O PHE C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 201 Processing helix chain 'C' and resid 210 through 237 removed outlier: 3.511A pdb=" N LEU C 230 " --> pdb=" O GLY C 226 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 244 removed outlier: 3.871A pdb=" N SER C 244 " --> pdb=" O SER C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 272 removed outlier: 3.504A pdb=" N LEU C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE C 272 " --> pdb=" O HIS C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 309 removed outlier: 3.505A pdb=" N PHE C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU C 297 " --> pdb=" O ILE C 293 " (cutoff:3.500A) Proline residue: C 298 - end of helix Processing helix chain 'L' and resid 86 through 88 No H-bonds generated for 'chain 'L' and resid 86 through 88' Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 88 through 90 No H-bonds generated for 'chain 'I' and resid 88 through 90' Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' Processing helix chain 'M' and resid 86 through 88 No H-bonds generated for 'chain 'M' and resid 86 through 88' Processing helix chain 'N' and resid 86 through 88 No H-bonds generated for 'chain 'N' and resid 86 through 88' Processing helix chain 'A' and resid 69 through 93 removed outlier: 3.818A pdb=" N HIS A 72 " --> pdb=" O PRO A 69 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LEU A 73 " --> pdb=" O GLN A 70 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 3.597A pdb=" N ILE A 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 83 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 84 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 87 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 90 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU A 93 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 114 through 143 Proline residue: A 119 - end of helix removed outlier: 4.064A pdb=" N TYR A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Proline residue: A 132 - end of helix removed outlier: 3.653A pdb=" N ALA A 137 " --> pdb=" O GLY A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 180 removed outlier: 3.802A pdb=" N THR A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG A 161 " --> pdb=" O TRP A 157 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS A 162 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLN A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 201 Processing helix chain 'A' and resid 210 through 237 removed outlier: 3.512A pdb=" N LEU A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 removed outlier: 3.871A pdb=" N SER A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 272 removed outlier: 3.504A pdb=" N LEU A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A 272 " --> pdb=" O HIS A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 309 removed outlier: 3.505A pdb=" N PHE A 296 " --> pdb=" O MET A 292 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU A 297 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Proline residue: A 298 - end of helix Processing helix chain 'B' and resid 69 through 93 removed outlier: 3.818A pdb=" N HIS B 72 " --> pdb=" O PRO B 69 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LEU B 73 " --> pdb=" O GLN B 70 " (cutoff:3.500A) Proline residue: B 74 - end of helix removed outlier: 3.597A pdb=" N ILE B 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 83 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 84 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 87 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 90 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU B 93 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 114 through 143 Proline residue: B 119 - end of helix removed outlier: 4.063A pdb=" N TYR B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Proline residue: B 132 - end of helix removed outlier: 3.652A pdb=" N ALA B 137 " --> pdb=" O GLY B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 180 removed outlier: 3.803A pdb=" N THR B 160 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG B 161 " --> pdb=" O TRP B 157 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS B 162 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLN B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 174 " --> pdb=" O PHE B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 201 Processing helix chain 'B' and resid 210 through 237 removed outlier: 3.512A pdb=" N LEU B 230 " --> pdb=" O GLY B 226 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 removed outlier: 3.872A pdb=" N SER B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 272 removed outlier: 3.503A pdb=" N LEU B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 272 " --> pdb=" O HIS B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 309 removed outlier: 3.505A pdb=" N PHE B 296 " --> pdb=" O MET B 292 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU B 297 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Proline residue: B 298 - end of helix Processing sheet with id= A, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.404A pdb=" N LYS L 109 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL L 13 " --> pdb=" O LYS L 109 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLU L 111 " --> pdb=" O VAL L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'L' and resid 19 through 24 removed outlier: 4.020A pdb=" N ASP L 76 " --> pdb=" O SER L 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'L' and resid 90 through 96 removed outlier: 6.119A pdb=" N GLN L 43 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LEU L 52 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 18 through 21 removed outlier: 3.739A pdb=" N LEU H 83 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 118 through 120 removed outlier: 6.773A pdb=" N ARG H 39 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N TRP H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE H 41 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU H 46 " --> pdb=" O PHE H 41 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'I' and resid 18 through 21 removed outlier: 3.739A pdb=" N LEU I 83 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU I 81 " --> pdb=" O LEU I 20 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'I' and resid 118 through 120 removed outlier: 6.773A pdb=" N ARG I 39 " --> pdb=" O TRP I 48 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N TRP I 48 " --> pdb=" O ARG I 39 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE I 41 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU I 46 " --> pdb=" O PHE I 41 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 18 through 21 removed outlier: 3.739A pdb=" N LEU J 83 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU J 81 " --> pdb=" O LEU J 20 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'J' and resid 118 through 120 removed outlier: 6.773A pdb=" N ARG J 39 " --> pdb=" O TRP J 48 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TRP J 48 " --> pdb=" O ARG J 39 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE J 41 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU J 46 " --> pdb=" O PHE J 41 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.403A pdb=" N LYS M 109 " --> pdb=" O LEU M 11 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL M 13 " --> pdb=" O LYS M 109 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLU M 111 " --> pdb=" O VAL M 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'M' and resid 19 through 24 removed outlier: 4.021A pdb=" N ASP M 76 " --> pdb=" O SER M 73 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'M' and resid 90 through 96 removed outlier: 6.119A pdb=" N GLN M 43 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU M 52 " --> pdb=" O GLN M 43 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.404A pdb=" N LYS N 109 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL N 13 " --> pdb=" O LYS N 109 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLU N 111 " --> pdb=" O VAL N 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'N' and resid 19 through 24 removed outlier: 4.021A pdb=" N ASP N 76 " --> pdb=" O SER N 73 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'N' and resid 90 through 96 removed outlier: 6.118A pdb=" N GLN N 43 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LEU N 52 " --> pdb=" O GLN N 43 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1278 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: 3.26 Time building geometry restraints manager: 5.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 4690 1.38 - 1.56: 7472 1.56 - 1.74: 3 1.74 - 1.92: 72 1.92 - 2.10: 9 Bond restraints: 12246 Sorted by residual: bond pdb=" C18 XP4 C 402 " pdb=" O7 XP4 C 402 " ideal model delta sigma weight residual 1.430 1.342 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C18 XP4 B 402 " pdb=" O7 XP4 B 402 " ideal model delta sigma weight residual 1.430 1.342 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C18 XP4 A 402 " pdb=" O7 XP4 A 402 " ideal model delta sigma weight residual 1.430 1.343 0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C4 XP4 C 402 " pdb=" O5 XP4 C 402 " ideal model delta sigma weight residual 1.404 1.328 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C4 XP4 B 402 " pdb=" O5 XP4 B 402 " ideal model delta sigma weight residual 1.404 1.328 0.076 2.00e-02 2.50e+03 1.44e+01 ... (remaining 12241 not shown) Histogram of bond angle deviations from ideal: 86.45 - 104.85: 218 104.85 - 123.24: 15816 123.24 - 141.63: 661 141.63 - 160.02: 0 160.02 - 178.41: 6 Bond angle restraints: 16701 Sorted by residual: angle pdb=" C5 XP4 A 402 " pdb=" C4 XP4 A 402 " pdb=" O5 XP4 A 402 " ideal model delta sigma weight residual 120.01 110.81 9.20 3.00e+00 1.11e-01 9.39e+00 angle pdb=" C5 XP4 B 402 " pdb=" C4 XP4 B 402 " pdb=" O5 XP4 B 402 " ideal model delta sigma weight residual 120.01 110.86 9.15 3.00e+00 1.11e-01 9.31e+00 angle pdb=" C5 XP4 C 402 " pdb=" C4 XP4 C 402 " pdb=" O5 XP4 C 402 " ideal model delta sigma weight residual 120.01 110.87 9.14 3.00e+00 1.11e-01 9.28e+00 angle pdb=" C19 XP4 A 402 " pdb=" C18 XP4 A 402 " pdb=" O7 XP4 A 402 " ideal model delta sigma weight residual 119.97 110.94 9.03 3.00e+00 1.11e-01 9.06e+00 angle pdb=" C19 XP4 C 402 " pdb=" C18 XP4 C 402 " pdb=" O7 XP4 C 402 " ideal model delta sigma weight residual 119.97 110.94 9.03 3.00e+00 1.11e-01 9.05e+00 ... (remaining 16696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 6751 17.66 - 35.32: 245 35.32 - 52.98: 69 52.98 - 70.64: 15 70.64 - 88.30: 15 Dihedral angle restraints: 7095 sinusoidal: 2850 harmonic: 4245 Sorted by residual: dihedral pdb=" C2C HEM B 401 " pdb=" C3C HEM B 401 " pdb=" CAC HEM B 401 " pdb=" CBC HEM B 401 " ideal model delta sinusoidal sigma weight residual 0.00 -71.90 71.90 2 1.00e+01 1.00e-02 4.34e+01 dihedral pdb=" C2C HEM C 401 " pdb=" C3C HEM C 401 " pdb=" CAC HEM C 401 " pdb=" CBC HEM C 401 " ideal model delta sinusoidal sigma weight residual 0.00 -71.88 71.88 2 1.00e+01 1.00e-02 4.34e+01 dihedral pdb=" C2C HEM A 401 " pdb=" C3C HEM A 401 " pdb=" CAC HEM A 401 " pdb=" CBC HEM A 401 " ideal model delta sinusoidal sigma weight residual 0.00 -71.77 71.77 2 1.00e+01 1.00e-02 4.33e+01 ... (remaining 7092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1073 0.026 - 0.053: 473 0.053 - 0.079: 167 0.079 - 0.105: 87 0.105 - 0.132: 33 Chirality restraints: 1833 Sorted by residual: chirality pdb=" CA ILE B 238 " pdb=" N ILE B 238 " pdb=" C ILE B 238 " pdb=" CB ILE B 238 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE A 238 " pdb=" N ILE A 238 " pdb=" C ILE A 238 " pdb=" CB ILE A 238 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA ILE C 238 " pdb=" N ILE C 238 " pdb=" C ILE C 238 " pdb=" CB ILE C 238 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 1830 not shown) Planarity restraints: 2004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 XP4 C 402 " -0.022 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" C19 XP4 C 402 " 0.006 2.00e-02 2.50e+03 pdb=" O7 XP4 C 402 " 0.007 2.00e-02 2.50e+03 pdb=" O8 XP4 C 402 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM B 401 " 0.010 2.00e-02 2.50e+03 8.54e-03 1.64e+00 pdb=" C2A HEM B 401 " 0.005 2.00e-02 2.50e+03 pdb=" C3A HEM B 401 " -0.001 2.00e-02 2.50e+03 pdb=" C4A HEM B 401 " 0.006 2.00e-02 2.50e+03 pdb=" CAA HEM B 401 " -0.008 2.00e-02 2.50e+03 pdb=" CHA HEM B 401 " 0.005 2.00e-02 2.50e+03 pdb=" CHB HEM B 401 " 0.003 2.00e-02 2.50e+03 pdb=" CMA HEM B 401 " 0.000 2.00e-02 2.50e+03 pdb=" NA HEM B 401 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM C 401 " -0.009 2.00e-02 2.50e+03 8.54e-03 1.64e+00 pdb=" C2A HEM C 401 " -0.006 2.00e-02 2.50e+03 pdb=" C3A HEM C 401 " 0.000 2.00e-02 2.50e+03 pdb=" C4A HEM C 401 " -0.006 2.00e-02 2.50e+03 pdb=" CAA HEM C 401 " 0.008 2.00e-02 2.50e+03 pdb=" CHA HEM C 401 " -0.005 2.00e-02 2.50e+03 pdb=" CHB HEM C 401 " -0.003 2.00e-02 2.50e+03 pdb=" CMA HEM C 401 " 0.000 2.00e-02 2.50e+03 pdb=" NA HEM C 401 " 0.020 2.00e-02 2.50e+03 ... (remaining 2001 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 93 2.57 - 3.15: 9918 3.15 - 3.74: 17961 3.74 - 4.32: 26598 4.32 - 4.90: 45185 Nonbonded interactions: 99755 Sorted by model distance: nonbonded pdb=" NE2 HIS C 268 " pdb="FE HEM C 401 " model vdw 1.990 3.080 nonbonded pdb=" NE2 HIS B 268 " pdb="FE HEM B 401 " model vdw 1.991 3.080 nonbonded pdb=" NE2 HIS A 268 " pdb="FE HEM A 401 " model vdw 1.991 3.080 nonbonded pdb=" OH TYR A 88 " pdb=" O PRO A 288 " model vdw 2.232 2.440 nonbonded pdb=" OH TYR C 88 " pdb=" O PRO C 288 " model vdw 2.232 2.440 ... (remaining 99750 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' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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 individual isotropic 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: 1.310 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: 6.870 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 36.150 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.090 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:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.217 12246 Z= 0.485 Angle : 0.698 9.195 16701 Z= 0.306 Chirality : 0.039 0.132 1833 Planarity : 0.003 0.026 2004 Dihedral : 11.435 88.295 4353 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.17 % Allowed : 5.37 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -4.00 (0.18), residues: 1410 helix: -2.56 (0.15), residues: 597 sheet: -2.91 (0.23), residues: 315 loop : -2.17 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 285 HIS 0.001 0.000 HIS C 152 PHE 0.007 0.001 PHE B 291 TYR 0.016 0.001 TYR B 219 ARG 0.002 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 260 time to evaluate : 1.445 Fit side-chains revert: symmetry clash REVERT: C 93 GLU cc_start: 0.8480 (mm-30) cc_final: 0.7818 (mp0) REVERT: C 158 MET cc_start: 0.8607 (mmm) cc_final: 0.8387 (mmm) REVERT: C 274 TRP cc_start: 0.7875 (t-100) cc_final: 0.7177 (t-100) REVERT: C 279 ASP cc_start: 0.8757 (t0) cc_final: 0.8304 (t0) REVERT: L 85 LYS cc_start: 0.9020 (mttt) cc_final: 0.8764 (mmmm) REVERT: H 3 GLN cc_start: 0.8011 (tp40) cc_final: 0.7600 (tm-30) REVERT: H 5 GLN cc_start: 0.8623 (tt0) cc_final: 0.8155 (pp30) REVERT: H 13 LYS cc_start: 0.8773 (mmtm) cc_final: 0.8424 (mmmt) REVERT: H 47 GLU cc_start: 0.8544 (tt0) cc_final: 0.8195 (tt0) REVERT: H 73 ASP cc_start: 0.8597 (t0) cc_final: 0.8377 (t0) REVERT: H 100 ARG cc_start: 0.8391 (ttm-80) cc_final: 0.8108 (mtp85) REVERT: H 103 ASP cc_start: 0.8263 (t0) cc_final: 0.7879 (t70) REVERT: H 105 ASP cc_start: 0.8208 (m-30) cc_final: 0.7910 (m-30) REVERT: I 3 GLN cc_start: 0.8189 (tp40) cc_final: 0.7781 (tm-30) REVERT: I 5 GLN cc_start: 0.8584 (tt0) cc_final: 0.8171 (pp30) REVERT: I 13 LYS cc_start: 0.8751 (mmtm) cc_final: 0.8512 (mmmt) REVERT: I 44 ASN cc_start: 0.8557 (m110) cc_final: 0.7873 (p0) REVERT: I 45 LYS cc_start: 0.8472 (tttt) cc_final: 0.8207 (tttp) REVERT: I 73 ASP cc_start: 0.8467 (t0) cc_final: 0.7968 (t0) REVERT: I 103 ASP cc_start: 0.8106 (t0) cc_final: 0.7496 (t0) REVERT: I 105 ASP cc_start: 0.8403 (m-30) cc_final: 0.8198 (m-30) REVERT: J 3 GLN cc_start: 0.8071 (tp40) cc_final: 0.7660 (tm-30) REVERT: J 5 GLN cc_start: 0.8566 (tt0) cc_final: 0.8085 (pp30) REVERT: J 22 CYS cc_start: 0.6565 (t) cc_final: 0.6308 (t) REVERT: J 73 ASP cc_start: 0.8730 (t0) cc_final: 0.8218 (t0) REVERT: J 78 GLN cc_start: 0.9004 (mt0) cc_final: 0.8770 (mt0) REVERT: J 87 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8457 (t) REVERT: J 103 ASP cc_start: 0.8165 (t0) cc_final: 0.7688 (t70) REVERT: J 105 ASP cc_start: 0.8201 (m-30) cc_final: 0.7932 (m-30) REVERT: M 55 TYR cc_start: 0.8787 (p90) cc_final: 0.8494 (p90) REVERT: M 85 LYS cc_start: 0.9015 (mttt) cc_final: 0.8382 (mtpm) REVERT: M 87 GLU cc_start: 0.8526 (pm20) cc_final: 0.7550 (pm20) REVERT: M 88 ASP cc_start: 0.8651 (m-30) cc_final: 0.8396 (m-30) REVERT: N 85 LYS cc_start: 0.8830 (mttt) cc_final: 0.8500 (mtmt) REVERT: N 87 GLU cc_start: 0.8711 (pm20) cc_final: 0.8465 (pm20) REVERT: N 111 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8300 (mt-10) REVERT: A 93 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8171 (mm-30) REVERT: A 212 ASP cc_start: 0.8648 (t0) cc_final: 0.8111 (t0) REVERT: A 274 TRP cc_start: 0.7829 (t-100) cc_final: 0.7298 (t-100) REVERT: A 279 ASP cc_start: 0.8940 (t0) cc_final: 0.8514 (t0) REVERT: B 93 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7804 (mp0) REVERT: B 143 ASN cc_start: 0.8225 (m110) cc_final: 0.7999 (p0) REVERT: B 243 ASP cc_start: 0.8112 (m-30) cc_final: 0.7869 (m-30) REVERT: B 274 TRP cc_start: 0.7925 (t-100) cc_final: 0.7328 (t-100) REVERT: B 279 ASP cc_start: 0.8957 (t0) cc_final: 0.8542 (t0) REVERT: B 292 MET cc_start: 0.8502 (mtp) cc_final: 0.8217 (mtt) outliers start: 15 outliers final: 4 residues processed: 272 average time/residue: 1.4966 time to fit residues: 435.1240 Evaluate side-chains 192 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 187 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 107 TYR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 107 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 96 HIS C 143 ASN C 202 GLN C 254 GLN L 37 ASN M 37 ASN N 37 ASN A 96 HIS A 143 ASN A 202 GLN A 254 GLN B 96 HIS B 202 GLN B 254 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12246 Z= 0.266 Angle : 0.626 12.171 16701 Z= 0.299 Chirality : 0.041 0.172 1833 Planarity : 0.004 0.034 2004 Dihedral : 9.810 82.708 1689 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.49 % Allowed : 12.31 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.92 (0.21), residues: 1410 helix: -0.36 (0.20), residues: 603 sheet: -2.25 (0.24), residues: 315 loop : -1.48 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 274 HIS 0.004 0.001 HIS A 268 PHE 0.008 0.001 PHE B 291 TYR 0.030 0.001 TYR C 219 ARG 0.008 0.001 ARG I 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 208 time to evaluate : 1.585 Fit side-chains revert: symmetry clash REVERT: C 93 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7803 (mp0) REVERT: C 120 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7390 (tpp) REVERT: C 274 TRP cc_start: 0.7758 (t-100) cc_final: 0.7044 (t-100) REVERT: C 279 ASP cc_start: 0.8742 (t0) cc_final: 0.8278 (t0) REVERT: L 17 GLU cc_start: 0.8420 (tt0) cc_final: 0.7990 (tt0) REVERT: L 35 GLN cc_start: 0.8723 (mt0) cc_final: 0.8386 (mt0) REVERT: L 76 ASP cc_start: 0.8087 (m-30) cc_final: 0.7861 (m-30) REVERT: H 3 GLN cc_start: 0.8059 (tp40) cc_final: 0.7688 (tm-30) REVERT: H 5 GLN cc_start: 0.8601 (tt0) cc_final: 0.8090 (pp30) REVERT: H 13 LYS cc_start: 0.8761 (mmtm) cc_final: 0.8438 (mmmt) REVERT: H 45 LYS cc_start: 0.8633 (ttpp) cc_final: 0.8410 (tttp) REVERT: H 73 ASP cc_start: 0.8352 (t0) cc_final: 0.7782 (t0) REVERT: H 100 ARG cc_start: 0.8282 (ttm-80) cc_final: 0.8040 (mtp85) REVERT: H 103 ASP cc_start: 0.8222 (t0) cc_final: 0.7685 (t70) REVERT: H 105 ASP cc_start: 0.8231 (m-30) cc_final: 0.7937 (m-30) REVERT: I 3 GLN cc_start: 0.8169 (tp40) cc_final: 0.7799 (tm-30) REVERT: I 44 ASN cc_start: 0.8598 (m110) cc_final: 0.7884 (p0) REVERT: I 45 LYS cc_start: 0.8544 (tttt) cc_final: 0.8265 (tttm) REVERT: I 73 ASP cc_start: 0.8318 (t0) cc_final: 0.7765 (t0) REVERT: I 82 GLN cc_start: 0.7663 (mp10) cc_final: 0.7349 (mp10) REVERT: I 103 ASP cc_start: 0.8082 (t0) cc_final: 0.7489 (t0) REVERT: I 105 ASP cc_start: 0.8424 (m-30) cc_final: 0.8216 (m-30) REVERT: J 3 GLN cc_start: 0.8087 (tp40) cc_final: 0.7645 (tm-30) REVERT: J 5 GLN cc_start: 0.8632 (tt0) cc_final: 0.8146 (pp30) REVERT: J 13 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8762 (mmtt) REVERT: J 73 ASP cc_start: 0.8484 (t0) cc_final: 0.7898 (t0) REVERT: J 87 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8726 (t) REVERT: J 100 ARG cc_start: 0.8397 (mtp85) cc_final: 0.8073 (ttp-110) REVERT: J 103 ASP cc_start: 0.8154 (t0) cc_final: 0.7648 (t70) REVERT: J 105 ASP cc_start: 0.8239 (m-30) cc_final: 0.7955 (m-30) REVERT: M 85 LYS cc_start: 0.9006 (mttt) cc_final: 0.8406 (mtpm) REVERT: M 87 GLU cc_start: 0.8520 (pm20) cc_final: 0.7707 (pm20) REVERT: N 17 GLU cc_start: 0.8377 (tt0) cc_final: 0.7750 (tt0) REVERT: N 85 LYS cc_start: 0.8847 (mttt) cc_final: 0.8552 (mmmm) REVERT: N 87 GLU cc_start: 0.8629 (pm20) cc_final: 0.8403 (pm20) REVERT: N 111 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8347 (mt-10) REVERT: A 93 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7873 (mp0) REVERT: A 120 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7535 (tpp) REVERT: A 274 TRP cc_start: 0.7384 (t-100) cc_final: 0.6993 (t-100) REVERT: A 279 ASP cc_start: 0.8937 (t0) cc_final: 0.8519 (t0) REVERT: B 93 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7780 (mp0) REVERT: B 243 ASP cc_start: 0.8243 (m-30) cc_final: 0.8022 (m-30) REVERT: B 248 ARG cc_start: 0.8503 (mmm160) cc_final: 0.8238 (tmm-80) REVERT: B 274 TRP cc_start: 0.7912 (t-100) cc_final: 0.7182 (t-100) REVERT: B 279 ASP cc_start: 0.8940 (t0) cc_final: 0.8515 (t0) REVERT: B 292 MET cc_start: 0.8612 (mtp) cc_final: 0.8378 (mtt) outliers start: 32 outliers final: 15 residues processed: 225 average time/residue: 1.5110 time to fit residues: 364.2771 Evaluate side-chains 207 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 189 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 107 TYR Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 275 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 106 optimal weight: 0.0970 chunk 87 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 128 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12246 Z= 0.203 Angle : 0.587 11.441 16701 Z= 0.273 Chirality : 0.040 0.174 1833 Planarity : 0.004 0.029 2004 Dihedral : 8.548 75.701 1689 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.74 % Allowed : 13.24 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.03 (0.22), residues: 1410 helix: 0.51 (0.22), residues: 600 sheet: -1.87 (0.25), residues: 315 loop : -1.16 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 214 HIS 0.003 0.001 HIS A 268 PHE 0.009 0.001 PHE B 291 TYR 0.026 0.001 TYR B 219 ARG 0.006 0.000 ARG N 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 216 time to evaluate : 1.498 Fit side-chains revert: symmetry clash REVERT: C 93 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7780 (mp0) REVERT: C 120 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7845 (tpt) REVERT: C 274 TRP cc_start: 0.7700 (t-100) cc_final: 0.7058 (t-100) REVERT: L 17 GLU cc_start: 0.8387 (tt0) cc_final: 0.7984 (tt0) REVERT: L 35 GLN cc_start: 0.8701 (mt0) cc_final: 0.8362 (mt0) REVERT: L 76 ASP cc_start: 0.8038 (m-30) cc_final: 0.7808 (m-30) REVERT: L 85 LYS cc_start: 0.9125 (mtpp) cc_final: 0.8904 (mtpt) REVERT: H 3 GLN cc_start: 0.8096 (tp40) cc_final: 0.7749 (tm-30) REVERT: H 5 GLN cc_start: 0.8604 (tt0) cc_final: 0.8146 (pp30) REVERT: H 13 LYS cc_start: 0.8749 (mmtm) cc_final: 0.8401 (mmmt) REVERT: H 45 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8378 (tttp) REVERT: H 73 ASP cc_start: 0.8310 (t0) cc_final: 0.7789 (t0) REVERT: H 100 ARG cc_start: 0.8227 (ttm-80) cc_final: 0.8025 (mtp85) REVERT: H 103 ASP cc_start: 0.8165 (t0) cc_final: 0.7606 (t70) REVERT: H 105 ASP cc_start: 0.8220 (m-30) cc_final: 0.7915 (m-30) REVERT: I 3 GLN cc_start: 0.8167 (tp40) cc_final: 0.7809 (tm-30) REVERT: I 44 ASN cc_start: 0.8653 (m110) cc_final: 0.7923 (p0) REVERT: I 45 LYS cc_start: 0.8543 (tttt) cc_final: 0.8233 (tttp) REVERT: I 73 ASP cc_start: 0.8289 (t0) cc_final: 0.7836 (t0) REVERT: I 103 ASP cc_start: 0.8032 (t0) cc_final: 0.7481 (t0) REVERT: J 3 GLN cc_start: 0.8120 (tp40) cc_final: 0.7741 (tm-30) REVERT: J 5 GLN cc_start: 0.8417 (tt0) cc_final: 0.8205 (tp-100) REVERT: J 67 ARG cc_start: 0.8681 (ptt90) cc_final: 0.8450 (ptt90) REVERT: J 73 ASP cc_start: 0.8376 (t0) cc_final: 0.7828 (t0) REVERT: J 87 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8774 (t) REVERT: J 89 GLU cc_start: 0.8314 (mp0) cc_final: 0.8005 (mp0) REVERT: J 103 ASP cc_start: 0.8098 (t0) cc_final: 0.7526 (t70) REVERT: J 105 ASP cc_start: 0.8244 (m-30) cc_final: 0.7947 (m-30) REVERT: M 61 GLU cc_start: 0.8472 (tp30) cc_final: 0.8254 (tp30) REVERT: M 85 LYS cc_start: 0.9001 (mttt) cc_final: 0.8382 (mtpm) REVERT: M 87 GLU cc_start: 0.8540 (pm20) cc_final: 0.7758 (pm20) REVERT: N 17 GLU cc_start: 0.8338 (tt0) cc_final: 0.7757 (tt0) REVERT: N 85 LYS cc_start: 0.8878 (mttt) cc_final: 0.8574 (mmmm) REVERT: N 87 GLU cc_start: 0.8634 (pm20) cc_final: 0.8403 (pm20) REVERT: N 111 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8419 (mt-10) REVERT: A 93 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7842 (mp0) REVERT: A 212 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7575 (t0) REVERT: A 274 TRP cc_start: 0.7255 (t-100) cc_final: 0.6980 (t-100) REVERT: A 279 ASP cc_start: 0.8917 (t0) cc_final: 0.8543 (t0) REVERT: B 93 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7777 (mp0) REVERT: B 201 GLN cc_start: 0.8963 (tp40) cc_final: 0.8743 (tp40) REVERT: B 243 ASP cc_start: 0.8296 (m-30) cc_final: 0.8081 (m-30) REVERT: B 274 TRP cc_start: 0.7938 (t-100) cc_final: 0.7223 (t-100) REVERT: B 279 ASP cc_start: 0.8955 (t0) cc_final: 0.8500 (t0) REVERT: B 292 MET cc_start: 0.8589 (mtp) cc_final: 0.8356 (mtt) outliers start: 48 outliers final: 19 residues processed: 242 average time/residue: 1.5023 time to fit residues: 389.3559 Evaluate side-chains 214 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 192 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 107 TYR Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 1.9990 chunk 96 optimal weight: 0.0040 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 128 optimal weight: 0.1980 chunk 136 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12246 Z= 0.164 Angle : 0.574 10.656 16701 Z= 0.265 Chirality : 0.040 0.178 1833 Planarity : 0.003 0.029 2004 Dihedral : 7.740 77.523 1689 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.57 % Allowed : 16.51 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.22), residues: 1410 helix: 0.87 (0.22), residues: 600 sheet: -1.65 (0.26), residues: 330 loop : -0.94 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 214 HIS 0.002 0.000 HIS A 268 PHE 0.009 0.001 PHE B 291 TYR 0.025 0.001 TYR B 219 ARG 0.006 0.001 ARG I 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 201 time to evaluate : 1.579 Fit side-chains revert: symmetry clash REVERT: C 93 GLU cc_start: 0.8407 (mm-30) cc_final: 0.7726 (mp0) REVERT: C 274 TRP cc_start: 0.7553 (t-100) cc_final: 0.7025 (t-100) REVERT: L 17 GLU cc_start: 0.8392 (tt0) cc_final: 0.8064 (tt0) REVERT: L 35 GLN cc_start: 0.8632 (mt0) cc_final: 0.8420 (mt0) REVERT: L 85 LYS cc_start: 0.9144 (mtpp) cc_final: 0.8905 (mtpt) REVERT: H 3 GLN cc_start: 0.8052 (tp40) cc_final: 0.7686 (tm-30) REVERT: H 5 GLN cc_start: 0.8587 (tt0) cc_final: 0.8150 (pp30) REVERT: H 13 LYS cc_start: 0.8754 (mmtm) cc_final: 0.8412 (mmmt) REVERT: H 45 LYS cc_start: 0.8626 (ttpp) cc_final: 0.8381 (tttp) REVERT: H 73 ASP cc_start: 0.8341 (t0) cc_final: 0.7884 (t0) REVERT: H 103 ASP cc_start: 0.8093 (t0) cc_final: 0.7548 (t70) REVERT: H 105 ASP cc_start: 0.8201 (m-30) cc_final: 0.7889 (m-30) REVERT: I 3 GLN cc_start: 0.8186 (tp40) cc_final: 0.7842 (tm-30) REVERT: I 44 ASN cc_start: 0.8624 (m110) cc_final: 0.7880 (p0) REVERT: I 45 LYS cc_start: 0.8517 (tttt) cc_final: 0.8216 (tttm) REVERT: I 73 ASP cc_start: 0.8209 (t0) cc_final: 0.7817 (t0) REVERT: I 100 ARG cc_start: 0.8166 (mtp85) cc_final: 0.7947 (mmm-85) REVERT: I 103 ASP cc_start: 0.7890 (t0) cc_final: 0.7366 (t0) REVERT: J 3 GLN cc_start: 0.8103 (tp40) cc_final: 0.7712 (tm-30) REVERT: J 5 GLN cc_start: 0.8534 (tt0) cc_final: 0.8138 (tm-30) REVERT: J 67 ARG cc_start: 0.8486 (ptt90) cc_final: 0.8282 (ptt90) REVERT: J 73 ASP cc_start: 0.8341 (t0) cc_final: 0.7836 (t0) REVERT: J 87 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8718 (t) REVERT: J 103 ASP cc_start: 0.8028 (t0) cc_final: 0.7464 (t70) REVERT: J 105 ASP cc_start: 0.8255 (m-30) cc_final: 0.7969 (m-30) REVERT: M 61 GLU cc_start: 0.8450 (tp30) cc_final: 0.8248 (tp30) REVERT: M 85 LYS cc_start: 0.8993 (mttt) cc_final: 0.8497 (mtpt) REVERT: M 87 GLU cc_start: 0.8538 (pm20) cc_final: 0.8008 (pm20) REVERT: N 17 GLU cc_start: 0.8294 (tt0) cc_final: 0.7744 (tt0) REVERT: N 85 LYS cc_start: 0.8932 (mttt) cc_final: 0.8453 (mtpp) REVERT: N 87 GLU cc_start: 0.8634 (pm20) cc_final: 0.8315 (pm20) REVERT: N 111 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8358 (mt-10) REVERT: A 93 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7824 (mp0) REVERT: A 274 TRP cc_start: 0.7164 (t-100) cc_final: 0.6955 (t-100) REVERT: A 279 ASP cc_start: 0.8914 (t0) cc_final: 0.8543 (t0) REVERT: B 93 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7794 (mp0) REVERT: B 243 ASP cc_start: 0.8288 (m-30) cc_final: 0.8085 (m-30) REVERT: B 274 TRP cc_start: 0.7879 (t-100) cc_final: 0.7157 (t-100) REVERT: B 279 ASP cc_start: 0.8961 (t0) cc_final: 0.8518 (t0) REVERT: B 292 MET cc_start: 0.8575 (mtp) cc_final: 0.8346 (mtt) outliers start: 33 outliers final: 18 residues processed: 225 average time/residue: 1.5053 time to fit residues: 362.6296 Evaluate side-chains 201 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 182 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 107 TYR Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain M residue 95 GLN Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.3980 chunk 77 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12246 Z= 0.232 Angle : 0.603 12.570 16701 Z= 0.274 Chirality : 0.041 0.172 1833 Planarity : 0.003 0.029 2004 Dihedral : 7.702 79.056 1689 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.19 % Allowed : 16.98 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.23), residues: 1410 helix: 1.04 (0.23), residues: 603 sheet: -1.39 (0.26), residues: 324 loop : -0.88 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 48 HIS 0.003 0.001 HIS A 268 PHE 0.008 0.001 PHE A 291 TYR 0.025 0.001 TYR B 219 ARG 0.007 0.001 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 196 time to evaluate : 1.508 Fit side-chains revert: symmetry clash REVERT: C 93 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7747 (mp0) REVERT: C 104 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.7130 (tp40) REVERT: C 274 TRP cc_start: 0.7614 (t-100) cc_final: 0.7035 (t-100) REVERT: L 17 GLU cc_start: 0.8401 (tt0) cc_final: 0.8018 (tt0) REVERT: L 35 GLN cc_start: 0.8702 (mt0) cc_final: 0.8491 (mt0) REVERT: L 61 GLU cc_start: 0.8561 (tp30) cc_final: 0.8295 (tp30) REVERT: H 3 GLN cc_start: 0.8195 (tp40) cc_final: 0.7823 (tm-30) REVERT: H 5 GLN cc_start: 0.8614 (tt0) cc_final: 0.8157 (pp30) REVERT: H 13 LYS cc_start: 0.8740 (mmtm) cc_final: 0.8357 (mmmt) REVERT: H 45 LYS cc_start: 0.8644 (ttpp) cc_final: 0.8401 (tttp) REVERT: H 65 LYS cc_start: 0.8623 (ttpp) cc_final: 0.8420 (ttpt) REVERT: H 73 ASP cc_start: 0.8355 (t0) cc_final: 0.7940 (t0) REVERT: H 103 ASP cc_start: 0.8210 (t0) cc_final: 0.7607 (t70) REVERT: H 105 ASP cc_start: 0.8271 (m-30) cc_final: 0.7972 (m-30) REVERT: I 3 GLN cc_start: 0.8178 (tp40) cc_final: 0.7876 (tm-30) REVERT: I 44 ASN cc_start: 0.8663 (m110) cc_final: 0.7962 (p0) REVERT: I 45 LYS cc_start: 0.8532 (tttt) cc_final: 0.8223 (tttm) REVERT: I 73 ASP cc_start: 0.8228 (t0) cc_final: 0.7830 (t0) REVERT: I 100 ARG cc_start: 0.8208 (mtp85) cc_final: 0.7981 (mmm-85) REVERT: I 103 ASP cc_start: 0.7929 (t0) cc_final: 0.7473 (t0) REVERT: J 3 GLN cc_start: 0.8215 (tp40) cc_final: 0.7832 (tm-30) REVERT: J 5 GLN cc_start: 0.8558 (tt0) cc_final: 0.8163 (tm-30) REVERT: J 67 ARG cc_start: 0.8480 (ptt90) cc_final: 0.8273 (ptt90) REVERT: J 73 ASP cc_start: 0.8316 (t0) cc_final: 0.7830 (t0) REVERT: J 87 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8299 (t) REVERT: J 103 ASP cc_start: 0.8107 (t0) cc_final: 0.7524 (t70) REVERT: J 105 ASP cc_start: 0.8251 (m-30) cc_final: 0.7948 (m-30) REVERT: M 61 GLU cc_start: 0.8457 (tp30) cc_final: 0.8234 (tp30) REVERT: M 85 LYS cc_start: 0.8970 (mttt) cc_final: 0.8497 (mtpt) REVERT: M 87 GLU cc_start: 0.8600 (pm20) cc_final: 0.8182 (pm20) REVERT: M 113 LYS cc_start: 0.7875 (ttpp) cc_final: 0.7620 (ttpp) REVERT: N 17 GLU cc_start: 0.8344 (tt0) cc_final: 0.7792 (tt0) REVERT: N 85 LYS cc_start: 0.8917 (mttt) cc_final: 0.8414 (mtpp) REVERT: N 87 GLU cc_start: 0.8640 (pm20) cc_final: 0.8297 (pm20) REVERT: A 93 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7873 (mp0) REVERT: A 279 ASP cc_start: 0.8912 (t0) cc_final: 0.8540 (t0) REVERT: B 93 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7773 (mp0) REVERT: B 274 TRP cc_start: 0.7957 (t-100) cc_final: 0.7231 (t-100) REVERT: B 279 ASP cc_start: 0.8959 (t0) cc_final: 0.8507 (t0) REVERT: B 292 MET cc_start: 0.8592 (mtp) cc_final: 0.8352 (mtt) outliers start: 41 outliers final: 24 residues processed: 223 average time/residue: 1.4725 time to fit residues: 352.6647 Evaluate side-chains 213 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 187 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 107 TYR Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain M residue 95 GLN Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.0270 chunk 136 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12246 Z= 0.176 Angle : 0.572 11.276 16701 Z= 0.262 Chirality : 0.040 0.178 1833 Planarity : 0.003 0.028 2004 Dihedral : 7.619 83.850 1689 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.41 % Allowed : 18.54 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.23), residues: 1410 helix: 1.18 (0.23), residues: 600 sheet: -1.28 (0.27), residues: 324 loop : -0.85 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 274 HIS 0.002 0.000 HIS A 268 PHE 0.009 0.001 PHE C 291 TYR 0.025 0.001 TYR B 219 ARG 0.006 0.001 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 199 time to evaluate : 1.489 Fit side-chains revert: symmetry clash REVERT: C 93 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7723 (mp0) REVERT: C 274 TRP cc_start: 0.7562 (t-100) cc_final: 0.7032 (t-100) REVERT: L 17 GLU cc_start: 0.8405 (tt0) cc_final: 0.8016 (tt0) REVERT: L 35 GLN cc_start: 0.8660 (mt0) cc_final: 0.8413 (mt0) REVERT: L 61 GLU cc_start: 0.8529 (tp30) cc_final: 0.8298 (tp30) REVERT: H 3 GLN cc_start: 0.8219 (tp40) cc_final: 0.7852 (tm-30) REVERT: H 5 GLN cc_start: 0.8594 (tt0) cc_final: 0.8165 (pp30) REVERT: H 13 LYS cc_start: 0.8726 (mmtm) cc_final: 0.8342 (mmmt) REVERT: H 45 LYS cc_start: 0.8657 (ttpp) cc_final: 0.8397 (tttp) REVERT: H 65 LYS cc_start: 0.8584 (ttpp) cc_final: 0.8382 (ttpt) REVERT: H 73 ASP cc_start: 0.8348 (t0) cc_final: 0.7963 (t0) REVERT: H 103 ASP cc_start: 0.8140 (t0) cc_final: 0.7550 (t70) REVERT: H 105 ASP cc_start: 0.8256 (m-30) cc_final: 0.7969 (m-30) REVERT: I 3 GLN cc_start: 0.8188 (tp40) cc_final: 0.7885 (tm-30) REVERT: I 44 ASN cc_start: 0.8627 (m110) cc_final: 0.7912 (p0) REVERT: I 45 LYS cc_start: 0.8536 (tttt) cc_final: 0.8230 (tttm) REVERT: I 73 ASP cc_start: 0.8215 (t0) cc_final: 0.7818 (t0) REVERT: I 100 ARG cc_start: 0.8179 (mtp85) cc_final: 0.7951 (mmm-85) REVERT: I 103 ASP cc_start: 0.7893 (t0) cc_final: 0.7431 (t0) REVERT: J 3 GLN cc_start: 0.8223 (tp40) cc_final: 0.7813 (tm-30) REVERT: J 5 GLN cc_start: 0.8549 (tt0) cc_final: 0.8189 (tm-30) REVERT: J 6 GLU cc_start: 0.8415 (mp0) cc_final: 0.7758 (mp0) REVERT: J 67 ARG cc_start: 0.8448 (ptt90) cc_final: 0.8239 (ptt90) REVERT: J 73 ASP cc_start: 0.8331 (t0) cc_final: 0.7780 (t0) REVERT: J 87 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8798 (t) REVERT: J 103 ASP cc_start: 0.8102 (t0) cc_final: 0.7498 (t70) REVERT: J 105 ASP cc_start: 0.8253 (m-30) cc_final: 0.7965 (m-30) REVERT: M 17 GLU cc_start: 0.8433 (tt0) cc_final: 0.8217 (tt0) REVERT: M 61 GLU cc_start: 0.8444 (tp30) cc_final: 0.8227 (tp30) REVERT: M 85 LYS cc_start: 0.8990 (mttt) cc_final: 0.8501 (mtpt) REVERT: M 87 GLU cc_start: 0.8592 (pm20) cc_final: 0.8176 (pm20) REVERT: M 113 LYS cc_start: 0.8174 (ttpp) cc_final: 0.7951 (ttpp) REVERT: N 17 GLU cc_start: 0.8278 (tt0) cc_final: 0.7743 (tt0) REVERT: N 85 LYS cc_start: 0.8921 (mttt) cc_final: 0.8429 (mtpp) REVERT: N 87 GLU cc_start: 0.8634 (pm20) cc_final: 0.8324 (pm20) REVERT: A 93 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7791 (mp0) REVERT: A 120 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7843 (tpp) REVERT: A 279 ASP cc_start: 0.8911 (t0) cc_final: 0.8538 (t0) REVERT: B 93 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7808 (mp0) REVERT: B 158 MET cc_start: 0.8444 (tpp) cc_final: 0.8189 (tpp) REVERT: B 249 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8262 (mp0) REVERT: B 274 TRP cc_start: 0.7888 (t-100) cc_final: 0.7192 (t-100) REVERT: B 279 ASP cc_start: 0.8956 (t0) cc_final: 0.8519 (t0) REVERT: B 292 MET cc_start: 0.8586 (mtp) cc_final: 0.8336 (mtt) outliers start: 31 outliers final: 19 residues processed: 221 average time/residue: 1.5148 time to fit residues: 357.9505 Evaluate side-chains 207 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 185 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain I residue 101 ASN Chi-restraints excluded: chain I residue 107 TYR Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain M residue 95 GLN Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 275 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 82 GLN M 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12246 Z= 0.246 Angle : 0.609 13.260 16701 Z= 0.275 Chirality : 0.041 0.177 1833 Planarity : 0.003 0.028 2004 Dihedral : 7.745 86.872 1689 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.12 % Allowed : 18.07 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.23), residues: 1410 helix: 1.14 (0.22), residues: 603 sheet: -1.21 (0.27), residues: 324 loop : -0.79 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 48 HIS 0.003 0.001 HIS A 268 PHE 0.008 0.001 PHE C 291 TYR 0.025 0.001 TYR B 219 ARG 0.007 0.001 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 190 time to evaluate : 1.553 Fit side-chains revert: symmetry clash REVERT: C 93 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7732 (mp0) REVERT: C 104 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.7025 (tp40) REVERT: C 158 MET cc_start: 0.8574 (tpp) cc_final: 0.8324 (mmm) REVERT: C 274 TRP cc_start: 0.7571 (t-100) cc_final: 0.7001 (t-100) REVERT: C 279 ASP cc_start: 0.8807 (t0) cc_final: 0.8339 (t0) REVERT: L 17 GLU cc_start: 0.8399 (tt0) cc_final: 0.7989 (tt0) REVERT: L 35 GLN cc_start: 0.8695 (mt0) cc_final: 0.8449 (mt0) REVERT: L 61 GLU cc_start: 0.8518 (tp30) cc_final: 0.8288 (tp30) REVERT: H 3 GLN cc_start: 0.8247 (tp40) cc_final: 0.7866 (tm-30) REVERT: H 5 GLN cc_start: 0.8616 (tt0) cc_final: 0.8150 (pp30) REVERT: H 13 LYS cc_start: 0.8762 (mmtm) cc_final: 0.8353 (mmmt) REVERT: H 45 LYS cc_start: 0.8653 (ttpp) cc_final: 0.8397 (tttp) REVERT: H 73 ASP cc_start: 0.8317 (t0) cc_final: 0.7885 (t0) REVERT: H 103 ASP cc_start: 0.8140 (t0) cc_final: 0.7460 (t70) REVERT: H 105 ASP cc_start: 0.8294 (m-30) cc_final: 0.8006 (m-30) REVERT: I 3 GLN cc_start: 0.8201 (tp40) cc_final: 0.7907 (tm-30) REVERT: I 44 ASN cc_start: 0.8698 (m110) cc_final: 0.8043 (p0) REVERT: I 45 LYS cc_start: 0.8538 (tttt) cc_final: 0.8223 (tttm) REVERT: I 73 ASP cc_start: 0.8231 (t0) cc_final: 0.7808 (t0) REVERT: I 103 ASP cc_start: 0.7952 (t0) cc_final: 0.7451 (t0) REVERT: J 3 GLN cc_start: 0.8262 (tp40) cc_final: 0.7906 (tm-30) REVERT: J 5 GLN cc_start: 0.8569 (tt0) cc_final: 0.8226 (tm-30) REVERT: J 6 GLU cc_start: 0.8412 (mp0) cc_final: 0.7819 (mp0) REVERT: J 67 ARG cc_start: 0.8476 (ptt90) cc_final: 0.8265 (ptt90) REVERT: J 73 ASP cc_start: 0.8325 (t0) cc_final: 0.7820 (t0) REVERT: J 87 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.8979 (t) REVERT: J 103 ASP cc_start: 0.8182 (t0) cc_final: 0.7546 (t70) REVERT: J 105 ASP cc_start: 0.8261 (m-30) cc_final: 0.7957 (m-30) REVERT: M 61 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8229 (tp30) REVERT: M 85 LYS cc_start: 0.8977 (mttt) cc_final: 0.8454 (mtpt) REVERT: M 87 GLU cc_start: 0.8632 (pm20) cc_final: 0.8245 (pm20) REVERT: M 113 LYS cc_start: 0.8162 (ttpp) cc_final: 0.7949 (ttpp) REVERT: N 17 GLU cc_start: 0.8282 (tt0) cc_final: 0.7722 (tt0) REVERT: N 85 LYS cc_start: 0.8926 (mttt) cc_final: 0.8605 (mmmm) REVERT: N 87 GLU cc_start: 0.8663 (pm20) cc_final: 0.8406 (pm20) REVERT: A 93 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7846 (mp0) REVERT: A 279 ASP cc_start: 0.8889 (t0) cc_final: 0.8494 (t0) REVERT: B 93 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7794 (mp0) REVERT: B 158 MET cc_start: 0.8498 (tpp) cc_final: 0.8227 (tpp) REVERT: B 274 TRP cc_start: 0.7932 (t-100) cc_final: 0.7221 (t-100) REVERT: B 279 ASP cc_start: 0.8958 (t0) cc_final: 0.8492 (t0) REVERT: B 292 MET cc_start: 0.8531 (mtp) cc_final: 0.8272 (mtt) outliers start: 40 outliers final: 22 residues processed: 216 average time/residue: 1.5093 time to fit residues: 348.7223 Evaluate side-chains 210 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 185 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain I residue 107 TYR Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 95 GLN Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12246 Z= 0.175 Angle : 0.579 11.385 16701 Z= 0.264 Chirality : 0.040 0.183 1833 Planarity : 0.003 0.029 2004 Dihedral : 7.680 89.813 1689 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.18 % Allowed : 18.77 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.23), residues: 1410 helix: 1.23 (0.23), residues: 603 sheet: -1.08 (0.28), residues: 324 loop : -0.77 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 274 HIS 0.002 0.000 HIS A 268 PHE 0.008 0.001 PHE B 291 TYR 0.024 0.001 TYR B 219 ARG 0.007 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 189 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: C 93 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7727 (mp0) REVERT: C 104 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.6956 (tp40) REVERT: C 274 TRP cc_start: 0.7570 (t-100) cc_final: 0.7021 (t-100) REVERT: C 279 ASP cc_start: 0.8803 (t0) cc_final: 0.8341 (t0) REVERT: L 17 GLU cc_start: 0.8401 (tt0) cc_final: 0.8148 (tt0) REVERT: L 35 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8432 (mt0) REVERT: L 61 GLU cc_start: 0.8522 (tp30) cc_final: 0.8281 (tp30) REVERT: H 3 GLN cc_start: 0.8242 (tp40) cc_final: 0.7914 (tm-30) REVERT: H 5 GLN cc_start: 0.8598 (tt0) cc_final: 0.8109 (pp30) REVERT: H 13 LYS cc_start: 0.8761 (mmtm) cc_final: 0.8353 (mmmt) REVERT: H 45 LYS cc_start: 0.8674 (ttpp) cc_final: 0.8404 (tttp) REVERT: H 73 ASP cc_start: 0.8296 (t0) cc_final: 0.7857 (t0) REVERT: H 103 ASP cc_start: 0.8045 (t0) cc_final: 0.7414 (t70) REVERT: H 105 ASP cc_start: 0.8274 (m-30) cc_final: 0.7995 (m-30) REVERT: I 3 GLN cc_start: 0.8189 (tp40) cc_final: 0.7881 (tm-30) REVERT: I 44 ASN cc_start: 0.8697 (m110) cc_final: 0.8052 (p0) REVERT: I 45 LYS cc_start: 0.8536 (tttt) cc_final: 0.8236 (tttm) REVERT: I 73 ASP cc_start: 0.8215 (t0) cc_final: 0.7796 (t0) REVERT: I 103 ASP cc_start: 0.7900 (t0) cc_final: 0.7420 (t0) REVERT: J 3 GLN cc_start: 0.8221 (tp40) cc_final: 0.7937 (tm-30) REVERT: J 5 GLN cc_start: 0.8553 (tt0) cc_final: 0.8226 (tm-30) REVERT: J 6 GLU cc_start: 0.8391 (mp0) cc_final: 0.7777 (mp0) REVERT: J 67 ARG cc_start: 0.8479 (ptt90) cc_final: 0.8268 (ptt90) REVERT: J 73 ASP cc_start: 0.8312 (t0) cc_final: 0.7821 (t0) REVERT: J 87 THR cc_start: 0.9205 (OUTLIER) cc_final: 0.8972 (t) REVERT: J 103 ASP cc_start: 0.8125 (t0) cc_final: 0.7518 (t70) REVERT: J 105 ASP cc_start: 0.8238 (m-30) cc_final: 0.7942 (m-30) REVERT: M 61 GLU cc_start: 0.8441 (tp30) cc_final: 0.8222 (tp30) REVERT: M 85 LYS cc_start: 0.8966 (mttt) cc_final: 0.8499 (mtpp) REVERT: M 113 LYS cc_start: 0.8080 (ttpp) cc_final: 0.7880 (ttpp) REVERT: N 17 GLU cc_start: 0.8273 (tt0) cc_final: 0.7734 (tt0) REVERT: N 42 TYR cc_start: 0.8914 (m-80) cc_final: 0.8604 (m-80) REVERT: N 85 LYS cc_start: 0.8901 (mttt) cc_final: 0.8544 (mmmm) REVERT: N 87 GLU cc_start: 0.8633 (pm20) cc_final: 0.8372 (pm20) REVERT: A 93 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7824 (mp0) REVERT: A 120 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7864 (tpp) REVERT: A 279 ASP cc_start: 0.8887 (t0) cc_final: 0.8494 (t0) REVERT: B 93 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7790 (mp0) REVERT: B 158 MET cc_start: 0.8441 (tpp) cc_final: 0.8178 (tpp) REVERT: B 249 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8235 (mp0) REVERT: B 274 TRP cc_start: 0.7863 (t-100) cc_final: 0.7196 (t-100) REVERT: B 279 ASP cc_start: 0.8953 (t0) cc_final: 0.8504 (t0) REVERT: B 292 MET cc_start: 0.8522 (mtp) cc_final: 0.8272 (mtt) outliers start: 28 outliers final: 13 residues processed: 208 average time/residue: 1.6072 time to fit residues: 357.1068 Evaluate side-chains 203 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 185 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain L residue 35 GLN Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain I residue 107 TYR Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain M residue 95 GLN Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 249 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 82 GLN M 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12246 Z= 0.194 Angle : 0.596 12.012 16701 Z= 0.271 Chirality : 0.040 0.205 1833 Planarity : 0.003 0.030 2004 Dihedral : 7.651 89.285 1689 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.95 % Allowed : 19.47 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.23), residues: 1410 helix: 1.27 (0.23), residues: 600 sheet: -0.99 (0.28), residues: 324 loop : -0.81 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 274 HIS 0.002 0.000 HIS A 268 PHE 0.010 0.001 PHE A 291 TYR 0.024 0.001 TYR B 219 ARG 0.008 0.001 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 1.546 Fit side-chains revert: symmetry clash REVERT: C 93 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7729 (mp0) REVERT: C 104 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6964 (tp40) REVERT: C 274 TRP cc_start: 0.7558 (t-100) cc_final: 0.7035 (t-100) REVERT: C 279 ASP cc_start: 0.8814 (t0) cc_final: 0.8325 (t0) REVERT: L 17 GLU cc_start: 0.8435 (tt0) cc_final: 0.8114 (tt0) REVERT: L 35 GLN cc_start: 0.8663 (mt0) cc_final: 0.8423 (mt0) REVERT: L 61 GLU cc_start: 0.8505 (tp30) cc_final: 0.8300 (tp30) REVERT: H 3 GLN cc_start: 0.8225 (tp40) cc_final: 0.7846 (tm-30) REVERT: H 5 GLN cc_start: 0.8603 (tt0) cc_final: 0.8111 (pp30) REVERT: H 13 LYS cc_start: 0.8759 (mmtm) cc_final: 0.8360 (mmmt) REVERT: H 45 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8401 (tttp) REVERT: H 73 ASP cc_start: 0.8293 (t0) cc_final: 0.7854 (t0) REVERT: H 103 ASP cc_start: 0.8036 (t0) cc_final: 0.7396 (t70) REVERT: H 105 ASP cc_start: 0.8287 (m-30) cc_final: 0.8005 (m-30) REVERT: I 3 GLN cc_start: 0.8194 (tp40) cc_final: 0.7904 (tm-30) REVERT: I 44 ASN cc_start: 0.8700 (m110) cc_final: 0.8062 (p0) REVERT: I 45 LYS cc_start: 0.8547 (tttt) cc_final: 0.8246 (tttm) REVERT: I 73 ASP cc_start: 0.8215 (t0) cc_final: 0.7796 (t0) REVERT: I 103 ASP cc_start: 0.7897 (t0) cc_final: 0.7415 (t0) REVERT: J 3 GLN cc_start: 0.8232 (tp40) cc_final: 0.7942 (tm-30) REVERT: J 5 GLN cc_start: 0.8545 (tt0) cc_final: 0.8132 (tm-30) REVERT: J 67 ARG cc_start: 0.8456 (ptt90) cc_final: 0.8088 (ptm-80) REVERT: J 73 ASP cc_start: 0.8310 (t0) cc_final: 0.7814 (t0) REVERT: J 87 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.8986 (t) REVERT: J 103 ASP cc_start: 0.8101 (t0) cc_final: 0.7500 (t70) REVERT: J 105 ASP cc_start: 0.8244 (m-30) cc_final: 0.7947 (m-30) REVERT: M 61 GLU cc_start: 0.8442 (tp30) cc_final: 0.8220 (tp30) REVERT: M 87 GLU cc_start: 0.8716 (pm20) cc_final: 0.8445 (pm20) REVERT: N 17 GLU cc_start: 0.8275 (tt0) cc_final: 0.7736 (tt0) REVERT: N 85 LYS cc_start: 0.8905 (mttt) cc_final: 0.8541 (mmmm) REVERT: N 87 GLU cc_start: 0.8630 (pm20) cc_final: 0.8370 (pm20) REVERT: A 93 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7825 (mp0) REVERT: A 120 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7868 (tpp) REVERT: A 279 ASP cc_start: 0.8885 (t0) cc_final: 0.8491 (t0) REVERT: B 93 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7776 (mp0) REVERT: B 158 MET cc_start: 0.8436 (tpp) cc_final: 0.8233 (tpp) REVERT: B 248 ARG cc_start: 0.8629 (mmm-85) cc_final: 0.8261 (mmm160) REVERT: B 249 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8280 (mp0) REVERT: B 274 TRP cc_start: 0.7864 (t-100) cc_final: 0.7203 (t-100) REVERT: B 279 ASP cc_start: 0.8952 (t0) cc_final: 0.8499 (t0) REVERT: B 292 MET cc_start: 0.8497 (mtp) cc_final: 0.8258 (mtt) outliers start: 25 outliers final: 15 residues processed: 210 average time/residue: 1.6096 time to fit residues: 361.2311 Evaluate side-chains 207 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 189 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 107 TYR Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain M residue 95 GLN Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 84 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 chunk 111 optimal weight: 0.0570 chunk 11 optimal weight: 0.9990 chunk 86 optimal weight: 0.1980 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12246 Z= 0.165 Angle : 0.583 10.897 16701 Z= 0.267 Chirality : 0.040 0.192 1833 Planarity : 0.003 0.032 2004 Dihedral : 7.485 87.931 1689 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.56 % Allowed : 20.17 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.23), residues: 1410 helix: 1.35 (0.23), residues: 597 sheet: -0.96 (0.28), residues: 324 loop : -0.83 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 274 HIS 0.002 0.000 HIS A 268 PHE 0.012 0.001 PHE A 291 TYR 0.023 0.001 TYR B 219 ARG 0.008 0.001 ARG A 248 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 195 time to evaluate : 1.421 Fit side-chains revert: symmetry clash REVERT: C 93 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7707 (mp0) REVERT: C 104 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6927 (tp40) REVERT: C 274 TRP cc_start: 0.7535 (t-100) cc_final: 0.7030 (t-100) REVERT: C 279 ASP cc_start: 0.8817 (t0) cc_final: 0.8398 (t0) REVERT: L 4 MET cc_start: 0.8656 (mmm) cc_final: 0.8344 (mmm) REVERT: L 17 GLU cc_start: 0.8431 (tt0) cc_final: 0.8089 (tt0) REVERT: L 35 GLN cc_start: 0.8627 (mt0) cc_final: 0.8386 (mt0) REVERT: L 61 GLU cc_start: 0.8509 (tp30) cc_final: 0.8278 (tp30) REVERT: L 113 LYS cc_start: 0.8090 (ttpp) cc_final: 0.7859 (ttpp) REVERT: H 3 GLN cc_start: 0.8220 (tp40) cc_final: 0.7892 (tm-30) REVERT: H 5 GLN cc_start: 0.8640 (tt0) cc_final: 0.8208 (pp30) REVERT: H 13 LYS cc_start: 0.8765 (mmtm) cc_final: 0.8369 (mmmt) REVERT: H 45 LYS cc_start: 0.8644 (ttpp) cc_final: 0.8348 (tttp) REVERT: H 73 ASP cc_start: 0.8246 (t0) cc_final: 0.7805 (t0) REVERT: H 103 ASP cc_start: 0.7971 (t0) cc_final: 0.7354 (t70) REVERT: H 105 ASP cc_start: 0.8274 (m-30) cc_final: 0.7996 (m-30) REVERT: I 3 GLN cc_start: 0.8177 (tp40) cc_final: 0.7906 (tm-30) REVERT: I 45 LYS cc_start: 0.8524 (tttt) cc_final: 0.8250 (tttm) REVERT: I 73 ASP cc_start: 0.8204 (t0) cc_final: 0.7803 (t0) REVERT: I 103 ASP cc_start: 0.7849 (t0) cc_final: 0.7376 (t0) REVERT: J 3 GLN cc_start: 0.8152 (tp40) cc_final: 0.7849 (tm-30) REVERT: J 5 GLN cc_start: 0.8597 (tt0) cc_final: 0.8196 (tm-30) REVERT: J 67 ARG cc_start: 0.8461 (ptt90) cc_final: 0.8103 (ptm-80) REVERT: J 73 ASP cc_start: 0.8291 (t0) cc_final: 0.7779 (t0) REVERT: J 87 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8966 (t) REVERT: J 103 ASP cc_start: 0.8058 (t0) cc_final: 0.7468 (t70) REVERT: J 105 ASP cc_start: 0.8224 (m-30) cc_final: 0.7929 (m-30) REVERT: M 61 GLU cc_start: 0.8433 (tp30) cc_final: 0.8215 (tp30) REVERT: N 17 GLU cc_start: 0.8273 (tt0) cc_final: 0.7748 (tt0) REVERT: N 85 LYS cc_start: 0.8901 (mttt) cc_final: 0.8631 (mmmm) REVERT: A 93 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7830 (mp0) REVERT: A 279 ASP cc_start: 0.8884 (t0) cc_final: 0.8490 (t0) REVERT: B 93 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7781 (mp0) REVERT: B 249 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8284 (mp0) REVERT: B 274 TRP cc_start: 0.7800 (t-100) cc_final: 0.7173 (t-100) REVERT: B 279 ASP cc_start: 0.8946 (t0) cc_final: 0.8489 (t0) REVERT: B 292 MET cc_start: 0.8419 (mtp) cc_final: 0.8172 (mtt) outliers start: 20 outliers final: 14 residues processed: 210 average time/residue: 1.5471 time to fit residues: 347.4212 Evaluate side-chains 200 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 183 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain I residue 107 TYR Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain M residue 95 GLN Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 249 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 31 optimal weight: 0.0970 chunk 112 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 115 optimal weight: 0.0470 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.077390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.058520 restraints weight = 25832.065| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.58 r_work: 0.2702 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12246 Z= 0.161 Angle : 0.589 10.661 16701 Z= 0.270 Chirality : 0.040 0.200 1833 Planarity : 0.003 0.033 2004 Dihedral : 7.284 86.758 1689 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.48 % Allowed : 21.03 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.23), residues: 1410 helix: 1.39 (0.23), residues: 597 sheet: -0.95 (0.29), residues: 318 loop : -0.86 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 274 HIS 0.002 0.000 HIS A 268 PHE 0.009 0.001 PHE B 291 TYR 0.023 0.001 TYR B 219 ARG 0.009 0.001 ARG C 248 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5647.05 seconds wall clock time: 100 minutes 54.53 seconds (6054.53 seconds total)