Starting phenix.real_space_refine on Wed Jul 30 10:17:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8es8_28571/07_2025/8es8_28571.cif Found real_map, /net/cci-nas-00/data/ceres_data/8es8_28571/07_2025/8es8_28571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8es8_28571/07_2025/8es8_28571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8es8_28571/07_2025/8es8_28571.map" model { file = "/net/cci-nas-00/data/ceres_data/8es8_28571/07_2025/8es8_28571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8es8_28571/07_2025/8es8_28571.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11976 Number of models: 1 Model: "" Number of chains: 21 Chain: "Z" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 281 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "Y" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 249 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "D" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 821 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "G" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 913 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "E" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "A" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2008 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain: "B" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2292 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 273} Chain: "N" Number of atoms: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2246 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 263} Chain: "M" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 837 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Chain: "P" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 80 Classifications: {'peptide': 10} Modifications used: {'COO': 1} Link IDs: {'TRANS': 9} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.10, per 1000 atoms: 0.76 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: 3.55 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.82 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: 4.18 Time building geometry restraints manager: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3829 1.35 - 1.47: 3159 1.47 - 1.60: 5164 1.60 - 1.72: 0 1.72 - 1.84: 98 Bond restraints: 12250 Sorted by residual: bond pdb=" CAI Y01 Y 201 " pdb=" CAK Y01 Y 201 " ideal model delta sigma weight residual 1.492 1.404 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.54e+00 bond pdb=" C1 NAG A1701 " pdb=" O5 NAG A1701 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.29e+00 bond pdb=" CAI Y01 Y 201 " pdb=" CAZ Y01 Y 201 " ideal model delta sigma weight residual 1.332 1.381 -0.049 2.00e-02 2.50e+03 5.97e+00 bond pdb=" C1 NAG G1702 " pdb=" O5 NAG G1702 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.20e+00 ... (remaining 12245 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 16322 2.36 - 4.72: 249 4.72 - 7.08: 21 7.08 - 9.44: 6 9.44 - 11.79: 4 Bond angle restraints: 16602 Sorted by residual: angle pdb=" OAG Y01 Y 201 " pdb=" CAY Y01 Y 201 " pdb=" OAW Y01 Y 201 " ideal model delta sigma weight residual 123.38 111.59 11.79 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CAM Y01 Y 201 " pdb=" CAY Y01 Y 201 " pdb=" OAW Y01 Y 201 " ideal model delta sigma weight residual 111.19 122.45 -11.26 3.00e+00 1.11e-01 1.41e+01 angle pdb=" CA CYS F 119 " pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " ideal model delta sigma weight residual 114.40 122.07 -7.67 2.30e+00 1.89e-01 1.11e+01 angle pdb=" N ASN A 184 " pdb=" CA ASN A 184 " pdb=" CB ASN A 184 " ideal model delta sigma weight residual 110.29 103.12 7.17 2.15e+00 2.16e-01 1.11e+01 angle pdb=" CAV Y01 Y 201 " pdb=" CAZ Y01 Y 201 " pdb=" CBH Y01 Y 201 " ideal model delta sigma weight residual 116.96 126.57 -9.61 3.00e+00 1.11e-01 1.03e+01 ... (remaining 16597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.65: 7082 21.65 - 43.31: 405 43.31 - 64.96: 66 64.96 - 86.62: 27 86.62 - 108.27: 16 Dihedral angle restraints: 7596 sinusoidal: 3337 harmonic: 4259 Sorted by residual: dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 122 " pdb=" CB CYS E 122 " ideal model delta sinusoidal sigma weight residual 93.00 42.29 50.71 1 1.00e+01 1.00e-02 3.52e+01 dihedral pdb=" CB CYS M 25 " pdb=" SG CYS M 25 " pdb=" SG CYS M 80 " pdb=" CB CYS M 80 " ideal model delta sinusoidal sigma weight residual 93.00 44.59 48.41 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" CA ASN A 150 " pdb=" C ASN A 150 " pdb=" N VAL A 151 " pdb=" CA VAL A 151 " ideal model delta harmonic sigma weight residual -180.00 -154.68 -25.32 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 7593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1825 0.129 - 0.259: 30 0.259 - 0.388: 5 0.388 - 0.517: 0 0.517 - 0.646: 1 Chirality restraints: 1861 Sorted by residual: chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN A 150 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C1 NAG A1702 " pdb=" ND2 ASN A 184 " pdb=" C2 NAG A1702 " pdb=" O5 NAG A1702 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA ASN A 195 " pdb=" N ASN A 195 " pdb=" C ASN A 195 " pdb=" CB ASN A 195 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 1858 not shown) Planarity restraints: 2110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 205 " 0.065 5.00e-02 4.00e+02 9.90e-02 1.57e+01 pdb=" N PRO A 206 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 52 " -0.033 2.00e-02 2.50e+03 3.24e-02 1.31e+01 pdb=" CG ASN G 52 " 0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN G 52 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN G 52 " 0.020 2.00e-02 2.50e+03 pdb=" C1 NAG G1702 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 150 " 0.025 2.00e-02 2.50e+03 2.43e-02 7.37e+00 pdb=" CG ASN A 150 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 150 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 150 " -0.030 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.026 2.00e-02 2.50e+03 ... (remaining 2107 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 253 2.69 - 3.25: 11032 3.25 - 3.80: 17895 3.80 - 4.35: 24045 4.35 - 4.90: 40251 Nonbonded interactions: 93476 Sorted by model distance: nonbonded pdb=" O SER B 8 " pdb=" OG1 THR B 109 " model vdw 2.142 3.040 nonbonded pdb=" NZ LYS N 127 " pdb=" O TRP N 133 " model vdw 2.171 3.120 nonbonded pdb=" OG1 THR G 66 " pdb=" OD1 ASP G 68 " model vdw 2.205 3.040 nonbonded pdb=" O SER N 13 " pdb=" OG SER N 92 " model vdw 2.241 3.040 nonbonded pdb=" OD1 ASN G 52 " pdb=" N2 NAG G1702 " model vdw 2.245 3.120 ... (remaining 93471 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = (chain 'F' and resid 33 through 155) } ncs_group { reference = chain 'J' selection = chain 'Q' selection = chain 'T' selection = chain 'U' selection = chain 'V' } ncs_group { reference = (chain 'Y' and resid 25 through 55) selection = (chain 'Z' and resid 25 through 55) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 284.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 33.790 Find NCS groups from input model: 0.290 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: 0.000 Load rotamer database and sin/cos tables:14.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 334.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 12285 Z= 0.193 Angle : 0.799 23.688 16690 Z= 0.383 Chirality : 0.053 0.646 1861 Planarity : 0.005 0.099 2099 Dihedral : 14.956 108.272 4813 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.08 % Allowed : 0.23 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (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 TRP 0.018 0.002 TRP F 59 HIS 0.005 0.001 HIS N 70 PHE 0.025 0.002 PHE A 35 TYR 0.013 0.001 TYR D 71 ARG 0.004 0.001 ARG M 3 Details of bonding type rmsd link_NAG-ASN : bond 0.01659 ( 11) link_NAG-ASN : angle 7.65727 ( 33) link_BETA1-4 : bond 0.00482 ( 7) link_BETA1-4 : angle 2.52770 ( 21) hydrogen bonds : bond 0.13856 ( 565) hydrogen bonds : angle 5.68466 ( 1680) SS BOND : bond 0.00615 ( 17) SS BOND : angle 2.24286 ( 34) covalent geometry : bond 0.00418 (12250) covalent geometry : angle 0.71237 (16602) *********************** 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 : 1.516 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: 0.5415 (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: 1.8194 time to fit residues: 502.8405 Evaluate side-chains 196 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 2.026 ------------------------------------------------------------------------------- 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 119 optimal weight: 1.9990 chunk 107 optimal weight: 0.2980 chunk 59 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 43 optimal weight: 0.0870 chunk 67 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 GLN F 92 GLN G 77 ASN E 62 ASN E 81 HIS A 196 ASN N 115 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.146193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.099696 restraints weight = 18471.347| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.39 r_work: 0.3119 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 12285 Z= 0.128 Angle : 0.699 16.544 16690 Z= 0.344 Chirality : 0.046 0.336 1861 Planarity : 0.004 0.063 2099 Dihedral : 10.098 95.169 2048 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.25 % Allowed : 11.96 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.22), residues: 1442 helix: 2.64 (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 TRP 0.021 0.001 TRP F 151 HIS 0.004 0.001 HIS N 192 PHE 0.024 0.001 PHE G 118 TYR 0.022 0.001 TYR D 79 ARG 0.004 0.000 ARG N 35 Details of bonding type rmsd link_NAG-ASN : bond 0.01184 ( 11) link_NAG-ASN : angle 6.32256 ( 33) link_BETA1-4 : bond 0.00466 ( 7) link_BETA1-4 : angle 1.88779 ( 21) hydrogen bonds : bond 0.04446 ( 565) hydrogen bonds : angle 4.60080 ( 1680) SS BOND : bond 0.00507 ( 17) SS BOND : angle 2.07169 ( 34) covalent geometry : bond 0.00275 (12250) covalent geometry : angle 0.63126 (16602) *********************** 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: 29 poor density : 208 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 84 LEU cc_start: 0.8023 (mt) cc_final: 0.7818 (mt) REVERT: F 85 LYS cc_start: 0.8444 (mttp) cc_final: 0.7932 (mmtm) REVERT: F 99 TYR cc_start: 0.6173 (p90) cc_final: 0.5963 (p90) REVERT: F 121 ASN cc_start: 0.6993 (p0) cc_final: 0.6669 (p0) REVERT: F 144 LEU cc_start: 0.5172 (OUTLIER) cc_final: 0.4831 (mm) REVERT: G 129 LEU cc_start: 0.7263 (mm) cc_final: 0.6895 (mt) REVERT: E 37 LYS cc_start: 0.7777 (mtmt) cc_final: 0.7423 (mppt) REVERT: E 64 LYS cc_start: 0.7963 (mtpp) cc_final: 0.7732 (mmtp) REVERT: E 115 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7921 (ttt180) REVERT: A 109 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8386 (tpp80) outliers start: 29 outliers final: 13 residues processed: 221 average time/residue: 1.5874 time to fit residues: 378.5366 Evaluate side-chains 202 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 1.476 ------------------------------------------------------------------------------- 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 109 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 3 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 51 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN B 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.145000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.097689 restraints weight = 18539.081| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.57 r_work: 0.3081 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12285 Z= 0.142 Angle : 0.691 15.551 16690 Z= 0.340 Chirality : 0.047 0.332 1861 Planarity : 0.004 0.049 2099 Dihedral : 9.129 98.606 2048 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.33 % Allowed : 14.52 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.22), residues: 1442 helix: 2.57 (0.27), residues: 345 sheet: 1.25 (0.25), residues: 425 loop : -1.06 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 151 HIS 0.005 0.001 HIS N 70 PHE 0.024 0.001 PHE A 35 TYR 0.015 0.001 TYR F 111 ARG 0.004 0.000 ARG A 130 Details of bonding type rmsd link_NAG-ASN : bond 0.01051 ( 11) link_NAG-ASN : angle 6.04295 ( 33) link_BETA1-4 : bond 0.00428 ( 7) link_BETA1-4 : angle 1.94064 ( 21) hydrogen bonds : bond 0.04517 ( 565) hydrogen bonds : angle 4.48440 ( 1680) SS BOND : bond 0.00735 ( 17) SS BOND : angle 2.12860 ( 34) covalent geometry : bond 0.00318 (12250) covalent geometry : angle 0.62677 (16602) *********************** 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 233 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 85 LYS cc_start: 0.8426 (mttp) cc_final: 0.7903 (mmtm) REVERT: F 121 ASN cc_start: 0.6986 (p0) cc_final: 0.6642 (p0) REVERT: F 144 LEU cc_start: 0.4954 (OUTLIER) cc_final: 0.4651 (mm) REVERT: G 129 LEU cc_start: 0.7210 (mm) cc_final: 0.6839 (mt) REVERT: E 37 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7544 (mppt) REVERT: E 43 THR cc_start: 0.7866 (p) cc_final: 0.7520 (m) REVERT: E 64 LYS cc_start: 0.7957 (mtpp) cc_final: 0.7730 (mmtp) REVERT: E 120 GLU cc_start: 0.5951 (pp20) cc_final: 0.5526 (pm20) REVERT: A 109 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8539 (tpp-160) outliers start: 30 outliers final: 14 residues processed: 216 average time/residue: 1.2900 time to fit residues: 301.6807 Evaluate side-chains 201 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain A residue 2 GLN Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain N residue 261 VAL Chi-restraints excluded: chain M residue 34 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 88 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.141978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.094962 restraints weight = 18266.751| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.46 r_work: 0.3036 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 12285 Z= 0.240 Angle : 0.796 15.306 16690 Z= 0.400 Chirality : 0.051 0.380 1861 Planarity : 0.005 0.043 2099 Dihedral : 8.626 94.431 2048 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.96 % Allowed : 14.60 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.21), residues: 1442 helix: 2.09 (0.26), residues: 345 sheet: 1.07 (0.24), residues: 437 loop : -1.28 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 151 HIS 0.006 0.001 HIS N 70 PHE 0.028 0.002 PHE A 35 TYR 0.023 0.002 TYR F 111 ARG 0.006 0.001 ARG N 35 Details of bonding type rmsd link_NAG-ASN : bond 0.01010 ( 11) link_NAG-ASN : angle 6.00927 ( 33) link_BETA1-4 : bond 0.00515 ( 7) link_BETA1-4 : angle 2.08188 ( 21) hydrogen bonds : bond 0.05665 ( 565) hydrogen bonds : angle 4.70349 ( 1680) SS BOND : bond 0.01380 ( 17) SS BOND : angle 2.54880 ( 34) covalent geometry : bond 0.00566 (12250) covalent geometry : angle 0.73944 (16602) *********************** 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: 51 poor density : 201 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 99 TYR cc_start: 0.6077 (OUTLIER) cc_final: 0.5099 (p90) REVERT: F 121 ASN cc_start: 0.7260 (p0) cc_final: 0.6956 (p0) REVERT: F 144 LEU cc_start: 0.5056 (OUTLIER) cc_final: 0.4740 (mm) REVERT: E 37 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7675 (mppt) REVERT: E 115 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8061 (ttt180) REVERT: E 117 ARG cc_start: 0.8879 (ttm170) cc_final: 0.8679 (ttm-80) REVERT: B 253 GLN cc_start: 0.8411 (tt0) cc_final: 0.8139 (tt0) REVERT: B 254 GLN cc_start: 0.8434 (mm110) cc_final: 0.8120 (tp-100) REVERT: M 99 MET cc_start: 0.6470 (mtp) cc_final: 0.6227 (mtm) outliers start: 51 outliers final: 17 residues processed: 226 average time/residue: 1.4526 time to fit residues: 354.1174 Evaluate side-chains 207 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 98 CYS Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 261 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 2 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.143894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.097089 restraints weight = 18400.927| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.41 r_work: 0.3079 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12285 Z= 0.137 Angle : 0.698 14.555 16690 Z= 0.345 Chirality : 0.047 0.421 1861 Planarity : 0.004 0.037 2099 Dihedral : 7.765 59.935 2046 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.03 % Allowed : 17.24 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.22), residues: 1442 helix: 2.46 (0.27), residues: 342 sheet: 1.20 (0.25), residues: 430 loop : -1.15 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 151 HIS 0.004 0.001 HIS N 70 PHE 0.022 0.001 PHE G 118 TYR 0.017 0.001 TYR B 252 ARG 0.011 0.000 ARG A 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00993 ( 11) link_NAG-ASN : angle 5.94092 ( 33) link_BETA1-4 : bond 0.00470 ( 7) link_BETA1-4 : angle 1.91874 ( 21) hydrogen bonds : bond 0.04632 ( 565) hydrogen bonds : angle 4.46014 ( 1680) SS BOND : bond 0.00582 ( 17) SS BOND : angle 2.17254 ( 34) covalent geometry : bond 0.00305 (12250) covalent geometry : angle 0.63681 (16602) *********************** 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 238 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 85 LYS cc_start: 0.8328 (mttp) cc_final: 0.7767 (mmtm) REVERT: F 106 GLU cc_start: 0.6787 (tp30) cc_final: 0.6183 (tp30) REVERT: F 121 ASN cc_start: 0.7199 (p0) cc_final: 0.6974 (p0) REVERT: F 144 LEU cc_start: 0.4928 (OUTLIER) cc_final: 0.4630 (mm) REVERT: G 129 LEU cc_start: 0.7254 (mm) cc_final: 0.6890 (mt) REVERT: E 37 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7483 (mppt) REVERT: E 90 LEU cc_start: 0.8899 (mt) cc_final: 0.8342 (tp) REVERT: E 115 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7972 (ttt180) REVERT: B 254 GLN cc_start: 0.8322 (mm110) cc_final: 0.8019 (tp-100) REVERT: M 99 MET cc_start: 0.6441 (mtp) cc_final: 0.6209 (mtm) outliers start: 39 outliers final: 13 residues processed: 219 average time/residue: 1.6027 time to fit residues: 381.9323 Evaluate side-chains 204 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain 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 115 ARG Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain B residue 257 LEU 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 44 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 2 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.144453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.097890 restraints weight = 18532.795| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.33 r_work: 0.3088 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 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 : 0.003 0.045 12285 Z= 0.129 Angle : 0.691 14.112 16690 Z= 0.340 Chirality : 0.047 0.412 1861 Planarity : 0.004 0.036 2099 Dihedral : 7.333 59.954 2046 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.18 % Allowed : 18.25 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.22), residues: 1442 helix: 2.56 (0.27), residues: 342 sheet: 1.20 (0.25), residues: 432 loop : -1.11 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 151 HIS 0.004 0.001 HIS N 70 PHE 0.018 0.001 PHE A 35 TYR 0.024 0.001 TYR F 111 ARG 0.010 0.000 ARG A 170 Details of bonding type rmsd link_NAG-ASN : bond 0.01028 ( 11) link_NAG-ASN : angle 5.85633 ( 33) link_BETA1-4 : bond 0.00457 ( 7) link_BETA1-4 : angle 1.88249 ( 21) hydrogen bonds : bond 0.04354 ( 565) hydrogen bonds : angle 4.38129 ( 1680) SS BOND : bond 0.00574 ( 17) SS BOND : angle 2.52390 ( 34) covalent geometry : bond 0.00286 (12250) covalent geometry : angle 0.62741 (16602) *********************** 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 238 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 85 LYS cc_start: 0.8323 (mttp) cc_final: 0.7786 (mmtm) REVERT: F 99 TYR cc_start: 0.6091 (p90) cc_final: 0.5863 (p90) REVERT: F 121 ASN cc_start: 0.6964 (p0) cc_final: 0.6756 (p0) REVERT: F 144 LEU cc_start: 0.4891 (OUTLIER) cc_final: 0.4609 (mm) REVERT: G 129 LEU cc_start: 0.7235 (mm) cc_final: 0.6874 (mt) REVERT: E 37 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7581 (mppt) REVERT: E 115 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7952 (ttt180) REVERT: A 151 VAL cc_start: 0.9345 (OUTLIER) cc_final: 0.9140 (t) REVERT: A 222 GLU cc_start: 0.7711 (pt0) cc_final: 0.7460 (pm20) REVERT: A 230 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7892 (mt0) REVERT: B 48 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8134 (p90) REVERT: B 253 GLN cc_start: 0.8180 (tt0) cc_final: 0.7891 (tt0) REVERT: N 98 MET cc_start: 0.9024 (tmt) cc_final: 0.8610 (tpt) outliers start: 41 outliers final: 19 residues processed: 217 average time/residue: 1.2395 time to fit residues: 291.5683 Evaluate side-chains 213 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 190 CYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 2 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.143128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.096318 restraints weight = 18433.466| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.41 r_work: 0.3061 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12285 Z= 0.173 Angle : 0.730 14.309 16690 Z= 0.363 Chirality : 0.048 0.409 1861 Planarity : 0.004 0.037 2099 Dihedral : 7.322 59.702 2046 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.34 % Allowed : 18.40 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.22), residues: 1442 helix: 2.36 (0.26), residues: 343 sheet: 1.19 (0.25), residues: 427 loop : -1.14 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 151 HIS 0.005 0.001 HIS N 70 PHE 0.022 0.002 PHE G 118 TYR 0.023 0.002 TYR D 79 ARG 0.005 0.001 ARG A 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00926 ( 11) link_NAG-ASN : angle 5.75018 ( 33) link_BETA1-4 : bond 0.00487 ( 7) link_BETA1-4 : angle 1.94720 ( 21) hydrogen bonds : bond 0.04879 ( 565) hydrogen bonds : angle 4.49583 ( 1680) SS BOND : bond 0.00763 ( 17) SS BOND : angle 2.69615 ( 34) covalent geometry : bond 0.00401 (12250) covalent geometry : angle 0.67142 (16602) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 1.405 Fit side-chains revert: symmetry clash REVERT: F 85 LYS cc_start: 0.8300 (mttp) cc_final: 0.7759 (mmtm) REVERT: F 144 LEU cc_start: 0.4999 (OUTLIER) cc_final: 0.4717 (mm) REVERT: G 54 THR cc_start: 0.6244 (OUTLIER) cc_final: 0.5189 (p) REVERT: E 115 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7989 (ttt180) REVERT: A 230 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7907 (mt0) REVERT: B 48 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8160 (p90) REVERT: B 253 GLN cc_start: 0.8260 (tt0) cc_final: 0.7955 (tt0) REVERT: B 254 GLN cc_start: 0.8331 (mm110) cc_final: 0.8011 (tp-100) REVERT: M 99 MET cc_start: 0.6420 (mtp) cc_final: 0.6191 (mtm) outliers start: 43 outliers final: 19 residues processed: 215 average time/residue: 1.1811 time to fit residues: 275.7632 Evaluate side-chains 203 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 62 ILE Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain A residue 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 180 GLN Chi-restraints excluded: chain B residue 257 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 43 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 138 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 GLN E 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.144223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.097575 restraints weight = 18407.837| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.39 r_work: 0.3079 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12285 Z= 0.137 Angle : 0.708 12.235 16690 Z= 0.351 Chirality : 0.047 0.417 1861 Planarity : 0.004 0.035 2099 Dihedral : 7.096 59.196 2046 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.72 % Allowed : 19.57 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.22), residues: 1442 helix: 2.46 (0.27), residues: 342 sheet: 1.24 (0.25), residues: 424 loop : -1.14 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 151 HIS 0.005 0.001 HIS N 70 PHE 0.016 0.001 PHE A 35 TYR 0.013 0.001 TYR D 71 ARG 0.003 0.000 ARG A 130 Details of bonding type rmsd link_NAG-ASN : bond 0.00964 ( 11) link_NAG-ASN : angle 5.69750 ( 33) link_BETA1-4 : bond 0.00445 ( 7) link_BETA1-4 : angle 1.91077 ( 21) hydrogen bonds : bond 0.04465 ( 565) hydrogen bonds : angle 4.41294 ( 1680) SS BOND : bond 0.00582 ( 17) SS BOND : angle 2.42524 ( 34) covalent geometry : bond 0.00310 (12250) covalent geometry : angle 0.64972 (16602) *********************** 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 228 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: F 58 LEU cc_start: 0.6606 (mm) cc_final: 0.6307 (mp) REVERT: F 85 LYS cc_start: 0.8303 (mttp) cc_final: 0.7728 (mmtm) REVERT: F 144 LEU cc_start: 0.4878 (OUTLIER) cc_final: 0.4601 (mm) REVERT: E 115 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8005 (ttt180) REVERT: A 151 VAL cc_start: 0.9360 (OUTLIER) cc_final: 0.9159 (t) REVERT: A 230 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7877 (mt0) REVERT: B 48 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8145 (p90) REVERT: N 98 MET cc_start: 0.8968 (tmt) cc_final: 0.8540 (tpt) REVERT: M 99 MET cc_start: 0.6398 (mtp) cc_final: 0.6172 (mtm) outliers start: 35 outliers final: 16 residues processed: 214 average time/residue: 1.2815 time to fit residues: 296.9454 Evaluate side-chains 204 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 257 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 61 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 11 optimal weight: 0.0970 chunk 136 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 51 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.145593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.099201 restraints weight = 18379.277| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.28 r_work: 0.3110 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12285 Z= 0.119 Angle : 0.684 12.294 16690 Z= 0.337 Chirality : 0.046 0.399 1861 Planarity : 0.003 0.033 2099 Dihedral : 6.731 57.167 2046 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.17 % Allowed : 20.34 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.22), residues: 1442 helix: 2.55 (0.27), residues: 342 sheet: 1.27 (0.25), residues: 420 loop : -1.04 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP F 151 HIS 0.003 0.001 HIS N 70 PHE 0.023 0.001 PHE G 118 TYR 0.028 0.001 TYR D 79 ARG 0.003 0.000 ARG N 75 Details of bonding type rmsd link_NAG-ASN : bond 0.00983 ( 11) link_NAG-ASN : angle 5.57898 ( 33) link_BETA1-4 : bond 0.00435 ( 7) link_BETA1-4 : angle 1.85912 ( 21) hydrogen bonds : bond 0.04060 ( 565) hydrogen bonds : angle 4.31067 ( 1680) SS BOND : bond 0.00445 ( 17) SS BOND : angle 2.16147 ( 34) covalent geometry : bond 0.00262 (12250) covalent geometry : angle 0.62864 (16602) *********************** 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 220 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 58 LEU cc_start: 0.6508 (mm) cc_final: 0.6275 (mp) REVERT: F 85 LYS cc_start: 0.8333 (mttp) cc_final: 0.7768 (mmtm) REVERT: F 99 TYR cc_start: 0.6023 (p90) cc_final: 0.5821 (p90) REVERT: F 144 LEU cc_start: 0.4824 (OUTLIER) cc_final: 0.4555 (mm) REVERT: E 92 GLN cc_start: 0.8725 (mt0) cc_final: 0.8275 (mt0) REVERT: E 115 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7966 (ttt180) REVERT: A 151 VAL cc_start: 0.9311 (OUTLIER) cc_final: 0.9077 (t) REVERT: A 230 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7915 (mt0) REVERT: B 48 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8090 (p90) REVERT: B 253 GLN cc_start: 0.8147 (tt0) cc_final: 0.7886 (tt0) REVERT: N 98 MET cc_start: 0.8934 (tmt) cc_final: 0.8480 (tpt) REVERT: M 99 MET cc_start: 0.6392 (mtp) cc_final: 0.6160 (mtm) outliers start: 28 outliers final: 11 residues processed: 209 average time/residue: 1.2708 time to fit residues: 287.0378 Evaluate side-chains 201 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 266 LEU 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 49 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 120 optimal weight: 0.0870 chunk 46 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.142363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.095157 restraints weight = 18289.044| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.47 r_work: 0.3042 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12285 Z= 0.210 Angle : 0.778 12.625 16690 Z= 0.391 Chirality : 0.050 0.408 1861 Planarity : 0.004 0.038 2099 Dihedral : 7.182 59.197 2046 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.10 % Allowed : 20.50 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.22), residues: 1442 helix: 2.14 (0.26), residues: 343 sheet: 1.15 (0.25), residues: 434 loop : -1.18 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 151 HIS 0.006 0.001 HIS N 70 PHE 0.022 0.002 PHE A 35 TYR 0.015 0.002 TYR D 71 ARG 0.005 0.001 ARG Y 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00906 ( 11) link_NAG-ASN : angle 5.53525 ( 33) link_BETA1-4 : bond 0.00447 ( 7) link_BETA1-4 : angle 2.04906 ( 21) hydrogen bonds : bond 0.05309 ( 565) hydrogen bonds : angle 4.55881 ( 1680) SS BOND : bond 0.00891 ( 17) SS BOND : angle 2.56430 ( 34) covalent geometry : bond 0.00491 (12250) covalent geometry : angle 0.72723 (16602) ********************** 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 213 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 1.484 Fit side-chains revert: symmetry clash REVERT: F 58 LEU cc_start: 0.6496 (mm) cc_final: 0.6236 (mp) REVERT: F 85 LYS cc_start: 0.8198 (mttp) cc_final: 0.7656 (mmtm) REVERT: F 144 LEU cc_start: 0.4910 (OUTLIER) cc_final: 0.4620 (mm) REVERT: E 115 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8032 (ttt180) REVERT: A 230 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7881 (mt0) REVERT: B 48 PHE cc_start: 0.9204 (OUTLIER) cc_final: 0.8222 (p90) REVERT: B 254 GLN cc_start: 0.8432 (mm110) cc_final: 0.8099 (tp-100) REVERT: M 99 MET cc_start: 0.6434 (mtp) cc_final: 0.6178 (mtm) outliers start: 27 outliers final: 14 residues processed: 205 average time/residue: 1.3093 time to fit residues: 289.5892 Evaluate side-chains 201 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 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 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 30 optimal weight: 0.0670 chunk 119 optimal weight: 0.6980 chunk 40 optimal weight: 0.3980 chunk 65 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 GLN E 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.144348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.097901 restraints weight = 18331.935| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.39 r_work: 0.3081 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12285 Z= 0.129 Angle : 0.714 12.203 16690 Z= 0.355 Chirality : 0.047 0.424 1861 Planarity : 0.004 0.035 2099 Dihedral : 6.919 59.365 2046 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.68 % Favored : 96.26 % Rotamer: Outliers : 1.55 % Allowed : 21.12 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.22), residues: 1442 helix: 2.33 (0.27), residues: 342 sheet: 1.21 (0.25), residues: 419 loop : -1.06 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP F 151 HIS 0.004 0.001 HIS N 70 PHE 0.024 0.001 PHE G 118 TYR 0.028 0.001 TYR D 79 ARG 0.003 0.000 ARG A 130 Details of bonding type rmsd link_NAG-ASN : bond 0.00967 ( 11) link_NAG-ASN : angle 5.62337 ( 33) link_BETA1-4 : bond 0.00467 ( 7) link_BETA1-4 : angle 1.87375 ( 21) hydrogen bonds : bond 0.04441 ( 565) hydrogen bonds : angle 4.41633 ( 1680) SS BOND : bond 0.00511 ( 17) SS BOND : angle 2.50910 ( 34) covalent geometry : bond 0.00286 (12250) covalent geometry : angle 0.65786 (16602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13177.05 seconds wall clock time: 231 minutes 40.58 seconds (13900.58 seconds total)