Starting phenix.real_space_refine on Fri Jul 3 05:05:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8es8_28571/07_2026/8es8_28571.cif Found real_map, /net/cci-nas-00/data/ceres_data/8es8_28571/07_2026/8es8_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8es8_28571/07_2026/8es8_28571.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8es8_28571/07_2026/8es8_28571.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8es8_28571/07_2026/8es8_28571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8es8_28571/07_2026/8es8_28571.map" model { file = "/net/cci-nas-00/data/ceres_data/8es8_28571/07_2026/8es8_28571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8es8_28571/07_2026/8es8_28571.cif" } 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-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 2.88, per 1000 atoms: 0.24 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: 1.07 Conformation dependent library (CDL) restraints added in 600.2 milliseconds 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: 0.38 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: 2.23 Time building geometry restraints manager: 1.40 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 - 18.00: 6565 18.00 - 35.99: 474 35.99 - 53.99: 88 53.99 - 71.98: 22 71.98 - 89.98: 13 Dihedral angle restraints: 7162 sinusoidal: 2903 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 7159 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: 6.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 12.650 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:7.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 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 : 13.250 89.976 4379 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 are 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/Z covalent geometry : bond 0.00418 / 0.19 (12250) covalent geometry : angle 0.71237 / 0.36 (16602) SS BOND : bond 0.00615 / 0.41 ( 17) SS BOND : angle 2.24286 / 1.71 ( 34) hydrogen bonds : bond 0.13856 / 8.99 ( 565) hydrogen bonds : angle 5.68466 / 4.05 ( 1680) link_BETA1-4 : bond 0.00482 / 0.27 ( 7) link_BETA1-4 : angle 2.52770 / 1.65 ( 21) link_NAG-ASN : bond 0.01659 / 0.97 ( 11) link_NAG-ASN : angle 7.65727 / 4.94 ( 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 : 0.443 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: 0.6569 time to fit residues: 180.6109 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 : 0.437 ------------------------------------------------------------------------------- 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... 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 = 0.4016 r_free = 0.4016 target = 0.146192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.099510 restraints weight = 18457.111| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.54 r_work: 0.3102 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1261 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= 0.128 Angle : 0.692 16.376 16690 Z= 0.343 Chirality : 0.046 0.331 1861 Planarity : 0.004 0.063 2099 Dihedral : 5.660 97.258 1614 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.41 % Allowed : 11.65 % 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 are not related in a simple way. whole: 0.89 (0.22), residues: 1442 helix: 2.62 (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 0.021 0.001 TRP F 151 HIS 0.004 0.001 HIS N 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (12250) covalent geometry : angle 0.62479 / 0.33 (16602) SS BOND : bond 0.00564 / 0.38 ( 17) SS BOND : angle 2.26718 / 1.64 ( 34) hydrogen bonds : bond 0.04462 / 2.91 ( 565) hydrogen bonds : angle 4.63273 / 3.29 ( 1680) link_BETA1-4 : bond 0.00441 / 0.22 ( 7) link_BETA1-4 : angle 1.40371 / 0.97 ( 21) link_NAG-ASN : bond 0.01156 / 0.66 ( 11) link_NAG-ASN : angle 6.26102 / 4.05 ( 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 237 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 206 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 84 LEU cc_start: 0.8020 (mt) cc_final: 0.7819 (mt) REVERT: F 85 LYS cc_start: 0.8430 (mttp) cc_final: 0.7912 (mmtm) REVERT: F 88 SER cc_start: 0.8553 (t) cc_final: 0.8280 (t) REVERT: F 99 TYR cc_start: 0.6124 (p90) cc_final: 0.5915 (p90) REVERT: F 121 ASN cc_start: 0.6964 (p0) cc_final: 0.6630 (p0) REVERT: F 144 LEU cc_start: 0.5170 (OUTLIER) cc_final: 0.4842 (mm) REVERT: G 72 TRP cc_start: 0.7409 (t-100) cc_final: 0.7203 (t-100) REVERT: G 129 LEU cc_start: 0.7243 (mm) cc_final: 0.6871 (mt) REVERT: E 37 LYS cc_start: 0.7784 (mtmt) cc_final: 0.7434 (mppt) REVERT: E 115 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7893 (ttt180) REVERT: A 109 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8411 (tpp80) outliers start: 31 outliers final: 13 residues processed: 220 average time/residue: 0.6263 time to fit residues: 148.7474 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 : 0.474 ------------------------------------------------------------------------------- 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: 0.8980 chunk 74 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 51 GLN ** 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 = 0.3953 r_free = 0.3953 target = 0.141839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.095148 restraints weight = 18668.776| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.51 r_work: 0.2998 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 12285 Z= 0.275 Angle : 0.826 15.718 16690 Z= 0.418 Chirality : 0.053 0.337 1861 Planarity : 0.005 0.051 2099 Dihedral : 6.165 96.391 1614 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.95 % Allowed : 14.52 % Favored : 82.53 % 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 are not related in a simple way. whole: 0.41 (0.21), residues: 1442 helix: 1.97 (0.26), residues: 345 sheet: 1.06 (0.24), residues: 428 loop : -1.24 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 35 TYR 0.022 0.002 TYR E 95 PHE 0.030 0.003 PHE A 35 TRP 0.023 0.002 TRP F 151 HIS 0.006 0.001 HIS N 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.27 (12250) covalent geometry : angle 0.77205 / 0.40 (16602) SS BOND : bond 0.01139 / 0.80 ( 17) SS BOND : angle 2.61433 / 1.88 ( 34) hydrogen bonds : bond 0.05999 / 3.90 ( 565) hydrogen bonds : angle 4.78901 / 3.38 ( 1680) link_BETA1-4 : bond 0.00549 / 0.26 ( 7) link_BETA1-4 : angle 1.67052 / 1.14 ( 21) link_NAG-ASN : bond 0.01048 / 0.60 ( 11) link_NAG-ASN : angle 6.03773 / 3.84 ( 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 243 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 97 VAL cc_start: 0.6833 (t) cc_final: 0.6549 (m) REVERT: F 121 ASN cc_start: 0.7281 (p0) cc_final: 0.6959 (p0) REVERT: F 144 LEU cc_start: 0.5139 (OUTLIER) cc_final: 0.4744 (mm) REVERT: E 37 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7490 (mppt) REVERT: A 15 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8354 (mt-10) REVERT: B 254 GLN cc_start: 0.8486 (mm110) cc_final: 0.8181 (tp-100) REVERT: N 89 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8070 (mm-30) REVERT: M 99 MET cc_start: 0.6517 (mtp) cc_final: 0.6280 (mtm) outliers start: 38 outliers final: 11 residues processed: 223 average time/residue: 0.6152 time to fit residues: 148.1424 Evaluate side-chains 201 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 A residue 15 GLU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 261 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 87 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 97 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 65 ASN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 2 GLN B 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.143347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.096385 restraints weight = 18436.037| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.40 r_work: 0.3065 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12285 Z= 0.149 Angle : 0.700 14.615 16690 Z= 0.351 Chirality : 0.047 0.330 1861 Planarity : 0.004 0.041 2099 Dihedral : 5.944 100.242 1614 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.65 % Allowed : 15.45 % Favored : 80.90 % 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 are not related in a simple way. whole: 0.58 (0.21), residues: 1442 helix: 2.32 (0.27), residues: 345 sheet: 1.09 (0.24), residues: 430 loop : -1.22 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 130 TYR 0.017 0.001 TYR B 252 PHE 0.020 0.002 PHE G 118 TRP 0.024 0.001 TRP F 151 HIS 0.005 0.001 HIS N 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (12250) covalent geometry : angle 0.64305 / 0.34 (16602) SS BOND : bond 0.00672 / 0.46 ( 17) SS BOND : angle 2.11910 / 1.62 ( 34) hydrogen bonds : bond 0.04879 / 3.17 ( 565) hydrogen bonds : angle 4.56805 / 3.21 ( 1680) link_BETA1-4 : bond 0.00448 / 0.22 ( 7) link_BETA1-4 : angle 1.44927 / 0.97 ( 21) link_NAG-ASN : bond 0.01001 / 0.56 ( 11) link_NAG-ASN : angle 5.81068 / 3.70 ( 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 252 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 205 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 85 LYS cc_start: 0.8358 (mttp) cc_final: 0.7773 (mmtm) REVERT: F 88 SER cc_start: 0.8541 (t) cc_final: 0.8220 (t) REVERT: F 99 TYR cc_start: 0.6047 (p90) cc_final: 0.5788 (p90) REVERT: F 121 ASN cc_start: 0.7212 (p0) cc_final: 0.6943 (p0) REVERT: F 144 LEU cc_start: 0.4993 (OUTLIER) cc_final: 0.4675 (mm) REVERT: G 129 LEU cc_start: 0.7280 (mm) cc_final: 0.6918 (mt) REVERT: E 37 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7537 (mppt) REVERT: E 115 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7991 (ttt180) REVERT: E 117 ARG cc_start: 0.8861 (ttm170) cc_final: 0.8620 (ttp-170) REVERT: A 15 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8286 (mt-10) REVERT: A 222 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7745 (pt0) REVERT: B 253 GLN cc_start: 0.8275 (tt0) cc_final: 0.7927 (tt0) REVERT: B 254 GLN cc_start: 0.8322 (mm110) cc_final: 0.8030 (tp-100) REVERT: M 99 MET cc_start: 0.6435 (mtp) cc_final: 0.6204 (mtm) outliers start: 47 outliers final: 17 residues processed: 227 average time/residue: 0.5492 time to fit residues: 135.1983 Evaluate side-chains 212 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 ILE 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 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 114 LEU 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 A residue 186 SER Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain N residue 35 ARG Chi-restraints excluded: chain N residue 261 VAL Chi-restraints excluded: chain M residue 34 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 52 optimal weight: 0.0980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3957 r_free = 0.3957 target = 0.142222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.096107 restraints weight = 18491.832| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.57 r_work: 0.3018 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12285 Z= 0.197 Angle : 0.745 14.855 16690 Z= 0.376 Chirality : 0.049 0.328 1861 Planarity : 0.004 0.039 2099 Dihedral : 5.971 92.581 1614 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.04 % Allowed : 16.61 % Favored : 79.35 % 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 are not related in a simple way. whole: 0.51 (0.21), residues: 1442 helix: 2.22 (0.26), residues: 343 sheet: 1.11 (0.24), residues: 427 loop : -1.25 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 130 TYR 0.016 0.002 TYR D 71 PHE 0.024 0.002 PHE A 35 TRP 0.025 0.002 TRP F 151 HIS 0.006 0.001 HIS N 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (12250) covalent geometry : angle 0.69120 / 0.36 (16602) SS BOND : bond 0.00873 / 0.60 ( 17) SS BOND : angle 2.50433 / 1.94 ( 34) hydrogen bonds : bond 0.05266 / 3.42 ( 565) hydrogen bonds : angle 4.60173 / 3.24 ( 1680) link_BETA1-4 : bond 0.00437 / 0.21 ( 7) link_BETA1-4 : angle 1.54340 / 1.03 ( 21) link_NAG-ASN : bond 0.00962 / 0.54 ( 11) link_NAG-ASN : angle 5.71100 / 3.62 ( 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 248 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 196 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 85 LYS cc_start: 0.8277 (mttp) cc_final: 0.7726 (mmtm) REVERT: F 106 GLU cc_start: 0.6713 (tp30) cc_final: 0.6170 (tp30) REVERT: F 121 ASN cc_start: 0.7300 (p0) cc_final: 0.7009 (p0) REVERT: F 144 LEU cc_start: 0.5031 (OUTLIER) cc_final: 0.4711 (mm) REVERT: E 37 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7642 (mppt) REVERT: E 115 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8035 (ttt180) REVERT: A 222 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7830 (pt0) REVERT: B 48 PHE cc_start: 0.9222 (OUTLIER) cc_final: 0.8195 (p90) REVERT: B 254 GLN cc_start: 0.8423 (mm110) cc_final: 0.8142 (tp-100) REVERT: M 99 MET cc_start: 0.6437 (mtp) cc_final: 0.6181 (mtm) outliers start: 52 outliers final: 24 residues processed: 225 average time/residue: 0.6064 time to fit residues: 147.1645 Evaluate side-chains 219 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 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 62 ILE 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 114 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 110 ARG 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 35 ARG 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: 3.9990 chunk 58 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 2 GLN N 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.143324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.096731 restraints weight = 18459.740| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.40 r_work: 0.3065 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12285 Z= 0.149 Angle : 0.702 14.473 16690 Z= 0.351 Chirality : 0.047 0.324 1861 Planarity : 0.004 0.037 2099 Dihedral : 5.321 53.204 1612 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.49 % Allowed : 18.40 % Favored : 78.11 % 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 are not related in a simple way. whole: 0.62 (0.22), residues: 1442 helix: 2.39 (0.27), residues: 343 sheet: 1.11 (0.24), residues: 432 loop : -1.20 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 130 TYR 0.014 0.001 TYR F 99 PHE 0.018 0.001 PHE A 35 TRP 0.027 0.001 TRP F 151 HIS 0.005 0.001 HIS N 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (12250) covalent geometry : angle 0.64604 / 0.34 (16602) SS BOND : bond 0.00642 / 0.45 ( 17) SS BOND : angle 2.52612 / 1.92 ( 34) hydrogen bonds : bond 0.04741 / 3.09 ( 565) hydrogen bonds : angle 4.53100 / 3.19 ( 1680) link_BETA1-4 : bond 0.00439 / 0.23 ( 7) link_BETA1-4 : angle 1.46008 / 0.97 ( 21) link_NAG-ASN : bond 0.00979 / 0.54 ( 11) link_NAG-ASN : angle 5.61851 / 3.55 ( 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 244 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 85 LYS cc_start: 0.8280 (mttp) cc_final: 0.7716 (mmtm) REVERT: F 99 TYR cc_start: 0.6084 (p90) cc_final: 0.5856 (p90) REVERT: F 144 LEU cc_start: 0.4968 (OUTLIER) cc_final: 0.4667 (mm) REVERT: G 54 THR cc_start: 0.6288 (OUTLIER) cc_final: 0.5391 (p) REVERT: E 37 LYS cc_start: 0.7820 (mtmt) cc_final: 0.7508 (mppt) REVERT: E 90 LEU cc_start: 0.8906 (mt) cc_final: 0.8358 (tp) REVERT: E 115 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7995 (ttt180) REVERT: E 120 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.6212 (pp20) REVERT: A 15 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8294 (mt-10) REVERT: A 222 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7793 (pt0) REVERT: A 230 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7897 (mt0) REVERT: B 48 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8166 (p90) REVERT: B 253 GLN cc_start: 0.8193 (tt0) cc_final: 0.7898 (tt0) REVERT: B 254 GLN cc_start: 0.8334 (mm110) cc_final: 0.8019 (tp-100) REVERT: M 99 MET cc_start: 0.6397 (mtp) cc_final: 0.6146 (mtm) outliers start: 45 outliers final: 19 residues processed: 223 average time/residue: 0.5741 time to fit residues: 138.3914 Evaluate side-chains 215 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 114 LEU Chi-restraints excluded: chain F residue 127 VAL 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 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 E residue 120 GLU 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 184 ASN Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain N residue 35 ARG Chi-restraints excluded: chain N residue 163 THR 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: 1.9990 chunk 64 optimal weight: 0.0770 chunk 85 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3985 r_free = 0.3985 target = 0.144325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.097680 restraints weight = 18439.870| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.33 r_work: 0.3092 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12285 Z= 0.126 Angle : 0.674 13.892 16690 Z= 0.338 Chirality : 0.046 0.317 1861 Planarity : 0.003 0.034 2099 Dihedral : 5.145 51.335 1612 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.95 % Allowed : 19.02 % Favored : 78.03 % 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 are not related in a simple way. whole: 0.77 (0.22), residues: 1442 helix: 2.53 (0.27), residues: 342 sheet: 1.25 (0.25), residues: 431 loop : -1.14 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 130 TYR 0.013 0.001 TYR D 71 PHE 0.023 0.001 PHE G 118 TRP 0.030 0.001 TRP F 151 HIS 0.004 0.001 HIS N 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (12250) covalent geometry : angle 0.61769 / 0.32 (16602) SS BOND : bond 0.00709 / 0.42 ( 17) SS BOND : angle 2.52723 / 1.96 ( 34) hydrogen bonds : bond 0.04283 / 2.78 ( 565) hydrogen bonds : angle 4.41411 / 3.11 ( 1680) link_BETA1-4 : bond 0.00446 / 0.24 ( 7) link_BETA1-4 : angle 1.34402 / 0.89 ( 21) link_NAG-ASN : bond 0.01014 / 0.55 ( 11) link_NAG-ASN : angle 5.49410 / 3.48 ( 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 231 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 193 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: F 85 LYS cc_start: 0.8308 (mttp) cc_final: 0.7739 (mmtm) REVERT: F 144 LEU cc_start: 0.4932 (OUTLIER) cc_final: 0.4646 (mm) REVERT: G 129 LEU cc_start: 0.7305 (mm) cc_final: 0.6937 (mt) REVERT: E 37 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7601 (mppt) REVERT: E 115 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7996 (ttt180) REVERT: A 15 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8322 (mt-10) REVERT: A 230 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7825 (mt0) REVERT: B 48 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8115 (p90) REVERT: B 253 GLN cc_start: 0.8097 (tt0) cc_final: 0.7815 (tt0) REVERT: M 99 MET cc_start: 0.6413 (mtp) cc_final: 0.6190 (mtm) outliers start: 38 outliers final: 13 residues processed: 212 average time/residue: 0.5470 time to fit residues: 125.2573 Evaluate side-chains 205 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 E residue 37 LYS Chi-restraints excluded: chain E residue 39 SER 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 151 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 269 LYS 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: 5.9990 chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3975 r_free = 0.3975 target = 0.143479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.096285 restraints weight = 18309.307| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.50 r_work: 0.3054 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12285 Z= 0.159 Angle : 0.711 13.884 16690 Z= 0.355 Chirality : 0.047 0.319 1861 Planarity : 0.004 0.034 2099 Dihedral : 5.235 49.059 1612 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.87 % Allowed : 19.95 % Favored : 77.17 % 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 are not related in a simple way. whole: 0.68 (0.22), residues: 1442 helix: 2.39 (0.27), residues: 343 sheet: 1.24 (0.25), residues: 425 loop : -1.17 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 52 TYR 0.025 0.001 TYR D 79 PHE 0.020 0.002 PHE A 35 TRP 0.031 0.002 TRP F 151 HIS 0.005 0.001 HIS N 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (12250) covalent geometry : angle 0.65965 / 0.34 (16602) SS BOND : bond 0.00681 / 0.48 ( 17) SS BOND : angle 2.37715 / 1.77 ( 34) hydrogen bonds : bond 0.04651 / 3.01 ( 565) hydrogen bonds : angle 4.46368 / 3.15 ( 1680) link_BETA1-4 : bond 0.00509 / 0.26 ( 7) link_BETA1-4 : angle 1.42651 / 0.94 ( 21) link_NAG-ASN : bond 0.00958 / 0.53 ( 11) link_NAG-ASN : angle 5.42247 / 3.40 ( 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: 37 poor density : 189 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 58 LEU cc_start: 0.6569 (mm) cc_final: 0.6275 (mp) REVERT: F 85 LYS cc_start: 0.8298 (mttp) cc_final: 0.7740 (mmtm) REVERT: F 144 LEU cc_start: 0.5016 (OUTLIER) cc_final: 0.4729 (mm) REVERT: G 65 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5848 (mm) REVERT: E 37 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7593 (mppt) REVERT: E 115 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8004 (ttt180) REVERT: A 15 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8294 (mt-10) REVERT: A 230 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7872 (mt0) REVERT: B 48 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8174 (p90) REVERT: B 253 GLN cc_start: 0.8181 (tt0) cc_final: 0.7886 (tt0) REVERT: M 92 ILE cc_start: 0.9538 (OUTLIER) cc_final: 0.9176 (mp) REVERT: M 99 MET cc_start: 0.6420 (mtp) cc_final: 0.6173 (mtm) outliers start: 37 outliers final: 19 residues processed: 212 average time/residue: 0.5592 time to fit residues: 128.2228 Evaluate side-chains 211 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 62 ILE Chi-restraints excluded: chain G residue 65 LEU 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 15 GLU 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 230 GLN 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 B residue 269 LYS Chi-restraints excluded: chain N residue 35 ARG 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 Chi-restraints excluded: chain M residue 92 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 109 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 121 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 71 optimal weight: 0.0980 chunk 88 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.145135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.098901 restraints weight = 18322.753| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.28 r_work: 0.3109 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12285 Z= 0.121 Angle : 0.671 13.284 16690 Z= 0.335 Chirality : 0.045 0.311 1861 Planarity : 0.003 0.032 2099 Dihedral : 5.016 46.703 1612 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.41 % Allowed : 21.04 % Favored : 76.55 % 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 are not related in a simple way. whole: 0.82 (0.22), residues: 1442 helix: 2.52 (0.27), residues: 342 sheet: 1.31 (0.25), residues: 426 loop : -1.08 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 170 TYR 0.015 0.001 TYR F 99 PHE 0.021 0.001 PHE G 118 TRP 0.036 0.001 TRP F 151 HIS 0.004 0.001 HIS N 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (12250) covalent geometry : angle 0.62100 / 0.32 (16602) SS BOND : bond 0.00439 / 0.31 ( 17) SS BOND : angle 2.04990 / 1.55 ( 34) hydrogen bonds : bond 0.04073 / 2.64 ( 565) hydrogen bonds : angle 4.37401 / 3.08 ( 1680) link_BETA1-4 : bond 0.00471 / 0.26 ( 7) link_BETA1-4 : angle 1.30088 / 0.87 ( 21) link_NAG-ASN : bond 0.01012 / 0.54 ( 11) link_NAG-ASN : angle 5.33505 / 3.36 ( 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 223 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: F 58 LEU cc_start: 0.6542 (mm) cc_final: 0.6322 (mp) REVERT: F 85 LYS cc_start: 0.8349 (mttp) cc_final: 0.7793 (mmtm) REVERT: F 144 LEU cc_start: 0.4895 (OUTLIER) cc_final: 0.4631 (mm) REVERT: G 65 LEU cc_start: 0.6048 (OUTLIER) cc_final: 0.5689 (mm) REVERT: E 37 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7574 (mppt) REVERT: E 115 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7959 (ttt180) REVERT: A 230 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7861 (mt0) REVERT: B 48 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8087 (p90) REVERT: B 253 GLN cc_start: 0.8070 (tt0) cc_final: 0.7834 (tt0) REVERT: M 99 MET cc_start: 0.6381 (mtp) cc_final: 0.6153 (mtm) outliers start: 31 outliers final: 14 residues processed: 213 average time/residue: 0.5362 time to fit residues: 123.5327 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 : 0.478 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain N residue 35 ARG 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: 0.9980 chunk 96 optimal weight: 4.9990 chunk 97 optimal weight: 0.0980 chunk 25 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.143776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.096622 restraints weight = 18315.111| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.46 r_work: 0.3074 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12285 Z= 0.150 Angle : 0.703 13.464 16690 Z= 0.351 Chirality : 0.047 0.311 1861 Planarity : 0.004 0.035 2099 Dihedral : 5.137 44.627 1612 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.17 % Allowed : 21.74 % Favored : 76.09 % 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 are not related in a simple way. whole: 0.74 (0.22), residues: 1442 helix: 2.37 (0.27), residues: 343 sheet: 1.31 (0.25), residues: 424 loop : -1.12 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 170 TYR 0.027 0.001 TYR D 79 PHE 0.019 0.002 PHE A 35 TRP 0.035 0.002 TRP F 151 HIS 0.004 0.001 HIS N 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (12250) covalent geometry : angle 0.65562 / 0.34 (16602) SS BOND : bond 0.00649 / 0.46 ( 17) SS BOND : angle 2.16113 / 1.66 ( 34) hydrogen bonds : bond 0.04533 / 2.94 ( 565) hydrogen bonds : angle 4.46085 / 3.15 ( 1680) link_BETA1-4 : bond 0.00400 / 0.21 ( 7) link_BETA1-4 : angle 1.36729 / 0.90 ( 21) link_NAG-ASN : bond 0.00959 / 0.52 ( 11) link_NAG-ASN : angle 5.28885 / 3.30 ( 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 212 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: D 68 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7619 (mtt-85) REVERT: F 58 LEU cc_start: 0.6473 (mm) cc_final: 0.6261 (mp) REVERT: F 85 LYS cc_start: 0.8308 (mttp) cc_final: 0.7748 (mmtm) REVERT: F 130 VAL cc_start: 0.7983 (t) cc_final: 0.7780 (p) REVERT: F 144 LEU cc_start: 0.4968 (OUTLIER) cc_final: 0.4676 (mm) REVERT: G 65 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5759 (mm) REVERT: E 37 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7549 (mppt) REVERT: E 115 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7993 (ttt180) REVERT: A 230 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7894 (mt0) REVERT: A 238 ARG cc_start: 0.7367 (mmt90) cc_final: 0.7157 (mmt90) REVERT: B 48 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8160 (p90) REVERT: B 253 GLN cc_start: 0.8157 (tt0) cc_final: 0.7901 (tt0) REVERT: M 99 MET cc_start: 0.6422 (mtp) cc_final: 0.6176 (mtm) outliers start: 28 outliers final: 13 residues processed: 201 average time/residue: 0.5619 time to fit residues: 121.8865 Evaluate side-chains 200 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain D residue 84 SER 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 65 LEU Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain N residue 35 ARG 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 56 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 23 GLN E 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.143381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.096383 restraints weight = 18371.282| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.48 r_work: 0.3063 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12285 Z= 0.160 Angle : 0.720 13.388 16690 Z= 0.361 Chirality : 0.047 0.311 1861 Planarity : 0.004 0.034 2099 Dihedral : 5.223 47.842 1612 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.47 % Favored : 96.46 % Rotamer: Outliers : 2.17 % Allowed : 21.82 % Favored : 76.01 % 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 are not related in a simple way. whole: 0.66 (0.22), residues: 1442 helix: 2.30 (0.27), residues: 343 sheet: 1.23 (0.25), residues: 425 loop : -1.15 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 170 TYR 0.015 0.001 TYR D 71 PHE 0.022 0.002 PHE G 118 TRP 0.039 0.002 TRP F 151 HIS 0.005 0.001 HIS N 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (12250) covalent geometry : angle 0.67319 / 0.35 (16602) SS BOND : bond 0.00685 / 0.48 ( 17) SS BOND : angle 2.15811 / 1.66 ( 34) hydrogen bonds : bond 0.04711 / 3.06 ( 565) hydrogen bonds : angle 4.50477 / 3.18 ( 1680) link_BETA1-4 : bond 0.00443 / 0.23 ( 7) link_BETA1-4 : angle 1.41536 / 0.93 ( 21) link_NAG-ASN : bond 0.00969 / 0.52 ( 11) link_NAG-ASN : angle 5.27702 / 3.28 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5701.91 seconds wall clock time: 97 minutes 37.38 seconds (5857.38 seconds total)