Starting phenix.real_space_refine on Sun Oct 13 10:19:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8es9_28572/10_2024/8es9_28572.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8es9_28572/10_2024/8es9_28572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8es9_28572/10_2024/8es9_28572.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8es9_28572/10_2024/8es9_28572.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8es9_28572/10_2024/8es9_28572.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8es9_28572/10_2024/8es9_28572.cif" } resolution = 3.25 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 Anisotropic ADP refinement not supported. Converting 3163 atoms to isotropic. 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 64 5.16 5 C 7526 2.51 5 N 1968 2.21 5 O 2286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 11844 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1972 Classifications: {'peptide': 251} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 238} Chain: "B" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2261 Classifications: {'peptide': 287} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 274} Chain: "Z" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 286 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 34} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: "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: "H" 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: "L" 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: "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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'NAG': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 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 Time building chain proxies: 9.50, per 1000 atoms: 0.80 Number of scatterers: 11844 At special positions: 0 Unit cell: (95.2, 100.3, 195.5, 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 64 16.00 O 2286 8.00 N 1968 7.00 C 7526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 146 " - pdb=" SG CYS B 211 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS D 93 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 98 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 98 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 122 " distance=2.03 Simple disulfide: pdb=" SG CYS N 101 " - pdb=" SG CYS N 164 " distance=2.03 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 H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG L 1 " - " NAG L 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1701 " - " ASN A 191 " " NAG A1702 " - " ASN A 180 " " NAG A1703 " - " ASN A 22 " " NAG B1701 " - " ASN B 185 " " NAG G1701 " - " ASN G 52 " " NAG G1702 " - " ASN G 92 " " NAG H 1 " - " ASN D 38 " " NAG L 1 " - " ASN D 74 " " NAG T 1 " - " ASN A 146 " Time building additional restraints: 3.87 Conformation dependent library (CDL) restraints added in 1.7 seconds 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 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: 23 helices and 26 sheets defined 25.8% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 209 through 216 removed outlier: 3.830A pdb=" N SER A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.644A pdb=" N ASN A 224 " --> pdb=" O ASP A 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 removed outlier: 3.617A pdb=" N SER B 89 " --> pdb=" O PRO B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 140 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 249 through 289 removed outlier: 3.548A pdb=" N LEU B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing helix chain 'Z' and resid 29 through 57 Processing helix chain 'Y' and resid 28 through 55 removed outlier: 4.395A pdb=" N CYS Y 32 " --> pdb=" O ASP Y 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 127 removed outlier: 3.752A pdb=" N GLY D 127 " --> pdb=" O PHE D 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 93 removed outlier: 3.675A pdb=" N SER F 93 " --> pdb=" O GLU F 89 " (cutoff:3.500A) 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 removed outlier: 3.513A pdb=" N ILE G 115 " --> pdb=" O ASN G 111 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE G 136 " --> pdb=" O GLY G 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 93 Processing helix chain 'E' and resid 126 through 155 removed outlier: 3.625A pdb=" N VAL E 130 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN E 154 " --> pdb=" O TYR E 150 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG E 155 " --> pdb=" O TRP E 151 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 53 removed outlier: 3.620A pdb=" N GLU N 53 " --> pdb=" O PRO N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 86 removed outlier: 3.559A pdb=" N GLY N 83 " --> pdb=" O GLY N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 138 through 149 removed outlier: 4.254A pdb=" N THR N 142 " --> pdb=" O MET N 138 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR N 143 " --> pdb=" O ALA N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 151 through 162 removed outlier: 3.844A pdb=" N GLN N 155 " --> pdb=" O HIS N 151 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR N 159 " --> pdb=" O GLN N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 175 Processing helix chain 'N' and resid 175 through 180 removed outlier: 3.657A pdb=" N GLN N 180 " --> pdb=" O LYS N 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 255 No H-bonds generated for 'chain 'N' and resid 253 through 255' Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 14 removed outlier: 3.507A pdb=" N ALA A 110 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 49 removed outlier: 6.478A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR A 49 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 33 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 32 " --> pdb=" O GLN A 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 121 through 124 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 14 removed outlier: 3.572A pdb=" N CYS B 13 " --> pdb=" O THR B 113 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 19 through 22 Processing sheet with id=AA8, first strand: chain 'B' and resid 57 through 58 removed outlier: 5.195A pdb=" N LEU B 46 " --> pdb=" O ARG B 37 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ARG B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 125 through 129 removed outlier: 5.628A pdb=" N TYR B 189 " --> pdb=" O GLY B 150 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 125 through 129 removed outlier: 5.628A pdb=" N TYR B 189 " --> pdb=" O GLY B 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 165 through 166 Processing sheet with id=AB3, first strand: chain 'D' and resid 26 through 28 removed outlier: 6.146A pdb=" N VAL D 33 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 42 through 46 removed outlier: 6.556A pdb=" N ILE D 70 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLY D 46 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ARG D 68 " --> pdb=" O GLY D 46 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N THR D 85 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N TYR E 113 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN D 87 " --> pdb=" O TYR E 113 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ARG E 115 " --> pdb=" O GLN D 87 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N HIS D 89 " --> pdb=" O ARG E 115 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE E 110 " --> pdb=" O CYS E 98 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N CYS E 98 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TRP E 59 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 96 through 98 Processing sheet with id=AB6, first strand: chain 'F' and resid 37 through 41 Processing sheet with id=AB7, first strand: chain 'F' and resid 64 through 66 removed outlier: 4.085A pdb=" N TRP F 59 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG F 115 " --> pdb=" O TYR G 100 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY G 63 " --> pdb=" O TRP G 55 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LYS G 57 " --> pdb=" O MET G 61 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N MET G 61 " --> pdb=" O LYS G 57 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 122 through 123 Processing sheet with id=AB9, first strand: chain 'G' and resid 32 through 34 removed outlier: 5.633A pdb=" N VAL G 42 " --> pdb=" O LEU G 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 37 through 41 Processing sheet with id=AC2, first strand: chain 'N' and resid 46 through 47 removed outlier: 6.765A pdb=" N GLY N 26 " --> pdb=" O PHE N 33 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG N 35 " --> pdb=" O ALA N 24 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA N 24 " --> pdb=" O ARG N 35 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ASP N 37 " --> pdb=" O PHE N 22 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N PHE N 22 " --> pdb=" O ASP N 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG N 111 " --> pdb=" O ASP N 102 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N HIS N 114 " --> pdb=" O LEU N 126 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE N 124 " --> pdb=" O TYR N 116 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N TYR N 118 " --> pdb=" O ASP N 122 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ASP N 122 " --> pdb=" O TYR N 118 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 189 through 193 removed outlier: 5.816A pdb=" N PHE N 241 " --> pdb=" O SER N 207 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 189 through 193 removed outlier: 5.816A pdb=" N PHE N 241 " --> pdb=" O SER N 207 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 222 through 223 Processing sheet with id=AC6, first strand: chain 'M' and resid 6 through 11 removed outlier: 5.980A pdb=" N PHE M 62 " --> pdb=" O GLY M 29 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU M 50 " --> pdb=" O TYR M 67 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 6 through 11 removed outlier: 5.980A pdb=" N PHE M 62 " --> pdb=" O GLY M 29 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER M 55 " --> pdb=" O TYR M 63 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 44 through 45 601 hydrogen bonds defined for protein. 1653 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: 4.23 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3371 1.33 - 1.46: 2787 1.46 - 1.58: 5870 1.58 - 1.70: 0 1.70 - 1.83: 89 Bond restraints: 12117 Sorted by residual: bond pdb=" CAI Y01 B1702 " pdb=" CAK Y01 B1702 " ideal model delta sigma weight residual 1.492 1.405 0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C1 NAG G1702 " pdb=" O5 NAG G1702 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 9.02e+00 bond pdb=" CAI Y01 B1702 " pdb=" CAZ Y01 B1702 " ideal model delta sigma weight residual 1.332 1.382 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C1 NAG B1701 " pdb=" O5 NAG B1701 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.35e+00 bond pdb=" CAY Y01 B1702 " pdb=" OAG Y01 B1702 " ideal model delta sigma weight residual 1.207 1.252 -0.045 2.00e-02 2.50e+03 5.00e+00 ... (remaining 12112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 16131 2.23 - 4.45: 268 4.45 - 6.68: 27 6.68 - 8.91: 6 8.91 - 11.14: 4 Bond angle restraints: 16436 Sorted by residual: angle pdb=" CA GLN E 60 " pdb=" CB GLN E 60 " pdb=" CG GLN E 60 " ideal model delta sigma weight residual 114.10 123.21 -9.11 2.00e+00 2.50e-01 2.08e+01 angle pdb=" C GLY B 107 " pdb=" N GLN B 108 " pdb=" CA GLN B 108 " ideal model delta sigma weight residual 121.54 129.05 -7.51 1.91e+00 2.74e-01 1.55e+01 angle pdb=" CAM Y01 B1702 " pdb=" CAY Y01 B1702 " pdb=" OAW Y01 B1702 " ideal model delta sigma weight residual 111.19 122.33 -11.14 3.00e+00 1.11e-01 1.38e+01 angle pdb=" OAG Y01 B1702 " pdb=" CAY Y01 B1702 " pdb=" OAW Y01 B1702 " ideal model delta sigma weight residual 123.38 112.86 10.52 3.00e+00 1.11e-01 1.23e+01 angle pdb=" CAV Y01 B1702 " pdb=" CAZ Y01 B1702 " pdb=" CBH Y01 B1702 " ideal model delta sigma weight residual 116.96 126.79 -9.83 3.00e+00 1.11e-01 1.07e+01 ... (remaining 16431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.22: 6902 22.22 - 44.43: 470 44.43 - 66.65: 56 66.65 - 88.86: 21 88.86 - 111.08: 4 Dihedral angle restraints: 7453 sinusoidal: 3207 harmonic: 4246 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 42.75 50.25 1 1.00e+01 1.00e-02 3.46e+01 dihedral pdb=" CB CYS Z 32 " pdb=" SG CYS Z 32 " pdb=" SG CYS Y 32 " pdb=" CB CYS Y 32 " ideal model delta sinusoidal sigma weight residual 93.00 142.21 -49.21 1 1.00e+01 1.00e-02 3.33e+01 dihedral pdb=" CA GLY B 107 " pdb=" C GLY B 107 " pdb=" N GLN B 108 " pdb=" CA GLN B 108 " ideal model delta harmonic sigma weight residual 180.00 153.01 26.99 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 7450 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 1788 0.114 - 0.227: 47 0.227 - 0.341: 7 0.341 - 0.454: 1 0.454 - 0.568: 1 Chirality restraints: 1844 Sorted by residual: chirality pdb=" C1 NAG A1703 " pdb=" ND2 ASN A 22 " pdb=" C2 NAG A1703 " pdb=" O5 NAG A1703 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.07e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN A 146 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" C1 NAG G1701 " pdb=" ND2 ASN G 52 " pdb=" C2 NAG G1701 " pdb=" O5 NAG G1701 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 1841 not shown) Planarity restraints: 2090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU N 154 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.85e+00 pdb=" C GLU N 154 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU N 154 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN N 155 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 55 " 0.011 2.00e-02 2.50e+03 1.54e-02 5.93e+00 pdb=" CG TRP G 55 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP G 55 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP G 55 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 55 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP G 55 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP G 55 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 55 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 55 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP G 55 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA N 153 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.71e+00 pdb=" C ALA N 153 " 0.041 2.00e-02 2.50e+03 pdb=" O ALA N 153 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU N 154 " -0.014 2.00e-02 2.50e+03 ... (remaining 2087 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 513 2.72 - 3.27: 11108 3.27 - 3.81: 18179 3.81 - 4.36: 21618 4.36 - 4.90: 39023 Nonbonded interactions: 90441 Sorted by model distance: nonbonded pdb=" NZ LYS N 66 " pdb=" O TYR P 3 " model vdw 2.176 3.120 nonbonded pdb=" O LYS E 73 " pdb=" NZ LYS E 85 " model vdw 2.202 3.120 nonbonded pdb=" NH1 ARG A 234 " pdb=" OD2 ASP Y 36 " model vdw 2.204 3.120 nonbonded pdb=" OG1 THR G 66 " pdb=" OD1 ASP G 68 " model vdw 2.241 3.040 nonbonded pdb=" OG SER Z 23 " pdb=" OE1 GLN D 94 " model vdw 2.265 3.040 ... (remaining 90436 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 'L' selection = chain 'T' } ncs_group { reference = chain 'Y' 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: 21.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.270 Process input model: 32.960 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.005 0.087 12117 Z= 0.296 Angle : 0.698 11.137 16436 Z= 0.349 Chirality : 0.051 0.568 1844 Planarity : 0.004 0.036 2081 Dihedral : 14.595 111.079 4670 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.36 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.26 (0.23), residues: 1437 helix: 2.28 (0.28), residues: 337 sheet: 0.72 (0.25), residues: 449 loop : -1.43 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP G 55 HIS 0.003 0.001 HIS N 151 PHE 0.016 0.002 PHE D 22 TYR 0.020 0.002 TYR M 67 ARG 0.007 0.001 ARG G 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8682 (tp) cc_final: 0.8482 (tp) REVERT: F 123 MET cc_start: 0.8081 (ppp) cc_final: 0.7685 (ppp) REVERT: G 55 TRP cc_start: 0.7607 (m100) cc_final: 0.7356 (m100) REVERT: E 65 ASN cc_start: 0.7551 (m-40) cc_final: 0.7250 (m-40) REVERT: E 66 ILE cc_start: 0.7723 (tp) cc_final: 0.7520 (tp) REVERT: E 92 GLN cc_start: 0.8343 (tp-100) cc_final: 0.7918 (tp-100) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2475 time to fit residues: 75.4925 Evaluate side-chains 179 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 59 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN F 65 ASN N 192 HIS M 31 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12117 Z= 0.321 Angle : 0.667 7.229 16436 Z= 0.345 Chirality : 0.049 0.508 1844 Planarity : 0.004 0.054 2081 Dihedral : 8.115 72.349 1926 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.22 % Favored : 94.71 % Rotamer: Outliers : 0.94 % Allowed : 7.57 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.36 (0.23), residues: 1437 helix: 2.37 (0.28), residues: 339 sheet: 0.76 (0.25), residues: 453 loop : -1.38 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 55 HIS 0.004 0.001 HIS N 151 PHE 0.019 0.002 PHE M 30 TYR 0.020 0.002 TYR G 34 ARG 0.005 0.001 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 193 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 274 TYR cc_start: 0.8505 (t80) cc_final: 0.8240 (t80) REVERT: F 123 MET cc_start: 0.8044 (ppp) cc_final: 0.7534 (ppp) REVERT: G 30 LEU cc_start: 0.7051 (mp) cc_final: 0.6838 (pp) REVERT: G 55 TRP cc_start: 0.7908 (m100) cc_final: 0.7700 (m100) REVERT: E 85 LYS cc_start: 0.9066 (pttt) cc_final: 0.8752 (pttm) REVERT: E 92 GLN cc_start: 0.8459 (tp-100) cc_final: 0.7938 (tp-100) outliers start: 12 outliers final: 9 residues processed: 196 average time/residue: 0.2510 time to fit residues: 73.3442 Evaluate side-chains 188 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 179 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain M residue 50 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 128 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 103 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN N 192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12117 Z= 0.203 Angle : 0.610 6.978 16436 Z= 0.316 Chirality : 0.046 0.461 1844 Planarity : 0.004 0.057 2081 Dihedral : 6.991 56.676 1926 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 0.94 % Allowed : 10.07 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.50 (0.23), residues: 1437 helix: 2.52 (0.28), residues: 339 sheet: 0.76 (0.25), residues: 462 loop : -1.28 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 43 HIS 0.003 0.001 HIS N 151 PHE 0.012 0.001 PHE B 28 TYR 0.018 0.001 TYR F 99 ARG 0.006 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 186 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 ASP cc_start: 0.6684 (t0) cc_final: 0.6430 (t0) REVERT: B 274 TYR cc_start: 0.8536 (t80) cc_final: 0.8328 (t80) REVERT: G 86 GLN cc_start: 0.7694 (mm-40) cc_final: 0.7356 (mm110) REVERT: E 85 LYS cc_start: 0.9033 (pttt) cc_final: 0.8716 (pttm) REVERT: E 92 GLN cc_start: 0.8385 (tp-100) cc_final: 0.7900 (tp-100) outliers start: 12 outliers final: 8 residues processed: 191 average time/residue: 0.2150 time to fit residues: 61.2097 Evaluate side-chains 185 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 177 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain D residue 73 CYS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain M residue 50 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 36 optimal weight: 0.0970 chunk 114 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 192 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 12117 Z= 0.453 Angle : 0.716 8.980 16436 Z= 0.366 Chirality : 0.050 0.554 1844 Planarity : 0.004 0.060 2081 Dihedral : 6.843 56.109 1926 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.29 % Favored : 94.64 % Rotamer: Outliers : 2.73 % Allowed : 11.40 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.32 (0.23), residues: 1437 helix: 2.51 (0.27), residues: 333 sheet: 0.65 (0.25), residues: 446 loop : -1.39 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 55 HIS 0.006 0.001 HIS B 71 PHE 0.024 0.002 PHE M 30 TYR 0.019 0.002 TYR G 34 ARG 0.006 0.001 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 183 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.7064 (tm130) REVERT: G 30 LEU cc_start: 0.7237 (mp) cc_final: 0.7030 (pp) REVERT: G 86 GLN cc_start: 0.7521 (mm-40) cc_final: 0.6996 (mm-40) REVERT: E 85 LYS cc_start: 0.9070 (pttt) cc_final: 0.8770 (pttm) REVERT: E 92 GLN cc_start: 0.8486 (tp-100) cc_final: 0.7909 (tp-100) REVERT: N 223 ASP cc_start: 0.8616 (m-30) cc_final: 0.8240 (p0) outliers start: 35 outliers final: 24 residues processed: 201 average time/residue: 0.2414 time to fit residues: 71.5094 Evaluate side-chains 198 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 173 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 73 CYS Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 194 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain M residue 59 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 117 optimal weight: 0.0970 chunk 94 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 192 HIS N 260 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12117 Z= 0.205 Angle : 0.619 7.762 16436 Z= 0.318 Chirality : 0.046 0.487 1844 Planarity : 0.004 0.062 2081 Dihedral : 6.326 52.590 1926 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.69 % Rotamer: Outliers : 1.95 % Allowed : 14.13 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.43 (0.23), residues: 1437 helix: 2.55 (0.27), residues: 340 sheet: 0.73 (0.25), residues: 450 loop : -1.35 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP G 55 HIS 0.003 0.001 HIS N 151 PHE 0.012 0.001 PHE B 28 TYR 0.036 0.001 TYR E 99 ARG 0.006 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 184 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8120 (pm20) REVERT: A 244 ASN cc_start: 0.5955 (t0) cc_final: 0.5558 (t0) REVERT: G 86 GLN cc_start: 0.7489 (mm-40) cc_final: 0.7062 (mm-40) REVERT: E 85 LYS cc_start: 0.9005 (pttt) cc_final: 0.8694 (pttm) REVERT: E 92 GLN cc_start: 0.8393 (tp-100) cc_final: 0.7877 (tp-100) REVERT: E 113 TYR cc_start: 0.7455 (t80) cc_final: 0.7206 (t80) REVERT: N 223 ASP cc_start: 0.8611 (m-30) cc_final: 0.8258 (p0) outliers start: 25 outliers final: 22 residues processed: 196 average time/residue: 0.2278 time to fit residues: 66.2434 Evaluate side-chains 199 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 73 CYS Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain N residue 189 MET Chi-restraints excluded: chain N residue 191 HIS Chi-restraints excluded: chain N residue 194 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain N residue 261 VAL Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain M residue 57 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 11 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 0.0040 chunk 132 optimal weight: 0.9990 overall best weight: 1.0176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 192 HIS N 260 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12117 Z= 0.258 Angle : 0.630 7.215 16436 Z= 0.323 Chirality : 0.047 0.486 1844 Planarity : 0.004 0.064 2081 Dihedral : 6.274 50.613 1926 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.22 % Favored : 94.71 % Rotamer: Outliers : 2.81 % Allowed : 14.52 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.48 (0.23), residues: 1437 helix: 2.57 (0.27), residues: 340 sheet: 0.78 (0.25), residues: 449 loop : -1.32 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP G 55 HIS 0.004 0.001 HIS N 151 PHE 0.015 0.002 PHE M 30 TYR 0.024 0.002 TYR E 99 ARG 0.003 0.000 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 180 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8167 (pm20) REVERT: A 244 ASN cc_start: 0.6030 (t0) cc_final: 0.5522 (t0) REVERT: F 59 TRP cc_start: 0.6830 (m100) cc_final: 0.6217 (m100) REVERT: F 128 MET cc_start: 0.7710 (tmm) cc_final: 0.7344 (tpp) REVERT: G 86 GLN cc_start: 0.7460 (mm-40) cc_final: 0.6984 (mm-40) REVERT: E 85 LYS cc_start: 0.9009 (pttt) cc_final: 0.8732 (pttm) REVERT: E 92 GLN cc_start: 0.8329 (tp-100) cc_final: 0.7883 (tp-100) REVERT: N 223 ASP cc_start: 0.8606 (m-30) cc_final: 0.8256 (p0) outliers start: 36 outliers final: 29 residues processed: 201 average time/residue: 0.2182 time to fit residues: 66.0575 Evaluate side-chains 208 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 178 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 73 CYS Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 189 MET Chi-restraints excluded: chain N residue 194 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain M residue 57 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.0970 chunk 78 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 115 optimal weight: 0.0980 chunk 76 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: