Starting phenix.real_space_refine on Sat Aug 23 13:07:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8es8_28571/08_2025/8es8_28571.cif Found real_map, /net/cci-nas-00/data/ceres_data/8es8_28571/08_2025/8es8_28571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8es8_28571/08_2025/8es8_28571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8es8_28571/08_2025/8es8_28571.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8es8_28571/08_2025/8es8_28571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8es8_28571/08_2025/8es8_28571.map" } resolution = 2.65 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 7602 2.51 5 N 1982 2.21 5 O 2324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11976 Number of models: 1 Model: "" Number of chains: 21 Chain: "Z" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 281 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "Y" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 249 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "D" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 821 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "G" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 913 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "E" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "A" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2008 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain: "B" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2292 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 273} Chain: "N" Number of atoms: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2246 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 263} Chain: "M" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 837 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Chain: "P" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 80 Classifications: {'peptide': 10} Modifications used: {'COO': 1} Link IDs: {'TRANS': 9} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.60, per 1000 atoms: 0.30 Number of scatterers: 11976 At special positions: 0 Unit cell: (95.2, 90.1, 201.45, 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 68 16.00 O 2324 8.00 N 1982 7.00 C 7602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS Z 32 " - pdb=" SG CYS Y 32 " distance=2.03 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 73 " distance=2.03 Simple disulfide: pdb=" SG CYS D 93 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 98 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 122 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 87 " distance=2.03 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 107 " distance=2.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 98 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 122 " distance=2.03 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 92 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 190 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS B 245 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 91 " distance=2.03 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 210 " distance=2.03 Simple disulfide: pdb=" SG CYS N 101 " - pdb=" SG CYS N 164 " distance=2.04 Simple disulfide: pdb=" SG CYS N 203 " - pdb=" SG CYS N 259 " distance=2.04 Simple disulfide: pdb=" SG CYS M 25 " - pdb=" SG CYS M 80 " distance=2.05 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG J 1 " - " NAG J 2 " " NAG Q 1 " - " NAG Q 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1701 " - " ASN A 195 " " NAG A1702 " - " ASN A 184 " " NAG B1701 " - " ASN B 184 " " NAG C 1 " - " ASN D 38 " " NAG G1701 " - " ASN G 92 " " NAG G1702 " - " ASN G 52 " " NAG J 1 " - " ASN A 58 " " NAG Q 1 " - " ASN B 84 " " NAG T 1 " - " ASN D 74 " " NAG U 1 " - " ASN B 107 " " NAG V 1 " - " ASN A 150 " Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 657.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2732 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 28 sheets defined 26.7% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'Z' and resid 29 through 56 Processing helix chain 'Y' and resid 28 through 55 removed outlier: 4.372A pdb=" N CYS Y 32 " --> pdb=" O ASP Y 28 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE Y 41 " --> pdb=" O GLY Y 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 100 through 127 removed outlier: 3.586A pdb=" N GLY D 127 " --> pdb=" O PHE D 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 93 Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 126 through 156 Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'G' and resid 111 through 136 Processing helix chain 'E' and resid 88 through 93 Processing helix chain 'E' and resid 126 through 154 removed outlier: 3.559A pdb=" N VAL E 130 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN E 154 " --> pdb=" O TYR E 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.676A pdb=" N SER A 87 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 220 removed outlier: 3.845A pdb=" N SER A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 257 Processing helix chain 'B' and resid 82 through 86 Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.525A pdb=" N LYS B 119 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 Processing helix chain 'B' and resid 198 through 202 Processing helix chain 'B' and resid 248 through 289 removed outlier: 3.571A pdb=" N LYS B 289 " --> pdb=" O MET B 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 55 removed outlier: 3.514A pdb=" N ILE N 52 " --> pdb=" O ALA N 49 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU N 53 " --> pdb=" O PRO N 50 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN N 54 " --> pdb=" O TRP N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 86 removed outlier: 3.515A pdb=" N TRP N 60 " --> pdb=" O GLY N 56 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY N 83 " --> pdb=" O GLY N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 151 removed outlier: 3.687A pdb=" N GLN N 141 " --> pdb=" O ASP N 137 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR N 142 " --> pdb=" O MET N 138 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR N 143 " --> pdb=" O ALA N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 151 through 162 removed outlier: 3.740A pdb=" N GLN N 155 " --> pdb=" O HIS N 151 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 175 Processing helix chain 'N' and resid 175 through 180 Processing sheet with id=AA1, first strand: chain 'D' and resid 26 through 28 removed outlier: 5.992A pdb=" N VAL D 33 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 42 through 46 removed outlier: 6.368A pdb=" N ILE D 70 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY D 46 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ARG D 68 " --> pdb=" O GLY D 46 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR D 85 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N TYR E 113 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLN D 87 " --> pdb=" O TYR E 113 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ARG E 115 " --> pdb=" O GLN D 87 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N HIS D 89 " --> pdb=" O ARG E 115 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N PHE E 110 " --> pdb=" O CYS E 98 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N CYS E 98 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TRP E 59 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.640A pdb=" N VAL D 97 " --> pdb=" O MET E 123 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET E 123 " --> pdb=" O VAL D 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 37 through 41 Processing sheet with id=AA5, first strand: chain 'F' and resid 64 through 66 removed outlier: 3.945A pdb=" N TRP F 59 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE G 53 " --> pdb=" O PHE G 64 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE G 64 " --> pdb=" O ILE G 53 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP G 55 " --> pdb=" O ILE G 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 122 through 123 removed outlier: 4.454A pdb=" N MET F 123 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE G 108 " --> pdb=" O MET F 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 31 through 34 removed outlier: 3.550A pdb=" N LEU G 43 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL G 42 " --> pdb=" O LEU G 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 37 through 41 removed outlier: 3.566A pdb=" N LYS E 37 " --> pdb=" O THR E 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'A' and resid 11 through 14 removed outlier: 6.445A pdb=" N MET A 11 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N HIS A 116 " --> pdb=" O MET A 11 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL A 13 " --> pdb=" O HIS A 116 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LYS A 38 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N PHE A 47 " --> pdb=" O LYS A 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 11 through 14 removed outlier: 6.445A pdb=" N MET A 11 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N HIS A 116 " --> pdb=" O MET A 11 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL A 13 " --> pdb=" O HIS A 116 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 19 through 21 Processing sheet with id=AB4, first strand: chain 'A' and resid 125 through 128 Processing sheet with id=AB5, first strand: chain 'A' and resid 125 through 128 Processing sheet with id=AB6, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'B' and resid 10 through 14 removed outlier: 6.494A pdb=" N LEU B 11 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N THR B 114 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS B 13 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET B 88 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N MET B 32 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE B 48 " --> pdb=" O MET B 32 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP B 34 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP B 38 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 10 through 14 removed outlier: 6.494A pdb=" N LEU B 11 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N THR B 114 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS B 13 " --> pdb=" O THR B 114 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 19 through 21 Processing sheet with id=AC1, first strand: chain 'B' and resid 124 through 128 removed outlier: 5.590A pdb=" N TYR B 188 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 124 through 128 removed outlier: 5.590A pdb=" N TYR B 188 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 164 through 166 removed outlier: 4.737A pdb=" N TRP B 159 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 46 through 47 removed outlier: 6.786A pdb=" N GLY N 26 " --> pdb=" O PHE N 33 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG N 35 " --> pdb=" O ALA N 24 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA N 24 " --> pdb=" O ARG N 35 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASP N 37 " --> pdb=" O PHE N 22 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N PHE N 22 " --> pdb=" O ASP N 37 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG N 111 " --> pdb=" O ASP N 102 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N HIS N 114 " --> pdb=" O LEU N 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE N 124 " --> pdb=" O TYR N 116 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N TYR N 118 " --> pdb=" O ASP N 122 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASP N 122 " --> pdb=" O TYR N 118 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 189 through 193 removed outlier: 5.871A pdb=" N PHE N 241 " --> pdb=" O SER N 207 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 189 through 193 removed outlier: 5.871A pdb=" N PHE N 241 " --> pdb=" O SER N 207 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 222 through 223 Processing sheet with id=AC8, first strand: chain 'M' and resid 6 through 11 removed outlier: 5.925A pdb=" N PHE M 62 " --> pdb=" O GLY M 29 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 6 through 11 removed outlier: 5.925A pdb=" N PHE M 62 " --> pdb=" O GLY M 29 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER M 55 " --> pdb=" O TYR M 63 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 44 through 45 624 hydrogen bonds defined for protein. 1680 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: 2.15 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3829 1.35 - 1.47: 3159 1.47 - 1.60: 5164 1.60 - 1.72: 0 1.72 - 1.84: 98 Bond restraints: 12250 Sorted by residual: bond pdb=" CAI Y01 Y 201 " pdb=" CAK Y01 Y 201 " ideal model delta sigma weight residual 1.492 1.404 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.54e+00 bond pdb=" C1 NAG A1701 " pdb=" O5 NAG A1701 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.29e+00 bond pdb=" CAI Y01 Y 201 " pdb=" CAZ Y01 Y 201 " ideal model delta sigma weight residual 1.332 1.381 -0.049 2.00e-02 2.50e+03 5.97e+00 bond pdb=" C1 NAG G1702 " pdb=" O5 NAG G1702 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.20e+00 ... (remaining 12245 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 16322 2.36 - 4.72: 249 4.72 - 7.08: 21 7.08 - 9.44: 6 9.44 - 11.79: 4 Bond angle restraints: 16602 Sorted by residual: angle pdb=" OAG Y01 Y 201 " pdb=" CAY Y01 Y 201 " pdb=" OAW Y01 Y 201 " ideal model delta sigma weight residual 123.38 111.59 11.79 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CAM Y01 Y 201 " pdb=" CAY Y01 Y 201 " pdb=" OAW Y01 Y 201 " ideal model delta sigma weight residual 111.19 122.45 -11.26 3.00e+00 1.11e-01 1.41e+01 angle pdb=" CA CYS F 119 " pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " ideal model delta sigma weight residual 114.40 122.07 -7.67 2.30e+00 1.89e-01 1.11e+01 angle pdb=" N ASN A 184 " pdb=" CA ASN A 184 " pdb=" CB ASN A 184 " ideal model delta sigma weight residual 110.29 103.12 7.17 2.15e+00 2.16e-01 1.11e+01 angle pdb=" CAV Y01 Y 201 " pdb=" CAZ Y01 Y 201 " pdb=" CBH Y01 Y 201 " ideal model delta sigma weight residual 116.96 126.57 -9.61 3.00e+00 1.11e-01 1.03e+01 ... (remaining 16597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.65: 7082 21.65 - 43.31: 405 43.31 - 64.96: 66 64.96 - 86.62: 27 86.62 - 108.27: 16 Dihedral angle restraints: 7596 sinusoidal: 3337 harmonic: 4259 Sorted by residual: dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 122 " pdb=" CB CYS E 122 " ideal model delta sinusoidal sigma weight residual 93.00 42.29 50.71 1 1.00e+01 1.00e-02 3.52e+01 dihedral pdb=" CB CYS M 25 " pdb=" SG CYS M 25 " pdb=" SG CYS M 80 " pdb=" CB CYS M 80 " ideal model delta sinusoidal sigma weight residual 93.00 44.59 48.41 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" CA ASN A 150 " pdb=" C ASN A 150 " pdb=" N VAL A 151 " pdb=" CA VAL A 151 " ideal model delta harmonic sigma weight residual -180.00 -154.68 -25.32 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 7593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1825 0.129 - 0.259: 30 0.259 - 0.388: 5 0.388 - 0.517: 0 0.517 - 0.646: 1 Chirality restraints: 1861 Sorted by residual: chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN A 150 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C1 NAG A1702 " pdb=" ND2 ASN A 184 " pdb=" C2 NAG A1702 " pdb=" O5 NAG A1702 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA ASN A 195 " pdb=" N ASN A 195 " pdb=" C ASN A 195 " pdb=" CB ASN A 195 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 1858 not shown) Planarity restraints: 2110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 205 " 0.065 5.00e-02 4.00e+02 9.90e-02 1.57e+01 pdb=" N PRO A 206 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 52 " -0.033 2.00e-02 2.50e+03 3.24e-02 1.31e+01 pdb=" CG ASN G 52 " 0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN G 52 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN G 52 " 0.020 2.00e-02 2.50e+03 pdb=" C1 NAG G1702 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 150 " 0.025 2.00e-02 2.50e+03 2.43e-02 7.37e+00 pdb=" CG ASN A 150 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 150 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 150 " -0.030 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.026 2.00e-02 2.50e+03 ... (remaining 2107 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 253 2.69 - 3.25: 11032 3.25 - 3.80: 17895 3.80 - 4.35: 24045 4.35 - 4.90: 40251 Nonbonded interactions: 93476 Sorted by model distance: nonbonded pdb=" O SER B 8 " pdb=" OG1 THR B 109 " model vdw 2.142 3.040 nonbonded pdb=" NZ LYS N 127 " pdb=" O TRP N 133 " model vdw 2.171 3.120 nonbonded pdb=" OG1 THR G 66 " pdb=" OD1 ASP G 68 " model vdw 2.205 3.040 nonbonded pdb=" O SER N 13 " pdb=" OG SER N 92 " model vdw 2.241 3.040 nonbonded pdb=" OD1 ASN G 52 " pdb=" N2 NAG G1702 " model vdw 2.245 3.120 ... (remaining 93471 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 'E' selection = (chain 'F' and resid 33 through 155) } ncs_group { reference = chain 'J' selection = chain 'Q' selection = chain 'T' selection = chain 'U' selection = chain 'V' } ncs_group { reference = (chain 'Y' and resid 25 through 55) selection = (chain 'Z' and resid 25 through 55) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.760 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 12285 Z= 0.193 Angle : 0.799 23.688 16690 Z= 0.383 Chirality : 0.053 0.646 1861 Planarity : 0.005 0.099 2099 Dihedral : 14.956 108.272 4813 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.08 % Allowed : 0.23 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: 0.76 (0.22), residues: 1442 helix: 2.49 (0.27), residues: 342 sheet: 1.24 (0.26), residues: 412 loop : -1.06 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 3 TYR 0.013 0.001 TYR D 71 PHE 0.025 0.002 PHE A 35 TRP 0.018 0.002 TRP F 59 HIS 0.005 0.001 HIS N 70 Details of bonding type rmsd covalent geometry : bond 0.00418 (12250) covalent geometry : angle 0.71237 (16602) SS BOND : bond 0.00615 ( 17) SS BOND : angle 2.24286 ( 34) hydrogen bonds : bond 0.13856 ( 565) hydrogen bonds : angle 5.68466 ( 1680) link_BETA1-4 : bond 0.00482 ( 7) link_BETA1-4 : angle 2.52770 ( 21) link_NAG-ASN : bond 0.01659 ( 11) link_NAG-ASN : angle 7.65727 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 255 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 121 ASN cc_start: 0.6982 (p0) cc_final: 0.6778 (p0) REVERT: F 123 MET cc_start: 0.5901 (ppp) cc_final: 0.5416 (ppp) REVERT: G 129 LEU cc_start: 0.7396 (mm) cc_final: 0.6970 (mt) outliers start: 1 outliers final: 1 residues processed: 256 average time/residue: 0.6779 time to fit residues: 186.0886 Evaluate side-chains 195 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 126 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.0970 chunk 55 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 GLN F 92 GLN G 77 ASN E 62 ASN E 81 HIS A 196 ASN N 115 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.146116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099298 restraints weight = 18453.720| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.47 r_work: 0.3114 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 12285 Z= 0.129 Angle : 0.705 16.893 16690 Z= 0.346 Chirality : 0.046 0.329 1861 Planarity : 0.004 0.063 2099 Dihedral : 10.343 98.493 2048 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.33 % Allowed : 11.72 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: 0.90 (0.22), residues: 1442 helix: 2.63 (0.27), residues: 345 sheet: 1.23 (0.25), residues: 417 loop : -0.95 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 35 TYR 0.021 0.001 TYR D 79 PHE 0.024 0.001 PHE G 118 TRP 0.020 0.001 TRP F 151 HIS 0.004 0.001 HIS N 192 Details of bonding type rmsd covalent geometry : bond 0.00280 (12250) covalent geometry : angle 0.63542 (16602) SS BOND : bond 0.00506 ( 17) SS BOND : angle 2.16275 ( 34) hydrogen bonds : bond 0.04496 ( 565) hydrogen bonds : angle 4.63701 ( 1680) link_BETA1-4 : bond 0.00542 ( 7) link_BETA1-4 : angle 1.92273 ( 21) link_NAG-ASN : bond 0.01178 ( 11) link_NAG-ASN : angle 6.38138 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 85 LYS cc_start: 0.8436 (mttp) cc_final: 0.7925 (mmtm) REVERT: F 88 SER cc_start: 0.8551 (t) cc_final: 0.8291 (t) REVERT: F 99 TYR cc_start: 0.6138 (p90) cc_final: 0.5935 (p90) REVERT: F 121 ASN cc_start: 0.6992 (p0) cc_final: 0.6666 (p0) REVERT: F 144 LEU cc_start: 0.5219 (OUTLIER) cc_final: 0.4851 (mm) REVERT: G 72 TRP cc_start: 0.7426 (t-100) cc_final: 0.7220 (t-100) REVERT: G 129 LEU cc_start: 0.7272 (mm) cc_final: 0.6890 (mt) REVERT: E 37 LYS cc_start: 0.7792 (mtmt) cc_final: 0.7447 (mppt) REVERT: E 115 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7911 (ttt180) REVERT: A 109 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8398 (tpp80) outliers start: 30 outliers final: 13 residues processed: 219 average time/residue: 0.6324 time to fit residues: 149.4335 Evaluate side-chains 203 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain N residue 128 GLU Chi-restraints excluded: chain N residue 261 VAL Chi-restraints excluded: chain M residue 34 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 53 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 51 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN B 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.144171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.096843 restraints weight = 18598.953| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.52 r_work: 0.3066 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12285 Z= 0.164 Angle : 0.721 15.690 16690 Z= 0.357 Chirality : 0.048 0.343 1861 Planarity : 0.004 0.049 2099 Dihedral : 9.022 93.042 2048 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.48 % Allowed : 14.21 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: 0.74 (0.22), residues: 1442 helix: 2.46 (0.27), residues: 345 sheet: 1.16 (0.24), residues: 437 loop : -1.12 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 130 TYR 0.017 0.002 TYR D 79 PHE 0.027 0.002 PHE A 35 TRP 0.023 0.002 TRP F 151 HIS 0.005 0.001 HIS N 70 Details of bonding type rmsd covalent geometry : bond 0.00376 (12250) covalent geometry : angle 0.65942 (16602) SS BOND : bond 0.00760 ( 17) SS BOND : angle 2.19015 ( 34) hydrogen bonds : bond 0.04862 ( 565) hydrogen bonds : angle 4.55578 ( 1680) link_BETA1-4 : bond 0.00475 ( 7) link_BETA1-4 : angle 1.97576 ( 21) link_NAG-ASN : bond 0.01038 ( 11) link_NAG-ASN : angle 6.04799 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 85 LYS cc_start: 0.8421 (mttp) cc_final: 0.7894 (mmtm) REVERT: F 121 ASN cc_start: 0.7111 (p0) cc_final: 0.6762 (p0) REVERT: F 144 LEU cc_start: 0.4992 (OUTLIER) cc_final: 0.4674 (mm) REVERT: E 37 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7578 (mppt) REVERT: E 43 THR cc_start: 0.7932 (p) cc_final: 0.7723 (m) REVERT: A 109 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8568 (tpp-160) REVERT: B 254 GLN cc_start: 0.8246 (mm110) cc_final: 0.7891 (tp-100) outliers start: 32 outliers final: 12 residues processed: 219 average time/residue: 0.6588 time to fit residues: 155.4983 Evaluate side-chains 202 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain N residue 261 VAL Chi-restraints excluded: chain M residue 34 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 87 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 120 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.142399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.096096 restraints weight = 18470.656| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.50 r_work: 0.3022 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 12285 Z= 0.221 Angle : 0.772 15.157 16690 Z= 0.386 Chirality : 0.050 0.390 1861 Planarity : 0.005 0.042 2099 Dihedral : 8.518 94.133 2048 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.88 % Allowed : 15.30 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: 0.53 (0.21), residues: 1442 helix: 2.18 (0.26), residues: 345 sheet: 1.12 (0.24), residues: 437 loop : -1.25 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 170 TYR 0.020 0.002 TYR F 111 PHE 0.025 0.002 PHE A 35 TRP 0.024 0.002 TRP F 151 HIS 0.006 0.001 HIS N 70 Details of bonding type rmsd covalent geometry : bond 0.00519 (12250) covalent geometry : angle 0.71423 (16602) SS BOND : bond 0.00998 ( 17) SS BOND : angle 2.40747 ( 34) hydrogen bonds : bond 0.05423 ( 565) hydrogen bonds : angle 4.64572 ( 1680) link_BETA1-4 : bond 0.00588 ( 7) link_BETA1-4 : angle 2.05911 ( 21) link_NAG-ASN : bond 0.01000 ( 11) link_NAG-ASN : angle 5.98751 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 197 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 99 TYR cc_start: 0.6084 (OUTLIER) cc_final: 0.4948 (p90) REVERT: F 121 ASN cc_start: 0.7253 (p0) cc_final: 0.6958 (p0) REVERT: F 144 LEU cc_start: 0.5040 (OUTLIER) cc_final: 0.4722 (mm) REVERT: E 37 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7650 (mppt) REVERT: E 115 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8074 (ttt180) REVERT: E 117 ARG cc_start: 0.8912 (ttm170) cc_final: 0.8694 (ttm-80) REVERT: A 15 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8331 (mt-10) REVERT: B 254 GLN cc_start: 0.8424 (mm110) cc_final: 0.8076 (tp-100) REVERT: M 99 MET cc_start: 0.6455 (mtp) cc_final: 0.6215 (mtm) outliers start: 50 outliers final: 18 residues processed: 220 average time/residue: 0.6415 time to fit residues: 152.2441 Evaluate side-chains 208 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 98 CYS Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain N residue 176 LYS Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 261 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 2 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.143714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.096878 restraints weight = 18479.547| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.42 r_work: 0.3064 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12285 Z= 0.146 Angle : 0.704 14.453 16690 Z= 0.348 Chirality : 0.047 0.419 1861 Planarity : 0.004 0.038 2099 Dihedral : 8.048 97.755 2048 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.26 % Allowed : 17.08 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: 0.68 (0.22), residues: 1442 helix: 2.42 (0.27), residues: 343 sheet: 1.17 (0.25), residues: 431 loop : -1.17 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 170 TYR 0.021 0.001 TYR F 111 PHE 0.019 0.001 PHE A 35 TRP 0.025 0.001 TRP F 151 HIS 0.004 0.001 HIS N 70 Details of bonding type rmsd covalent geometry : bond 0.00330 (12250) covalent geometry : angle 0.64318 (16602) SS BOND : bond 0.00646 ( 17) SS BOND : angle 2.22723 ( 34) hydrogen bonds : bond 0.04728 ( 565) hydrogen bonds : angle 4.46382 ( 1680) link_BETA1-4 : bond 0.00445 ( 7) link_BETA1-4 : angle 1.94507 ( 21) link_NAG-ASN : bond 0.00982 ( 11) link_NAG-ASN : angle 5.90399 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 198 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 85 LYS cc_start: 0.8339 (mttp) cc_final: 0.7753 (mmtm) REVERT: F 106 GLU cc_start: 0.6816 (tp30) cc_final: 0.6204 (tp30) REVERT: F 121 ASN cc_start: 0.7199 (p0) cc_final: 0.6975 (p0) REVERT: F 144 LEU cc_start: 0.4898 (OUTLIER) cc_final: 0.4606 (mm) REVERT: G 129 LEU cc_start: 0.7273 (mm) cc_final: 0.6930 (mt) REVERT: E 37 LYS cc_start: 0.7848 (mtmt) cc_final: 0.7522 (mppt) REVERT: E 90 LEU cc_start: 0.8904 (mt) cc_final: 0.8349 (tp) REVERT: E 115 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7988 (ttt180) REVERT: A 15 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8314 (mt-10) REVERT: A 222 GLU cc_start: 0.7729 (pt0) cc_final: 0.7430 (pm20) REVERT: B 48 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8150 (p90) REVERT: B 253 GLN cc_start: 0.8250 (tt0) cc_final: 0.7960 (tt0) REVERT: B 254 GLN cc_start: 0.8325 (mm110) cc_final: 0.8013 (tp-100) REVERT: M 99 MET cc_start: 0.6405 (mtp) cc_final: 0.6181 (mtm) outliers start: 42 outliers final: 18 residues processed: 218 average time/residue: 0.6421 time to fit residues: 151.3431 Evaluate side-chains 211 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 176 LYS Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 261 VAL Chi-restraints excluded: chain M residue 34 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 2 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.144365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.097672 restraints weight = 18461.094| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.45 r_work: 0.3089 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12285 Z= 0.132 Angle : 0.694 13.998 16690 Z= 0.343 Chirality : 0.047 0.412 1861 Planarity : 0.004 0.039 2099 Dihedral : 7.314 56.660 2046 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.11 % Allowed : 18.09 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: 0.77 (0.22), residues: 1442 helix: 2.53 (0.27), residues: 342 sheet: 1.20 (0.25), residues: 432 loop : -1.11 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 170 TYR 0.028 0.001 TYR F 111 PHE 0.022 0.001 PHE G 118 TRP 0.029 0.001 TRP F 151 HIS 0.004 0.001 HIS N 70 Details of bonding type rmsd covalent geometry : bond 0.00295 (12250) covalent geometry : angle 0.63212 (16602) SS BOND : bond 0.00576 ( 17) SS BOND : angle 2.47843 ( 34) hydrogen bonds : bond 0.04394 ( 565) hydrogen bonds : angle 4.36302 ( 1680) link_BETA1-4 : bond 0.00437 ( 7) link_BETA1-4 : angle 1.88051 ( 21) link_NAG-ASN : bond 0.01017 ( 11) link_NAG-ASN : angle 5.83978 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: F 85 LYS cc_start: 0.8286 (mttp) cc_final: 0.7757 (mmtm) REVERT: F 144 LEU cc_start: 0.4870 (OUTLIER) cc_final: 0.4599 (mm) REVERT: G 129 LEU cc_start: 0.7291 (mm) cc_final: 0.6946 (mt) REVERT: E 37 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7608 (mppt) REVERT: E 115 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7977 (ttt180) REVERT: A 15 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8311 (mt-10) REVERT: A 151 VAL cc_start: 0.9352 (OUTLIER) cc_final: 0.9149 (t) REVERT: A 186 SER cc_start: 0.7898 (OUTLIER) cc_final: 0.7574 (m) REVERT: A 230 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7856 (mt0) REVERT: B 48 PHE cc_start: 0.9153 (OUTLIER) cc_final: 0.8135 (p90) REVERT: B 253 GLN cc_start: 0.8173 (tt0) cc_final: 0.7895 (tt0) REVERT: M 99 MET cc_start: 0.6424 (mtp) cc_final: 0.6194 (mtm) outliers start: 40 outliers final: 18 residues processed: 216 average time/residue: 0.5863 time to fit residues: 136.5644 Evaluate side-chains 211 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 261 VAL Chi-restraints excluded: chain M residue 34 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 116 optimal weight: 0.6980 chunk 64 optimal weight: 0.0980 chunk 85 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN A 2 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.144912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.098380 restraints weight = 18470.582| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.39 r_work: 0.3101 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12285 Z= 0.125 Angle : 0.680 13.962 16690 Z= 0.335 Chirality : 0.046 0.400 1861 Planarity : 0.003 0.035 2099 Dihedral : 6.997 56.971 2046 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.87 % Allowed : 19.02 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: 0.83 (0.22), residues: 1442 helix: 2.57 (0.27), residues: 342 sheet: 1.26 (0.25), residues: 430 loop : -1.08 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 170 TYR 0.022 0.001 TYR D 79 PHE 0.016 0.001 PHE A 35 TRP 0.030 0.001 TRP F 151 HIS 0.004 0.001 HIS N 70 Details of bonding type rmsd covalent geometry : bond 0.00278 (12250) covalent geometry : angle 0.61876 (16602) SS BOND : bond 0.00583 ( 17) SS BOND : angle 2.45631 ( 34) hydrogen bonds : bond 0.04199 ( 565) hydrogen bonds : angle 4.32417 ( 1680) link_BETA1-4 : bond 0.00448 ( 7) link_BETA1-4 : angle 1.88830 ( 21) link_NAG-ASN : bond 0.00968 ( 11) link_NAG-ASN : angle 5.70863 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: F 85 LYS cc_start: 0.8323 (mttp) cc_final: 0.7726 (mmtm) REVERT: F 144 LEU cc_start: 0.4899 (OUTLIER) cc_final: 0.4610 (mm) REVERT: G 54 THR cc_start: 0.6163 (OUTLIER) cc_final: 0.5042 (p) REVERT: G 129 LEU cc_start: 0.7345 (mm) cc_final: 0.7017 (mt) REVERT: E 37 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7551 (mppt) REVERT: E 115 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7944 (ttt180) REVERT: A 151 VAL cc_start: 0.9335 (OUTLIER) cc_final: 0.9116 (t) REVERT: A 230 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7886 (mt0) REVERT: B 48 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8106 (p90) REVERT: B 253 GLN cc_start: 0.8126 (tt0) cc_final: 0.7849 (tt0) REVERT: M 99 MET cc_start: 0.6406 (mtp) cc_final: 0.6173 (mtm) outliers start: 37 outliers final: 13 residues processed: 219 average time/residue: 0.6507 time to fit residues: 153.8358 Evaluate side-chains 206 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 261 VAL Chi-restraints excluded: chain M residue 34 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 2 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 95 optimal weight: 0.0170 chunk 6 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 93 optimal weight: 0.0670 overall best weight: 0.6156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.145276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.098688 restraints weight = 18428.643| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.46 r_work: 0.3106 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12285 Z= 0.123 Angle : 0.678 12.204 16690 Z= 0.335 Chirality : 0.046 0.394 1861 Planarity : 0.003 0.033 2099 Dihedral : 6.801 57.560 2046 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.56 % Allowed : 19.57 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: 0.85 (0.22), residues: 1442 helix: 2.59 (0.27), residues: 342 sheet: 1.29 (0.25), residues: 426 loop : -1.07 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 35 TYR 0.027 0.001 TYR F 111 PHE 0.021 0.001 PHE G 118 TRP 0.032 0.001 TRP F 151 HIS 0.004 0.001 HIS N 70 Details of bonding type rmsd covalent geometry : bond 0.00273 (12250) covalent geometry : angle 0.62231 (16602) SS BOND : bond 0.00515 ( 17) SS BOND : angle 2.16887 ( 34) hydrogen bonds : bond 0.04117 ( 565) hydrogen bonds : angle 4.31287 ( 1680) link_BETA1-4 : bond 0.00428 ( 7) link_BETA1-4 : angle 1.88326 ( 21) link_NAG-ASN : bond 0.00976 ( 11) link_NAG-ASN : angle 5.55777 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 58 LEU cc_start: 0.6498 (mm) cc_final: 0.6211 (mp) REVERT: F 85 LYS cc_start: 0.8316 (mttp) cc_final: 0.7751 (mmtm) REVERT: F 144 LEU cc_start: 0.4871 (OUTLIER) cc_final: 0.4606 (mm) REVERT: G 129 LEU cc_start: 0.7277 (mm) cc_final: 0.6921 (mt) REVERT: E 37 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7536 (mppt) REVERT: E 115 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7951 (ttt180) REVERT: A 151 VAL cc_start: 0.9327 (OUTLIER) cc_final: 0.9104 (t) REVERT: A 222 GLU cc_start: 0.7653 (pt0) cc_final: 0.7346 (pm20) REVERT: A 230 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7902 (mt0) REVERT: B 48 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8092 (p90) REVERT: B 253 GLN cc_start: 0.8129 (tt0) cc_final: 0.7882 (tt0) REVERT: B 263 TYR cc_start: 0.7903 (m-80) cc_final: 0.7545 (m-80) REVERT: M 99 MET cc_start: 0.6397 (mtp) cc_final: 0.6162 (mtm) outliers start: 33 outliers final: 11 residues processed: 211 average time/residue: 0.6646 time to fit residues: 151.3880 Evaluate side-chains 203 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 261 VAL Chi-restraints excluded: chain M residue 34 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 109 optimal weight: 0.0970 chunk 78 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 chunk 71 optimal weight: 0.2980 chunk 88 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 GLN E 51 GLN E 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.144387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.097822 restraints weight = 18285.482| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.39 r_work: 0.3087 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12285 Z= 0.146 Angle : 0.702 12.171 16690 Z= 0.350 Chirality : 0.047 0.393 1861 Planarity : 0.004 0.034 2099 Dihedral : 6.796 58.977 2046 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.25 % Allowed : 19.72 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: 0.81 (0.22), residues: 1442 helix: 2.48 (0.27), residues: 342 sheet: 1.36 (0.25), residues: 421 loop : -1.09 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 238 TYR 0.028 0.001 TYR D 79 PHE 0.019 0.002 PHE A 35 TRP 0.033 0.002 TRP F 151 HIS 0.004 0.001 HIS N 70 Details of bonding type rmsd covalent geometry : bond 0.00335 (12250) covalent geometry : angle 0.64803 (16602) SS BOND : bond 0.00611 ( 17) SS BOND : angle 2.21535 ( 34) hydrogen bonds : bond 0.04435 ( 565) hydrogen bonds : angle 4.35431 ( 1680) link_BETA1-4 : bond 0.00420 ( 7) link_BETA1-4 : angle 1.90103 ( 21) link_NAG-ASN : bond 0.00941 ( 11) link_NAG-ASN : angle 5.50732 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 58 LEU cc_start: 0.6555 (mm) cc_final: 0.6277 (mp) REVERT: F 85 LYS cc_start: 0.8305 (mttp) cc_final: 0.7742 (mmtm) REVERT: F 130 VAL cc_start: 0.7923 (t) cc_final: 0.7715 (p) REVERT: F 144 LEU cc_start: 0.4826 (OUTLIER) cc_final: 0.4558 (mm) REVERT: G 129 LEU cc_start: 0.7242 (mm) cc_final: 0.6988 (mt) REVERT: E 82 LEU cc_start: 0.7360 (tt) cc_final: 0.6964 (tm) REVERT: E 115 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7971 (ttt180) REVERT: A 151 VAL cc_start: 0.9356 (OUTLIER) cc_final: 0.9135 (t) REVERT: A 222 GLU cc_start: 0.7675 (pt0) cc_final: 0.7378 (pm20) REVERT: A 230 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7861 (mt0) REVERT: B 48 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8131 (p90) REVERT: M 99 MET cc_start: 0.6408 (mtp) cc_final: 0.6181 (mtm) outliers start: 29 outliers final: 16 residues processed: 208 average time/residue: 0.5978 time to fit residues: 134.8022 Evaluate side-chains 204 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 261 VAL Chi-restraints excluded: chain M residue 34 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 28 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 97 optimal weight: 0.0170 chunk 25 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 GLN E 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.141622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.095040 restraints weight = 18358.535| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.38 r_work: 0.3039 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 12285 Z= 0.245 Angle : 0.808 12.663 16690 Z= 0.407 Chirality : 0.051 0.425 1861 Planarity : 0.005 0.043 2099 Dihedral : 7.402 57.986 2046 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.88 % Favored : 96.05 % Rotamer: Outliers : 2.64 % Allowed : 20.03 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: 0.44 (0.21), residues: 1442 helix: 1.97 (0.26), residues: 343 sheet: 1.20 (0.25), residues: 420 loop : -1.26 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 35 TYR 0.033 0.002 TYR F 111 PHE 0.022 0.002 PHE A 35 TRP 0.030 0.003 TRP F 151 HIS 0.006 0.001 HIS N 70 Details of bonding type rmsd covalent geometry : bond 0.00578 (12250) covalent geometry : angle 0.75792 (16602) SS BOND : bond 0.00962 ( 17) SS BOND : angle 2.57890 ( 34) hydrogen bonds : bond 0.05620 ( 565) hydrogen bonds : angle 4.66044 ( 1680) link_BETA1-4 : bond 0.00507 ( 7) link_BETA1-4 : angle 2.14262 ( 21) link_NAG-ASN : bond 0.00928 ( 11) link_NAG-ASN : angle 5.57660 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: F 58 LEU cc_start: 0.6557 (mm) cc_final: 0.6290 (mp) REVERT: F 144 LEU cc_start: 0.4948 (OUTLIER) cc_final: 0.4629 (mm) REVERT: E 37 LYS cc_start: 0.7705 (mtmm) cc_final: 0.7437 (mppt) REVERT: E 115 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8090 (ttt180) REVERT: E 123 MET cc_start: 0.7877 (ptm) cc_final: 0.7605 (pp-130) REVERT: A 230 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7880 (mt0) REVERT: A 238 ARG cc_start: 0.7611 (mmm-85) cc_final: 0.7366 (mmm-85) REVERT: B 48 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.8271 (p90) REVERT: B 254 GLN cc_start: 0.8459 (mm110) cc_final: 0.8155 (tp-100) REVERT: M 99 MET cc_start: 0.6436 (mtp) cc_final: 0.6184 (mtm) outliers start: 34 outliers final: 18 residues processed: 203 average time/residue: 0.6096 time to fit residues: 133.2856 Evaluate side-chains 197 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 261 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 28 optimal weight: 0.1980 chunk 114 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 GLN E 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.144084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.097791 restraints weight = 18448.977| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.39 r_work: 0.3091 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 12285 Z= 0.134 Angle : 0.716 12.010 16690 Z= 0.357 Chirality : 0.047 0.433 1861 Planarity : 0.004 0.035 2099 Dihedral : 7.094 59.635 2046 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.47 % Favored : 96.46 % Rotamer: Outliers : 2.17 % Allowed : 20.81 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: 0.66 (0.22), residues: 1442 helix: 2.28 (0.27), residues: 342 sheet: 1.23 (0.25), residues: 425 loop : -1.14 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 238 TYR 0.027 0.001 TYR D 79 PHE 0.015 0.001 PHE A 35 TRP 0.037 0.002 TRP F 151 HIS 0.004 0.001 HIS N 70 Details of bonding type rmsd covalent geometry : bond 0.00299 (12250) covalent geometry : angle 0.65713 (16602) SS BOND : bond 0.00534 ( 17) SS BOND : angle 2.73639 ( 34) hydrogen bonds : bond 0.04478 ( 565) hydrogen bonds : angle 4.45517 ( 1680) link_BETA1-4 : bond 0.00464 ( 7) link_BETA1-4 : angle 1.88274 ( 21) link_NAG-ASN : bond 0.00967 ( 11) link_NAG-ASN : angle 5.64620 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6408.46 seconds wall clock time: 109 minutes 40.39 seconds (6580.39 seconds total)