Starting phenix.real_space_refine on Tue Mar 3 19:50:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6j5a_0670/03_2026/6j5a_0670.cif Found real_map, /net/cci-nas-00/data/ceres_data/6j5a_0670/03_2026/6j5a_0670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6j5a_0670/03_2026/6j5a_0670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6j5a_0670/03_2026/6j5a_0670.map" model { file = "/net/cci-nas-00/data/ceres_data/6j5a_0670/03_2026/6j5a_0670.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6j5a_0670/03_2026/6j5a_0670.cif" } resolution = 4.35 write_initial_geo_file = False refinement { macro_cycles = 10 } 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: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 5542 2.51 5 N 1423 2.21 5 O 1530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8544 Number of models: 1 Model: "" Number of chains: 18 Chain: "b" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 440 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 5, 'TRANS': 76} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLU:plan': 5, 'HIS:plan': 1, 'ARG:plan': 1, 'PHE:plan': 5, 'GLN:plan1': 1, 'TYR:plan': 5} Unresolved non-hydrogen planarities: 99 Chain: "d" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 2, 'ASP:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "e" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 315 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'TRANS': 62} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'UNK:plan-1': 63} Unresolved non-hydrogen planarities: 63 Chain: "f" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 530 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 3, 'TRANS': 83} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 5, 'GLU:plan': 2, 'TRP:plan': 1, 'PHE:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 6, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 112 Chain: "g" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 420 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'TRANS': 83} Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'UNK:plan-1': 84} Unresolved non-hydrogen planarities: 84 Chain: "i" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 306 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 41} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "k" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 145 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'UNK:plan-1': 29} Unresolved non-hydrogen planarities: 29 Chain: "8" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 251 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "a" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1706 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 210} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "K" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "L" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "M" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "N" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "O" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "P" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "Q" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "R" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "u" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 210 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'TRANS': 41} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'UNK:plan-1': 42} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 1.98, per 1000 atoms: 0.23 Number of scatterers: 8544 At special positions: 0 Unit cell: (111.78, 109.02, 113.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 1530 8.00 N 1423 7.00 C 5542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 314.3 milliseconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2326 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 0 sheets defined 89.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'b' and resid 3 through 31 Proline residue: b 18 - end of helix Proline residue: b 27 - end of helix removed outlier: 3.504A pdb=" N VAL b 31 " --> pdb=" O PRO b 27 " (cutoff:3.500A) Processing helix chain 'b' and resid 37 through 42 removed outlier: 3.917A pdb=" N LEU b 41 " --> pdb=" O LEU b 37 " (cutoff:3.500A) Processing helix chain 'b' and resid 43 through 48 Processing helix chain 'b' and resid 49 through 51 No H-bonds generated for 'chain 'b' and resid 49 through 51' Processing helix chain 'b' and resid 61 through 83 removed outlier: 4.190A pdb=" N LEU b 67 " --> pdb=" O THR b 63 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL b 68 " --> pdb=" O ILE b 64 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR b 69 " --> pdb=" O GLY b 65 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE b 70 " --> pdb=" O VAL b 66 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL b 71 " --> pdb=" O LEU b 67 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS b 72 " --> pdb=" O VAL b 68 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS b 73 " --> pdb=" O TYR b 69 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY b 75 " --> pdb=" O VAL b 71 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLY b 79 " --> pdb=" O GLY b 75 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA b 80 " --> pdb=" O ALA b 76 " (cutoff:3.500A) Processing helix chain 'd' and resid 133 through 137 removed outlier: 3.864A pdb=" N GLU d 137 " --> pdb=" O ASP d 134 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 63 removed outlier: 3.501A pdb=" N UNK e 42 " --> pdb=" O UNK e 38 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 15 removed outlier: 3.502A pdb=" N LYS f 7 " --> pdb=" O VAL f 3 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP f 8 " --> pdb=" O VAL f 4 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG f 9 " --> pdb=" O PRO f 5 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU f 11 " --> pdb=" O LYS f 7 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL f 14 " --> pdb=" O ARG f 10 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS f 15 " --> pdb=" O LEU f 11 " (cutoff:3.500A) Processing helix chain 'f' and resid 27 through 35 removed outlier: 3.749A pdb=" N GLY f 32 " --> pdb=" O PHE f 28 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE f 33 " --> pdb=" O THR f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 36 through 41 Processing helix chain 'f' and resid 42 through 44 No H-bonds generated for 'chain 'f' and resid 42 through 44' Processing helix chain 'f' and resid 55 through 60 removed outlier: 3.617A pdb=" N LEU f 59 " --> pdb=" O SER f 55 " (cutoff:3.500A) Processing helix chain 'f' and resid 61 through 75 removed outlier: 3.526A pdb=" N VAL f 67 " --> pdb=" O LEU f 63 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL f 68 " --> pdb=" O ALA f 64 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N CYS f 72 " --> pdb=" O VAL f 68 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG f 73 " --> pdb=" O PHE f 69 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER f 74 " --> pdb=" O ASN f 70 " (cutoff:3.500A) Processing helix chain 'g' and resid 2 through 32 removed outlier: 3.669A pdb=" N UNK g 7 " --> pdb=" O UNK g 3 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N UNK g 8 " --> pdb=" O UNK g 4 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N UNK g 18 " --> pdb=" O UNK g 14 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N UNK g 21 " --> pdb=" O UNK g 17 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N UNK g 25 " --> pdb=" O UNK g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 65 Processing helix chain 'g' and resid 65 through 84 removed outlier: 3.564A pdb=" N UNK g 74 " --> pdb=" O UNK g 70 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N UNK g 77 " --> pdb=" O UNK g 73 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N UNK g 78 " --> pdb=" O UNK g 74 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N UNK g 79 " --> pdb=" O UNK g 75 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N UNK g 83 " --> pdb=" O UNK g 79 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N UNK g 84 " --> pdb=" O UNK g 80 " (cutoff:3.500A) Processing helix chain 'i' and resid 14 through 26 removed outlier: 3.975A pdb=" N ASN i 19 " --> pdb=" O LYS i 15 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER i 20 " --> pdb=" O LYS i 16 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU i 23 " --> pdb=" O ASN i 19 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N THR i 24 " --> pdb=" O SER i 20 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 48 removed outlier: 4.493A pdb=" N LEU i 31 " --> pdb=" O MET i 27 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 29 removed outlier: 3.818A pdb=" N UNK k 16 " --> pdb=" O UNK k 12 " (cutoff:3.500A) Processing helix chain '8' and resid 12 through 16 removed outlier: 3.667A pdb=" N SER 8 15 " --> pdb=" O THR 8 12 " (cutoff:3.500A) Processing helix chain '8' and resid 19 through 28 removed outlier: 3.706A pdb=" N LEU 8 23 " --> pdb=" O THR 8 19 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLN 8 25 " --> pdb=" O PHE 8 21 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU 8 26 " --> pdb=" O ILE 8 22 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 24 removed outlier: 4.165A pdb=" N ILE a 23 " --> pdb=" O ILE a 19 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 29 Processing helix chain 'a' and resid 43 through 54 removed outlier: 3.796A pdb=" N LEU a 49 " --> pdb=" O ILE a 45 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN a 51 " --> pdb=" O GLN a 47 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR a 53 " --> pdb=" O LEU a 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 68 through 73 removed outlier: 3.737A pdb=" N LEU a 72 " --> pdb=" O TRP a 68 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET a 73 " --> pdb=" O SER a 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 68 through 73' Processing helix chain 'a' and resid 73 through 82 removed outlier: 3.814A pdb=" N MET a 77 " --> pdb=" O MET a 73 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE a 79 " --> pdb=" O LEU a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 88 removed outlier: 3.820A pdb=" N LEU a 87 " --> pdb=" O ILE a 84 " (cutoff:3.500A) Processing helix chain 'a' and resid 93 through 96 Processing helix chain 'a' and resid 97 through 102 removed outlier: 4.551A pdb=" N ASN a 101 " --> pdb=" O GLN a 97 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU a 102 " --> pdb=" O LEU a 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 97 through 102' Processing helix chain 'a' and resid 105 through 117 removed outlier: 4.139A pdb=" N ALA a 111 " --> pdb=" O PRO a 107 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR a 112 " --> pdb=" O LEU a 108 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL a 113 " --> pdb=" O TRP a 109 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE a 114 " --> pdb=" O SER a 110 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR a 115 " --> pdb=" O ALA a 111 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY a 116 " --> pdb=" O THR a 112 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE a 117 " --> pdb=" O VAL a 113 " (cutoff:3.500A) Processing helix chain 'a' and resid 150 through 180 removed outlier: 4.580A pdb=" N VAL a 154 " --> pdb=" O PHE a 150 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG a 159 " --> pdb=" O ALA a 155 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN a 163 " --> pdb=" O ARG a 159 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE a 164 " --> pdb=" O LEU a 160 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR a 165 " --> pdb=" O THR a 161 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA a 166 " --> pdb=" O ALA a 162 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS a 168 " --> pdb=" O ILE a 164 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU a 170 " --> pdb=" O ALA a 166 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR a 178 " --> pdb=" O ILE a 174 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU a 179 " --> pdb=" O GLY a 175 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 202 removed outlier: 4.207A pdb=" N PHE a 190 " --> pdb=" O THR a 186 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR a 200 " --> pdb=" O LEU a 196 " (cutoff:3.500A) Processing helix chain 'a' and resid 206 through 222 removed outlier: 3.834A pdb=" N GLN a 210 " --> pdb=" O VAL a 206 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA a 211 " --> pdb=" O ALA a 207 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR a 212 " --> pdb=" O LEU a 208 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR a 215 " --> pdb=" O ALA a 211 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU a 216 " --> pdb=" O TYR a 212 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER a 219 " --> pdb=" O THR a 215 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 15 removed outlier: 3.700A pdb=" N ILE K 9 " --> pdb=" O ALA K 5 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY K 12 " --> pdb=" O PHE K 8 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR K 15 " --> pdb=" O ALA K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 37 removed outlier: 3.958A pdb=" N GLY K 26 " --> pdb=" O GLY K 22 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR K 27 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL K 28 " --> pdb=" O GLY K 24 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE K 29 " --> pdb=" O ILE K 25 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET K 32 " --> pdb=" O VAL K 28 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE K 33 " --> pdb=" O PHE K 29 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE K 34 " --> pdb=" O GLY K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 73 removed outlier: 4.206A pdb=" N SER K 48 " --> pdb=" O GLN K 44 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER K 57 " --> pdb=" O GLY K 53 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA K 59 " --> pdb=" O ALA K 55 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE K 63 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N CYS K 64 " --> pdb=" O MET K 60 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU K 65 " --> pdb=" O GLY K 61 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU K 72 " --> pdb=" O ALA K 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 15 removed outlier: 3.631A pdb=" N ILE L 9 " --> pdb=" O ALA L 5 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA L 11 " --> pdb=" O LYS L 7 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA L 13 " --> pdb=" O ILE L 9 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR L 15 " --> pdb=" O ALA L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 24 Processing helix chain 'L' and resid 24 through 29 removed outlier: 4.195A pdb=" N VAL L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 35 removed outlier: 3.546A pdb=" N ILE L 34 " --> pdb=" O GLY L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 73 removed outlier: 4.140A pdb=" N SER L 48 " --> pdb=" O GLN L 44 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA L 50 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER L 57 " --> pdb=" O GLY L 53 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY L 61 " --> pdb=" O SER L 57 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE L 63 " --> pdb=" O ALA L 59 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N CYS L 64 " --> pdb=" O MET L 60 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA L 68 " --> pdb=" O CYS L 64 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU L 72 " --> pdb=" O ALA L 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 14 removed outlier: 3.536A pdb=" N LYS M 7 " --> pdb=" O ASP M 3 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY M 12 " --> pdb=" O PHE M 8 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA M 14 " --> pdb=" O GLY M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 29 removed outlier: 4.418A pdb=" N SER M 21 " --> pdb=" O GLY M 17 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA M 23 " --> pdb=" O ALA M 19 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLY M 26 " --> pdb=" O GLY M 22 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL M 28 " --> pdb=" O GLY M 24 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE M 29 " --> pdb=" O ILE M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 39 removed outlier: 3.555A pdb=" N ARG M 38 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN M 39 " --> pdb=" O GLY M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 56 removed outlier: 4.172A pdb=" N SER M 48 " --> pdb=" O GLN M 44 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA M 50 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU M 52 " --> pdb=" O SER M 48 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY M 53 " --> pdb=" O TYR M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 71 removed outlier: 3.989A pdb=" N LEU M 65 " --> pdb=" O GLY M 61 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL M 67 " --> pdb=" O PHE M 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 13 removed outlier: 3.513A pdb=" N PHE N 8 " --> pdb=" O THR N 4 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY N 10 " --> pdb=" O ALA N 6 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA N 11 " --> pdb=" O LYS N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 19 removed outlier: 3.631A pdb=" N GLY N 17 " --> pdb=" O ALA N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 37 removed outlier: 3.569A pdb=" N ILE N 25 " --> pdb=" O SER N 21 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY N 26 " --> pdb=" O GLY N 22 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL N 28 " --> pdb=" O GLY N 24 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET N 32 " --> pdb=" O VAL N 28 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE N 33 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE N 34 " --> pdb=" O GLY N 30 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY N 35 " --> pdb=" O SER N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 63 removed outlier: 4.086A pdb=" N SER N 48 " --> pdb=" O GLN N 44 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE N 51 " --> pdb=" O PHE N 47 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU N 52 " --> pdb=" O SER N 48 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY N 53 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE N 63 " --> pdb=" O ALA N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 73 removed outlier: 3.511A pdb=" N PHE N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU N 70 " --> pdb=" O MET N 66 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE N 71 " --> pdb=" O VAL N 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 12 removed outlier: 3.695A pdb=" N PHE O 8 " --> pdb=" O THR O 4 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE O 9 " --> pdb=" O ALA O 5 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY O 10 " --> pdb=" O ALA O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 31 removed outlier: 3.633A pdb=" N ILE O 25 " --> pdb=" O SER O 21 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR O 27 " --> pdb=" O ALA O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 37 Processing helix chain 'O' and resid 44 through 71 removed outlier: 3.966A pdb=" N SER O 48 " --> pdb=" O GLN O 44 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA O 50 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU O 56 " --> pdb=" O LEU O 52 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N CYS O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU O 65 " --> pdb=" O GLY O 61 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N MET O 66 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL O 67 " --> pdb=" O PHE O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 14 removed outlier: 3.784A pdb=" N PHE P 8 " --> pdb=" O THR P 4 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE P 9 " --> pdb=" O ALA P 5 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA P 11 " --> pdb=" O LYS P 7 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY P 12 " --> pdb=" O PHE P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 26 removed outlier: 3.676A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY P 24 " --> pdb=" O GLY P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 Processing helix chain 'P' and resid 32 through 37 Processing helix chain 'P' and resid 44 through 73 removed outlier: 4.411A pdb=" N SER P 48 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA P 50 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA P 59 " --> pdb=" O ALA P 55 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE P 63 " --> pdb=" O ALA P 59 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N CYS P 64 " --> pdb=" O MET P 60 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU P 65 " --> pdb=" O GLY P 61 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU P 70 " --> pdb=" O MET P 66 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE P 71 " --> pdb=" O VAL P 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 15 removed outlier: 3.643A pdb=" N PHE Q 8 " --> pdb=" O THR Q 4 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY Q 10 " --> pdb=" O ALA Q 6 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA Q 11 " --> pdb=" O LYS Q 7 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY Q 12 " --> pdb=" O PHE Q 8 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA Q 13 " --> pdb=" O ILE Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 24 Processing helix chain 'Q' and resid 27 through 37 removed outlier: 3.952A pdb=" N MET Q 32 " --> pdb=" O VAL Q 28 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE Q 33 " --> pdb=" O PHE Q 29 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE Q 34 " --> pdb=" O GLY Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 73 removed outlier: 3.829A pdb=" N SER Q 48 " --> pdb=" O GLN Q 44 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR Q 49 " --> pdb=" O GLN Q 45 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA Q 50 " --> pdb=" O LEU Q 46 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU Q 52 " --> pdb=" O SER Q 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE Q 54 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS Q 64 " --> pdb=" O MET Q 60 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA Q 68 " --> pdb=" O CYS Q 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU Q 70 " --> pdb=" O MET Q 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 16 removed outlier: 3.812A pdb=" N PHE R 8 " --> pdb=" O THR R 4 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE R 9 " --> pdb=" O ALA R 5 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY R 10 " --> pdb=" O ALA R 6 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA R 14 " --> pdb=" O GLY R 10 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR R 15 " --> pdb=" O ALA R 11 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL R 16 " --> pdb=" O GLY R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 37 removed outlier: 4.294A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY R 22 " --> pdb=" O VAL R 18 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY R 26 " --> pdb=" O GLY R 22 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR R 27 " --> pdb=" O ALA R 23 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE R 29 " --> pdb=" O ILE R 25 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE R 33 " --> pdb=" O PHE R 29 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE R 34 " --> pdb=" O GLY R 30 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA R 37 " --> pdb=" O ILE R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 73 removed outlier: 3.664A pdb=" N SER R 48 " --> pdb=" O GLN R 44 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA R 50 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA R 55 " --> pdb=" O ILE R 51 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL R 67 " --> pdb=" O PHE R 63 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA R 68 " --> pdb=" O CYS R 64 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU R 72 " --> pdb=" O ALA R 68 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE R 73 " --> pdb=" O PHE R 69 " (cutoff:3.500A) Processing helix chain 'u' and resid 3 through 9 removed outlier: 3.632A pdb=" N UNK u 7 " --> pdb=" O UNK u 3 " (cutoff:3.500A) Processing helix chain 'u' and resid 16 through 35 removed outlier: 4.471A pdb=" N UNK u 20 " --> pdb=" O UNK u 16 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N UNK u 21 " --> pdb=" O UNK u 17 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N UNK u 29 " --> pdb=" O UNK u 25 " (cutoff:3.500A) 451 hydrogen bonds defined for protein. 1329 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: 1.17 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2698 1.34 - 1.46: 1859 1.46 - 1.58: 4020 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 8665 Sorted by residual: bond pdb=" C GLN a 152 " pdb=" N PRO a 153 " ideal model delta sigma weight residual 1.336 1.366 -0.030 1.20e-02 6.94e+03 6.41e+00 bond pdb=" CA THR b 32 " pdb=" C THR b 32 " ideal model delta sigma weight residual 1.523 1.553 -0.029 1.30e-02 5.92e+03 5.07e+00 bond pdb=" N ASN M 39 " pdb=" CA ASN M 39 " ideal model delta sigma weight residual 1.462 1.441 0.021 1.00e-02 1.00e+04 4.34e+00 bond pdb=" CB PHE a 214 " pdb=" CG PHE a 214 " ideal model delta sigma weight residual 1.502 1.454 0.048 2.30e-02 1.89e+03 4.31e+00 bond pdb=" N UNK g 38 " pdb=" CA UNK g 38 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.12e+00 ... (remaining 8660 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 11454 3.04 - 6.07: 286 6.07 - 9.11: 37 9.11 - 12.15: 9 12.15 - 15.18: 1 Bond angle restraints: 11787 Sorted by residual: angle pdb=" C UNK g 37 " pdb=" N UNK g 38 " pdb=" CA UNK g 38 " ideal model delta sigma weight residual 121.70 136.88 -15.18 1.80e+00 3.09e-01 7.11e+01 angle pdb=" C SER 8 7 " pdb=" N THR 8 8 " pdb=" CA THR 8 8 " ideal model delta sigma weight residual 121.54 133.17 -11.63 1.91e+00 2.74e-01 3.71e+01 angle pdb=" N LEU a 136 " pdb=" CA LEU a 136 " pdb=" C LEU a 136 " ideal model delta sigma weight residual 113.01 119.93 -6.92 1.20e+00 6.94e-01 3.32e+01 angle pdb=" N ALA a 135 " pdb=" CA ALA a 135 " pdb=" C ALA a 135 " ideal model delta sigma weight residual 111.69 118.55 -6.86 1.23e+00 6.61e-01 3.11e+01 angle pdb=" N THR b 32 " pdb=" CA THR b 32 " pdb=" C THR b 32 " ideal model delta sigma weight residual 111.28 117.21 -5.93 1.09e+00 8.42e-01 2.96e+01 ... (remaining 11782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.31: 4272 14.31 - 28.62: 521 28.62 - 42.94: 154 42.94 - 57.25: 41 57.25 - 71.56: 6 Dihedral angle restraints: 4994 sinusoidal: 1377 harmonic: 3617 Sorted by residual: dihedral pdb=" CA THR 8 6 " pdb=" C THR 8 6 " pdb=" N SER 8 7 " pdb=" CA SER 8 7 " ideal model delta harmonic sigma weight residual -180.00 -131.76 -48.24 0 5.00e+00 4.00e-02 9.31e+01 dihedral pdb=" CA ILE f 23 " pdb=" C ILE f 23 " pdb=" N LEU f 24 " pdb=" CA LEU f 24 " ideal model delta harmonic sigma weight residual -180.00 -133.31 -46.69 0 5.00e+00 4.00e-02 8.72e+01 dihedral pdb=" CA THR 8 8 " pdb=" C THR 8 8 " pdb=" N TRP 8 9 " pdb=" CA TRP 8 9 " ideal model delta harmonic sigma weight residual 180.00 140.95 39.05 0 5.00e+00 4.00e-02 6.10e+01 ... (remaining 4991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1035 0.047 - 0.095: 316 0.095 - 0.142: 88 0.142 - 0.190: 27 0.190 - 0.237: 12 Chirality restraints: 1478 Sorted by residual: chirality pdb=" CB THR 8 8 " pdb=" CA THR 8 8 " pdb=" OG1 THR 8 8 " pdb=" CG2 THR 8 8 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL L 28 " pdb=" CA VAL L 28 " pdb=" CG1 VAL L 28 " pdb=" CG2 VAL L 28 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB VAL K 18 " pdb=" CA VAL K 18 " pdb=" CG1 VAL K 18 " pdb=" CG2 VAL K 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1475 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN O 39 " 0.062 5.00e-02 4.00e+02 9.42e-02 1.42e+01 pdb=" N PRO O 40 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO O 40 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO O 40 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU f 16 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C LEU f 16 " -0.058 2.00e-02 2.50e+03 pdb=" O LEU f 16 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY f 17 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN M 39 " -0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO M 40 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO M 40 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO M 40 " -0.043 5.00e-02 4.00e+02 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 70 2.48 - 3.09: 5633 3.09 - 3.69: 13365 3.69 - 4.30: 17885 4.30 - 4.90: 27831 Nonbonded interactions: 64784 Sorted by model distance: nonbonded pdb=" O LYS f 53 " pdb=" O ARG a 41 " model vdw 1.880 3.040 nonbonded pdb=" O UNK e 21 " pdb=" CB UNK e 25 " model vdw 1.935 2.752 nonbonded pdb=" O GLU f 13 " pdb=" N GLU f 18 " model vdw 1.956 3.120 nonbonded pdb=" O UNK e 22 " pdb=" CB UNK e 26 " model vdw 1.975 2.752 nonbonded pdb=" CA VAL f 14 " pdb=" O GLU f 18 " model vdw 2.046 3.470 ... (remaining 64779 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'K' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'L' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'M' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = chain 'N' selection = (chain 'O' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'P' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'Q' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'R' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.140 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5646 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 : 0.008 0.091 8665 Z= 0.355 Angle : 1.250 15.182 11787 Z= 0.730 Chirality : 0.054 0.237 1478 Planarity : 0.008 0.094 1488 Dihedral : 15.225 71.561 2668 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.88 % Favored : 90.54 % Rotamer: Outliers : 1.18 % Allowed : 19.15 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.59 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.05 (0.19), residues: 1036 helix: -4.00 (0.12), residues: 734 sheet: None (None), residues: 0 loop : -3.38 (0.31), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG a 159 TYR 0.029 0.003 TYR i 21 PHE 0.023 0.003 PHE M 29 TRP 0.015 0.003 TRP a 68 HIS 0.007 0.002 HIS a 172 Details of bonding type rmsd covalent geometry : bond 0.00795 ( 8665) covalent geometry : angle 1.25042 (11787) hydrogen bonds : bond 0.30901 ( 451) hydrogen bonds : angle 10.00849 ( 1329) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 310 time to evaluate : 0.227 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLN i 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 49 LEU cc_start: 0.8203 (tt) cc_final: 0.7914 (mm) REVERT: a 121 THR cc_start: 0.4359 (OUTLIER) cc_final: 0.3609 (t) REVERT: a 183 ASN cc_start: 0.6252 (m-40) cc_final: 0.5730 (p0) REVERT: a 203 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7446 (mp0) REVERT: a 209 ILE cc_start: 0.7352 (mm) cc_final: 0.7035 (mm) REVERT: L 66 MET cc_start: 0.2629 (mtt) cc_final: 0.2178 (ppp) REVERT: M 42 LEU cc_start: 0.4779 (OUTLIER) cc_final: 0.4368 (pp) REVERT: N 63 PHE cc_start: 0.6845 (p90) cc_final: 0.6530 (p90) REVERT: O 3 ASP cc_start: 0.6181 (p0) cc_final: 0.5898 (t0) REVERT: O 56 LEU cc_start: 0.8723 (tp) cc_final: 0.8487 (mp) REVERT: P 62 LEU cc_start: 0.6854 (mt) cc_final: 0.6475 (mt) REVERT: Q 25 ILE cc_start: 0.7563 (pt) cc_final: 0.7247 (pt) REVERT: R 62 LEU cc_start: 0.7522 (mm) cc_final: 0.7283 (mm) outliers start: 8 outliers final: 2 residues processed: 314 average time/residue: 0.0705 time to fit residues: 32.1304 Evaluate side-chains 203 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 199 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.0970 chunk 49 optimal weight: 0.0870 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.2980 chunk 117 optimal weight: 0.9980 overall best weight: 0.2354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 39 ASN a 83 ASN a 97 GLN a 168 HIS a 172 HIS K 45 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.169169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.141921 restraints weight = 19136.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.143399 restraints weight = 13033.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.143762 restraints weight = 10848.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.144540 restraints weight = 9318.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.144624 restraints weight = 8778.604| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8665 Z= 0.146 Angle : 0.756 8.357 11787 Z= 0.378 Chirality : 0.039 0.187 1478 Planarity : 0.005 0.058 1488 Dihedral : 6.467 46.045 1306 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.27 % Favored : 93.34 % Rotamer: Outliers : 0.29 % Allowed : 5.89 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.69 (0.22), residues: 1036 helix: -2.78 (0.15), residues: 781 sheet: None (None), residues: 0 loop : -3.43 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 38 TYR 0.013 0.001 TYR i 21 PHE 0.031 0.002 PHE M 8 TRP 0.020 0.002 TRP 8 9 HIS 0.011 0.002 HIS a 168 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8665) covalent geometry : angle 0.75635 (11787) hydrogen bonds : bond 0.04163 ( 451) hydrogen bonds : angle 4.86518 ( 1329) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 249 time to evaluate : 0.238 Fit side-chains TARDY: cannot create tardy model for: "GLN i 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 76 LYS cc_start: 0.8848 (tttm) cc_final: 0.8439 (mmtp) REVERT: i 27 MET cc_start: 0.8857 (mmp) cc_final: 0.8424 (mmp) REVERT: 8 16 MET cc_start: 0.6337 (mpp) cc_final: 0.5967 (mtm) REVERT: a 49 LEU cc_start: 0.8626 (tt) cc_final: 0.8266 (mm) REVERT: a 73 MET cc_start: 0.8395 (mmm) cc_final: 0.7954 (mmp) REVERT: a 214 PHE cc_start: 0.7183 (t80) cc_final: 0.6685 (t80) REVERT: L 66 MET cc_start: 0.2888 (mtt) cc_final: 0.2153 (ppp) REVERT: L 73 PHE cc_start: 0.5048 (m-80) cc_final: 0.4760 (t80) REVERT: N 39 ASN cc_start: 0.7515 (t0) cc_final: 0.7173 (t0) REVERT: N 65 LEU cc_start: 0.8348 (mm) cc_final: 0.8129 (mm) REVERT: N 66 MET cc_start: 0.7166 (mmm) cc_final: 0.6828 (mmp) REVERT: O 56 LEU cc_start: 0.8839 (tp) cc_final: 0.8452 (mp) REVERT: P 60 MET cc_start: 0.7850 (tpt) cc_final: 0.7620 (tpt) REVERT: Q 66 MET cc_start: 0.7763 (tpp) cc_final: 0.7392 (mmt) REVERT: R 60 MET cc_start: 0.3244 (mtm) cc_final: 0.2519 (mmm) REVERT: R 63 PHE cc_start: 0.6360 (m-10) cc_final: 0.6117 (m-10) outliers start: 2 outliers final: 0 residues processed: 251 average time/residue: 0.0602 time to fit residues: 22.9747 Evaluate side-chains 195 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 49 optimal weight: 0.0270 overall best weight: 1.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.157927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.127534 restraints weight = 20121.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.129361 restraints weight = 14508.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.130303 restraints weight = 11671.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.131257 restraints weight = 10239.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.131516 restraints weight = 9410.046| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8665 Z= 0.191 Angle : 0.781 7.822 11787 Z= 0.390 Chirality : 0.042 0.279 1478 Planarity : 0.005 0.060 1488 Dihedral : 5.990 44.045 1306 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.82 % Favored : 91.80 % Rotamer: Outliers : 0.29 % Allowed : 8.84 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.23), residues: 1036 helix: -2.06 (0.17), residues: 763 sheet: None (None), residues: 0 loop : -3.01 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG a 159 TYR 0.016 0.002 TYR M 36 PHE 0.025 0.002 PHE Q 54 TRP 0.026 0.004 TRP a 68 HIS 0.005 0.001 HIS a 172 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 8665) covalent geometry : angle 0.78137 (11787) hydrogen bonds : bond 0.04074 ( 451) hydrogen bonds : angle 4.43541 ( 1329) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 232 time to evaluate : 0.196 Fit side-chains REVERT: f 66 TYR cc_start: 0.7455 (t80) cc_final: 0.7002 (t80) REVERT: f 76 LYS cc_start: 0.8753 (tttm) cc_final: 0.8419 (mmtp) REVERT: i 27 MET cc_start: 0.8982 (mmp) cc_final: 0.8761 (mmp) REVERT: a 46 GLN cc_start: 0.8251 (mt0) cc_final: 0.8028 (tm-30) REVERT: a 209 ILE cc_start: 0.7920 (mm) cc_final: 0.7660 (mm) REVERT: a 214 PHE cc_start: 0.7342 (t80) cc_final: 0.7026 (t80) REVERT: K 7 LYS cc_start: 0.4094 (tptt) cc_final: 0.3487 (tptp) REVERT: N 32 MET cc_start: 0.8555 (tmm) cc_final: 0.8293 (tmm) REVERT: N 39 ASN cc_start: 0.7643 (t0) cc_final: 0.7410 (t0) REVERT: N 46 LEU cc_start: 0.6271 (mm) cc_final: 0.5739 (mm) REVERT: O 56 LEU cc_start: 0.9048 (tp) cc_final: 0.8709 (mp) REVERT: R 42 LEU cc_start: 0.7875 (pt) cc_final: 0.7348 (pt) REVERT: R 43 LYS cc_start: 0.8361 (mptt) cc_final: 0.7741 (ttpp) REVERT: R 60 MET cc_start: 0.3704 (mtp) cc_final: 0.3169 (mmm) REVERT: R 63 PHE cc_start: 0.6584 (m-10) cc_final: 0.6335 (m-10) outliers start: 2 outliers final: 0 residues processed: 233 average time/residue: 0.0586 time to fit residues: 20.9578 Evaluate side-chains 190 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 52 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 112 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 66 GLN ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.150271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.123197 restraints weight = 21019.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.123406 restraints weight = 16362.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.123351 restraints weight = 15164.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.123857 restraints weight = 13025.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.123978 restraints weight = 12137.725| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.7204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8665 Z= 0.233 Angle : 0.831 7.376 11787 Z= 0.420 Chirality : 0.045 0.286 1478 Planarity : 0.006 0.064 1488 Dihedral : 6.421 45.664 1306 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.82 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.24), residues: 1036 helix: -1.74 (0.17), residues: 734 sheet: None (None), residues: 0 loop : -2.70 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG i 26 TYR 0.019 0.003 TYR M 49 PHE 0.026 0.003 PHE M 63 TRP 0.013 0.004 TRP a 48 HIS 0.007 0.002 HIS a 223 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 8665) covalent geometry : angle 0.83062 (11787) hydrogen bonds : bond 0.04149 ( 451) hydrogen bonds : angle 4.67452 ( 1329) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 76 LYS cc_start: 0.8926 (tttm) cc_final: 0.8379 (mmtt) REVERT: i 46 LEU cc_start: 0.7537 (tp) cc_final: 0.7329 (pp) REVERT: a 77 MET cc_start: 0.7278 (tpp) cc_final: 0.6738 (tpp) REVERT: a 128 PHE cc_start: 0.7005 (m-10) cc_final: 0.6665 (m-80) REVERT: a 199 LEU cc_start: 0.8652 (tp) cc_final: 0.8190 (tt) REVERT: a 209 ILE cc_start: 0.8009 (mm) cc_final: 0.7802 (mm) REVERT: a 214 PHE cc_start: 0.7511 (t80) cc_final: 0.7197 (t80) REVERT: K 71 ILE cc_start: 0.6553 (pt) cc_final: 0.6339 (pt) REVERT: L 8 PHE cc_start: 0.6730 (m-80) cc_final: 0.6377 (m-80) REVERT: L 66 MET cc_start: 0.5643 (mmp) cc_final: 0.3371 (ppp) REVERT: M 71 ILE cc_start: 0.8372 (mm) cc_final: 0.8024 (mm) REVERT: N 39 ASN cc_start: 0.7707 (t0) cc_final: 0.7439 (t0) REVERT: P 62 LEU cc_start: 0.7105 (mt) cc_final: 0.6863 (mt) REVERT: R 27 THR cc_start: 0.9227 (p) cc_final: 0.8839 (t) REVERT: R 63 PHE cc_start: 0.6730 (m-10) cc_final: 0.6440 (m-10) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.0679 time to fit residues: 23.0998 Evaluate side-chains 189 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 24 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 70 ASN ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.150108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.120247 restraints weight = 20844.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.122417 restraints weight = 13801.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.123801 restraints weight = 10547.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.124378 restraints weight = 8907.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.124378 restraints weight = 8118.813| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.7894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8665 Z= 0.199 Angle : 0.758 8.230 11787 Z= 0.378 Chirality : 0.042 0.232 1478 Planarity : 0.005 0.055 1488 Dihedral : 6.033 46.718 1306 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.78 % Favored : 91.02 % Rotamer: Outliers : 0.15 % Allowed : 4.71 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.25), residues: 1036 helix: -1.53 (0.18), residues: 753 sheet: None (None), residues: 0 loop : -2.53 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG i 26 TYR 0.023 0.002 TYR K 49 PHE 0.028 0.002 PHE M 63 TRP 0.011 0.002 TRP 8 9 HIS 0.006 0.002 HIS a 172 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 8665) covalent geometry : angle 0.75848 (11787) hydrogen bonds : bond 0.03694 ( 451) hydrogen bonds : angle 4.37878 ( 1329) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 76 LYS cc_start: 0.8837 (tttm) cc_final: 0.8405 (mmtp) REVERT: i 46 LEU cc_start: 0.7544 (tp) cc_final: 0.7340 (pp) REVERT: a 77 MET cc_start: 0.7356 (tpp) cc_final: 0.6762 (tpp) REVERT: a 128 PHE cc_start: 0.6747 (m-10) cc_final: 0.6232 (m-80) REVERT: a 199 LEU cc_start: 0.8797 (tp) cc_final: 0.8373 (tt) REVERT: a 209 ILE cc_start: 0.8107 (mm) cc_final: 0.7821 (mm) REVERT: a 214 PHE cc_start: 0.7596 (t80) cc_final: 0.7261 (t80) REVERT: K 3 ASP cc_start: 0.8239 (m-30) cc_final: 0.7378 (t0) REVERT: L 66 MET cc_start: 0.5705 (mmp) cc_final: 0.5401 (mmp) REVERT: M 71 ILE cc_start: 0.8152 (mm) cc_final: 0.7941 (mm) REVERT: N 54 PHE cc_start: 0.7032 (t80) cc_final: 0.6707 (t80) REVERT: N 63 PHE cc_start: 0.8571 (p90) cc_final: 0.8353 (p90) REVERT: O 63 PHE cc_start: 0.8061 (t80) cc_final: 0.7757 (t80) REVERT: R 27 THR cc_start: 0.9405 (p) cc_final: 0.9118 (t) REVERT: R 42 LEU cc_start: 0.7998 (pt) cc_final: 0.7458 (pt) REVERT: R 43 LYS cc_start: 0.8490 (mptt) cc_final: 0.7996 (ttpp) REVERT: R 63 PHE cc_start: 0.6672 (m-10) cc_final: 0.6367 (m-10) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.0645 time to fit residues: 22.2915 Evaluate side-chains 195 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 112 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 74 optimal weight: 0.3980 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 80 HIS ** a 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.155071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.125076 restraints weight = 19864.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.127321 restraints weight = 13112.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.128217 restraints weight = 9975.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.129562 restraints weight = 8620.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.129946 restraints weight = 7639.502| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.8057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8665 Z= 0.121 Angle : 0.666 7.380 11787 Z= 0.325 Chirality : 0.039 0.388 1478 Planarity : 0.004 0.050 1488 Dihedral : 5.441 42.267 1306 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.24 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.26), residues: 1036 helix: -1.07 (0.19), residues: 751 sheet: None (None), residues: 0 loop : -2.39 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG i 26 TYR 0.018 0.001 TYR i 21 PHE 0.020 0.001 PHE O 29 TRP 0.013 0.001 TRP 8 9 HIS 0.002 0.001 HIS f 80 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8665) covalent geometry : angle 0.66558 (11787) hydrogen bonds : bond 0.03120 ( 451) hydrogen bonds : angle 3.78892 ( 1329) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 76 LYS cc_start: 0.8823 (tttm) cc_final: 0.8271 (mmtm) REVERT: i 27 MET cc_start: 0.8958 (mmp) cc_final: 0.8369 (mmm) REVERT: i 46 LEU cc_start: 0.7781 (tp) cc_final: 0.7444 (pp) REVERT: a 57 MET cc_start: 0.6470 (mmm) cc_final: 0.5970 (mpp) REVERT: a 77 MET cc_start: 0.7292 (tpp) cc_final: 0.6930 (tpp) REVERT: a 90 HIS cc_start: 0.3021 (m-70) cc_final: 0.2727 (m-70) REVERT: a 128 PHE cc_start: 0.6931 (m-10) cc_final: 0.6533 (m-80) REVERT: a 199 LEU cc_start: 0.8840 (tp) cc_final: 0.8402 (tt) REVERT: a 209 ILE cc_start: 0.7927 (mm) cc_final: 0.7614 (mm) REVERT: a 214 PHE cc_start: 0.7292 (t80) cc_final: 0.7033 (t80) REVERT: K 3 ASP cc_start: 0.8217 (m-30) cc_final: 0.7227 (t0) REVERT: M 71 ILE cc_start: 0.8088 (mm) cc_final: 0.7871 (mm) REVERT: N 39 ASN cc_start: 0.7544 (t0) cc_final: 0.7311 (t0) REVERT: N 54 PHE cc_start: 0.7079 (t80) cc_final: 0.6598 (t80) REVERT: R 27 THR cc_start: 0.9421 (p) cc_final: 0.9129 (t) REVERT: R 42 LEU cc_start: 0.7939 (pt) cc_final: 0.7642 (pt) REVERT: R 43 LYS cc_start: 0.8366 (mptt) cc_final: 0.7588 (ttpp) REVERT: R 63 PHE cc_start: 0.6690 (m-10) cc_final: 0.6343 (m-10) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.0657 time to fit residues: 22.7300 Evaluate side-chains 188 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 3 optimal weight: 8.9990 chunk 81 optimal weight: 0.0570 chunk 101 optimal weight: 0.7980 chunk 15 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 114 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 82 optimal weight: 0.0770 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.156142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.125998 restraints weight = 20513.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.128153 restraints weight = 13598.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.129286 restraints weight = 10422.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.130316 restraints weight = 8941.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.130581 restraints weight = 8037.841| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.8263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8665 Z= 0.117 Angle : 0.662 8.451 11787 Z= 0.319 Chirality : 0.038 0.317 1478 Planarity : 0.004 0.046 1488 Dihedral : 5.151 41.883 1306 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.34 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.26), residues: 1036 helix: -0.83 (0.19), residues: 767 sheet: None (None), residues: 0 loop : -2.22 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG i 26 TYR 0.015 0.001 TYR i 21 PHE 0.027 0.001 PHE M 63 TRP 0.019 0.002 TRP 8 9 HIS 0.002 0.001 HIS a 223 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8665) covalent geometry : angle 0.66180 (11787) hydrogen bonds : bond 0.02955 ( 451) hydrogen bonds : angle 3.63530 ( 1329) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 67 LEU cc_start: 0.7695 (pp) cc_final: 0.6989 (mp) REVERT: f 76 LYS cc_start: 0.8779 (tttm) cc_final: 0.8220 (mmtp) REVERT: i 27 MET cc_start: 0.8951 (mmp) cc_final: 0.8706 (mmm) REVERT: i 46 LEU cc_start: 0.7750 (tp) cc_final: 0.7464 (pp) REVERT: a 57 MET cc_start: 0.6573 (mmm) cc_final: 0.5984 (mpp) REVERT: a 77 MET cc_start: 0.7095 (tpp) cc_final: 0.6654 (tpp) REVERT: a 90 HIS cc_start: 0.3208 (m-70) cc_final: 0.2910 (m-70) REVERT: a 128 PHE cc_start: 0.6809 (m-10) cc_final: 0.6513 (m-80) REVERT: a 199 LEU cc_start: 0.8641 (tp) cc_final: 0.8283 (tt) REVERT: a 209 ILE cc_start: 0.7843 (mm) cc_final: 0.7522 (mm) REVERT: a 214 PHE cc_start: 0.7226 (t80) cc_final: 0.7003 (t80) REVERT: K 3 ASP cc_start: 0.8181 (m-30) cc_final: 0.7171 (t0) REVERT: L 66 MET cc_start: 0.5434 (mmp) cc_final: 0.3609 (ppp) REVERT: M 71 ILE cc_start: 0.7959 (mm) cc_final: 0.7743 (mm) REVERT: N 54 PHE cc_start: 0.7030 (t80) cc_final: 0.6245 (t80) REVERT: O 63 PHE cc_start: 0.7919 (t80) cc_final: 0.7697 (t80) REVERT: O 66 MET cc_start: 0.8620 (ppp) cc_final: 0.8172 (ppp) REVERT: R 7 LYS cc_start: 0.7093 (mmtt) cc_final: 0.6831 (ptmm) REVERT: R 27 THR cc_start: 0.9431 (p) cc_final: 0.9118 (t) REVERT: R 63 PHE cc_start: 0.6861 (m-10) cc_final: 0.6567 (m-10) REVERT: R 71 ILE cc_start: 0.8232 (tt) cc_final: 0.7741 (tt) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.0667 time to fit residues: 22.8423 Evaluate side-chains 196 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 24 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 103 optimal weight: 0.0010 chunk 122 optimal weight: 20.0000 chunk 49 optimal weight: 0.4980 chunk 80 optimal weight: 0.3980 chunk 27 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.153256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.123436 restraints weight = 19959.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.125664 restraints weight = 13044.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.127076 restraints weight = 9884.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.127456 restraints weight = 8349.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.128015 restraints weight = 7756.621| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.8586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8665 Z= 0.135 Angle : 0.684 8.796 11787 Z= 0.333 Chirality : 0.039 0.278 1478 Planarity : 0.004 0.050 1488 Dihedral : 5.196 42.279 1306 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.27), residues: 1036 helix: -0.74 (0.19), residues: 759 sheet: None (None), residues: 0 loop : -2.08 (0.40), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG i 26 TYR 0.017 0.001 TYR i 21 PHE 0.026 0.002 PHE M 63 TRP 0.021 0.002 TRP 8 9 HIS 0.002 0.001 HIS a 127 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8665) covalent geometry : angle 0.68353 (11787) hydrogen bonds : bond 0.03112 ( 451) hydrogen bonds : angle 3.75546 ( 1329) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 76 LYS cc_start: 0.8856 (tttm) cc_final: 0.8292 (mmtp) REVERT: i 46 LEU cc_start: 0.7775 (tp) cc_final: 0.7485 (pp) REVERT: a 57 MET cc_start: 0.6740 (mmm) cc_final: 0.6096 (mpp) REVERT: a 77 MET cc_start: 0.7288 (tpp) cc_final: 0.6843 (tpp) REVERT: a 128 PHE cc_start: 0.6920 (m-10) cc_final: 0.6670 (m-80) REVERT: a 147 ILE cc_start: 0.8263 (pt) cc_final: 0.8063 (pt) REVERT: a 199 LEU cc_start: 0.8688 (tp) cc_final: 0.8383 (tt) REVERT: a 209 ILE cc_start: 0.7930 (mm) cc_final: 0.7667 (mm) REVERT: a 214 PHE cc_start: 0.7384 (t80) cc_final: 0.7159 (t80) REVERT: K 3 ASP cc_start: 0.8338 (m-30) cc_final: 0.7264 (t0) REVERT: L 66 MET cc_start: 0.5430 (mmp) cc_final: 0.3613 (ppp) REVERT: M 60 MET cc_start: 0.7804 (mpp) cc_final: 0.6959 (tpt) REVERT: M 71 ILE cc_start: 0.7921 (mm) cc_final: 0.7711 (mm) REVERT: N 54 PHE cc_start: 0.6686 (t80) cc_final: 0.5939 (t80) REVERT: O 63 PHE cc_start: 0.8002 (t80) cc_final: 0.7700 (t80) REVERT: R 27 THR cc_start: 0.9463 (p) cc_final: 0.9128 (t) REVERT: R 63 PHE cc_start: 0.6981 (m-10) cc_final: 0.6676 (m-10) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.0635 time to fit residues: 20.9302 Evaluate side-chains 186 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 4 optimal weight: 6.9990 chunk 73 optimal weight: 0.1980 chunk 14 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 1 optimal weight: 30.0000 chunk 70 optimal weight: 0.7980 chunk 22 optimal weight: 0.0970 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 39 ASN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.155458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.125503 restraints weight = 20070.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.127565 restraints weight = 13376.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.128493 restraints weight = 10304.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.128506 restraints weight = 8927.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.128506 restraints weight = 8899.762| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.8769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8665 Z= 0.118 Angle : 0.678 8.926 11787 Z= 0.328 Chirality : 0.040 0.536 1478 Planarity : 0.004 0.048 1488 Dihedral : 4.936 41.247 1306 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.27), residues: 1036 helix: -0.58 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -2.03 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 73 TYR 0.017 0.001 TYR i 21 PHE 0.031 0.001 PHE M 29 TRP 0.018 0.001 TRP 8 9 HIS 0.003 0.001 HIS a 127 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8665) covalent geometry : angle 0.67774 (11787) hydrogen bonds : bond 0.02911 ( 451) hydrogen bonds : angle 3.53114 ( 1329) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 76 LYS cc_start: 0.8828 (tttm) cc_final: 0.8324 (mmtp) REVERT: i 27 MET cc_start: 0.8975 (mmp) cc_final: 0.8516 (mmm) REVERT: i 46 LEU cc_start: 0.7789 (tp) cc_final: 0.7416 (pp) REVERT: a 57 MET cc_start: 0.6774 (mmm) cc_final: 0.6221 (mpp) REVERT: a 77 MET cc_start: 0.7057 (tpp) cc_final: 0.6628 (tpp) REVERT: a 199 LEU cc_start: 0.8826 (tp) cc_final: 0.8486 (tt) REVERT: a 209 ILE cc_start: 0.7851 (mm) cc_final: 0.7587 (mm) REVERT: K 3 ASP cc_start: 0.8430 (m-30) cc_final: 0.7305 (t0) REVERT: L 8 PHE cc_start: 0.6374 (m-80) cc_final: 0.6025 (m-10) REVERT: L 66 MET cc_start: 0.5243 (mmp) cc_final: 0.3577 (ppp) REVERT: M 71 ILE cc_start: 0.7877 (mm) cc_final: 0.7588 (mm) REVERT: N 54 PHE cc_start: 0.6865 (t80) cc_final: 0.6032 (t80) REVERT: O 63 PHE cc_start: 0.8175 (t80) cc_final: 0.7962 (t80) REVERT: Q 64 CYS cc_start: 0.8554 (m) cc_final: 0.8329 (m) REVERT: R 7 LYS cc_start: 0.6896 (mmtt) cc_final: 0.6439 (ptpt) REVERT: R 27 THR cc_start: 0.9427 (p) cc_final: 0.9113 (t) REVERT: R 63 PHE cc_start: 0.7223 (m-10) cc_final: 0.6833 (m-10) REVERT: R 71 ILE cc_start: 0.8235 (tt) cc_final: 0.7754 (tt) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.0688 time to fit residues: 22.3112 Evaluate side-chains 186 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 34 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 40 optimal weight: 0.0980 chunk 16 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 17 optimal weight: 0.0570 chunk 43 optimal weight: 0.0980 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 39 ASN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.158074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.131668 restraints weight = 20242.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.130644 restraints weight = 16571.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.131253 restraints weight = 15319.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.131479 restraints weight = 13226.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.131950 restraints weight = 12220.593| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.8921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8665 Z= 0.109 Angle : 0.657 8.406 11787 Z= 0.317 Chirality : 0.039 0.500 1478 Planarity : 0.004 0.046 1488 Dihedral : 4.771 40.416 1306 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.27), residues: 1036 helix: -0.45 (0.19), residues: 770 sheet: None (None), residues: 0 loop : -1.97 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 38 TYR 0.015 0.001 TYR i 21 PHE 0.026 0.001 PHE M 63 TRP 0.019 0.001 TRP 8 9 HIS 0.003 0.001 HIS a 127 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8665) covalent geometry : angle 0.65713 (11787) hydrogen bonds : bond 0.02727 ( 451) hydrogen bonds : angle 3.40549 ( 1329) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 76 LYS cc_start: 0.8883 (tttm) cc_final: 0.8326 (mmtp) REVERT: i 27 MET cc_start: 0.8949 (mmp) cc_final: 0.8541 (mmm) REVERT: i 46 LEU cc_start: 0.7613 (tp) cc_final: 0.7116 (pp) REVERT: 8 18 MET cc_start: 0.7915 (mtt) cc_final: 0.7596 (mtt) REVERT: a 57 MET cc_start: 0.6616 (mmm) cc_final: 0.6160 (mpp) REVERT: a 77 MET cc_start: 0.7069 (tpp) cc_final: 0.6794 (tpp) REVERT: a 199 LEU cc_start: 0.8642 (tp) cc_final: 0.8302 (tt) REVERT: a 209 ILE cc_start: 0.7812 (mm) cc_final: 0.7549 (mm) REVERT: K 3 ASP cc_start: 0.8431 (m-30) cc_final: 0.7256 (t0) REVERT: L 8 PHE cc_start: 0.6397 (m-80) cc_final: 0.6055 (m-10) REVERT: L 66 MET cc_start: 0.5265 (mmp) cc_final: 0.3563 (ppp) REVERT: M 71 ILE cc_start: 0.7897 (mm) cc_final: 0.7616 (mm) REVERT: N 32 MET cc_start: 0.8838 (tmm) cc_final: 0.8305 (tmm) REVERT: N 39 ASN cc_start: 0.8102 (t0) cc_final: 0.7850 (t0) REVERT: N 54 PHE cc_start: 0.6709 (t80) cc_final: 0.5828 (t80) REVERT: Q 64 CYS cc_start: 0.8549 (m) cc_final: 0.8295 (m) REVERT: R 7 LYS cc_start: 0.6912 (mmtt) cc_final: 0.6572 (ptmm) REVERT: R 27 THR cc_start: 0.9362 (p) cc_final: 0.9028 (t) REVERT: R 71 ILE cc_start: 0.8321 (tt) cc_final: 0.7999 (tt) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.0639 time to fit residues: 21.3234 Evaluate side-chains 196 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 48 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 121 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 43 optimal weight: 0.1980 chunk 71 optimal weight: 6.9990 chunk 88 optimal weight: 0.0010 chunk 47 optimal weight: 0.5980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 44 GLN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.155188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.128025 restraints weight = 19864.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.128392 restraints weight = 15516.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.128111 restraints weight = 16765.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.129847 restraints weight = 13433.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.129176 restraints weight = 11083.854| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.9065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8665 Z= 0.118 Angle : 0.666 8.411 11787 Z= 0.324 Chirality : 0.040 0.496 1478 Planarity : 0.004 0.047 1488 Dihedral : 4.762 41.284 1306 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.27), residues: 1036 helix: -0.29 (0.19), residues: 742 sheet: None (None), residues: 0 loop : -2.06 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG i 26 TYR 0.015 0.001 TYR i 21 PHE 0.027 0.001 PHE M 63 TRP 0.019 0.002 TRP 8 9 HIS 0.002 0.000 HIS a 127 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8665) covalent geometry : angle 0.66589 (11787) hydrogen bonds : bond 0.02796 ( 451) hydrogen bonds : angle 3.46655 ( 1329) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1395.64 seconds wall clock time: 24 minutes 42.95 seconds (1482.95 seconds total)