Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 12 15:01:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8es8_28571/08_2023/8es8_28571.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8es8_28571/08_2023/8es8_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8es8_28571/08_2023/8es8_28571.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8es8_28571/08_2023/8es8_28571.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8es8_28571/08_2023/8es8_28571.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8es8_28571/08_2023/8es8_28571.pdb" } 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 Residue "Z ASP 36": "OD1" <-> "OD2" Residue "Z PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 77": "OD1" <-> "OD2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "F GLU 91": "OE1" <-> "OE2" Residue "G GLU 122": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 44": "OE1" <-> "OE2" Residue "M TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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 chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.51, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 4.82 Conformation dependent library (CDL) restraints added in 1.9 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: 1.39 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: 4.09 Time building geometry restraints manager: 5.21 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: 98.05 - 105.24: 194 105.24 - 112.43: 6225 112.43 - 119.63: 4092 119.63 - 126.82: 5918 126.82 - 134.01: 173 Bond angle restraints: 16602 Sorted by residual: angle pdb=" OAG Y01 Y 201 " pdb=" CAY Y01 Y 201 " pdb=" OAW Y01 Y 201 " ideal model delta sigma weight residual 123.38 111.59 11.79 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CAM Y01 Y 201 " pdb=" CAY Y01 Y 201 " pdb=" OAW Y01 Y 201 " ideal model delta sigma weight residual 111.19 122.45 -11.26 3.00e+00 1.11e-01 1.41e+01 angle pdb=" CA CYS F 119 " pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " ideal model delta sigma weight residual 114.40 122.07 -7.67 2.30e+00 1.89e-01 1.11e+01 angle pdb=" N ASN A 184 " pdb=" CA ASN A 184 " pdb=" CB ASN A 184 " ideal model delta sigma weight residual 110.29 103.12 7.17 2.15e+00 2.16e-01 1.11e+01 angle pdb=" CAV Y01 Y 201 " pdb=" CAZ Y01 Y 201 " pdb=" CBH Y01 Y 201 " ideal model delta sigma weight residual 116.96 126.57 -9.61 3.00e+00 1.11e-01 1.03e+01 ... (remaining 16597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 6565 18.00 - 35.99: 474 35.99 - 53.99: 88 53.99 - 71.98: 22 71.98 - 89.98: 13 Dihedral angle restraints: 7162 sinusoidal: 2903 harmonic: 4259 Sorted by residual: dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 122 " pdb=" CB CYS E 122 " ideal model delta sinusoidal sigma weight residual 93.00 42.29 50.71 1 1.00e+01 1.00e-02 3.52e+01 dihedral pdb=" CB CYS M 25 " pdb=" SG CYS M 25 " pdb=" SG CYS M 80 " pdb=" CB CYS M 80 " ideal model delta sinusoidal sigma weight residual 93.00 44.59 48.41 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" CA ASN A 150 " pdb=" C ASN A 150 " pdb=" N VAL A 151 " pdb=" CA VAL A 151 " ideal model delta harmonic sigma weight residual -180.00 -154.68 -25.32 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 7159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1825 0.129 - 0.259: 30 0.259 - 0.388: 5 0.388 - 0.517: 0 0.517 - 0.646: 1 Chirality restraints: 1861 Sorted by residual: chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN A 150 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C1 NAG A1702 " pdb=" ND2 ASN A 184 " pdb=" C2 NAG A1702 " pdb=" O5 NAG A1702 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA ASN A 195 " pdb=" N ASN A 195 " pdb=" C ASN A 195 " pdb=" CB ASN A 195 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 1858 not shown) Planarity restraints: 2110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 205 " 0.065 5.00e-02 4.00e+02 9.90e-02 1.57e+01 pdb=" N PRO A 206 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 52 " -0.033 2.00e-02 2.50e+03 3.24e-02 1.31e+01 pdb=" CG ASN G 52 " 0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN G 52 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN G 52 " 0.020 2.00e-02 2.50e+03 pdb=" C1 NAG G1702 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 150 " 0.025 2.00e-02 2.50e+03 2.43e-02 7.37e+00 pdb=" CG ASN A 150 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 150 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 150 " -0.030 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.026 2.00e-02 2.50e+03 ... (remaining 2107 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 253 2.69 - 3.25: 11032 3.25 - 3.80: 17895 3.80 - 4.35: 24045 4.35 - 4.90: 40251 Nonbonded interactions: 93476 Sorted by model distance: nonbonded pdb=" O SER B 8 " pdb=" OG1 THR B 109 " model vdw 2.142 2.440 nonbonded pdb=" NZ LYS N 127 " pdb=" O TRP N 133 " model vdw 2.171 2.520 nonbonded pdb=" OG1 THR G 66 " pdb=" OD1 ASP G 68 " model vdw 2.205 2.440 nonbonded pdb=" O SER N 13 " pdb=" OG SER N 92 " model vdw 2.241 2.440 nonbonded pdb=" OD1 ASN G 52 " pdb=" N2 NAG G1702 " model vdw 2.245 2.520 ... (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 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: 3.580 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: 18.750 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 33.930 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 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:12.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.260 ------------------------------------------------------------------------------- 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 12250 Z= 0.267 Angle : 0.712 11.794 16602 Z= 0.362 Chirality : 0.053 0.646 1861 Planarity : 0.005 0.099 2099 Dihedral : 13.250 89.976 4379 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.08 % 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 255 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 256 average time/residue: 1.3857 time to fit residues: 381.1688 Evaluate side-chains 195 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 1.389 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2511 time to fit residues: 2.2372 ------------------------------------------------------------------------------- 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: 3.9990 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 GLN F 51 GLN F 92 GLN G 77 ASN E 62 ASN E 81 HIS ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN A 196 ASN N 115 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.105 12250 Z= 0.271 Angle : 0.668 7.431 16602 Z= 0.351 Chirality : 0.048 0.309 1861 Planarity : 0.004 0.064 2099 Dihedral : 5.251 55.613 1612 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 2.56 % 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: 0.75 (0.22), residues: 1442 helix: 2.40 (0.26), residues: 345 sheet: 1.21 (0.25), residues: 418 loop : -1.04 (0.22), residues: 679 *********************** 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 233 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 200 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 13 residues processed: 212 average time/residue: 1.3081 time to fit residues: 299.3382 Evaluate side-chains 197 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 184 time to evaluate : 1.334 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 7 average time/residue: 0.3437 time to fit residues: 4.8299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 35 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 GLN E 62 ASN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 12250 Z= 0.173 Angle : 0.597 7.802 16602 Z= 0.312 Chirality : 0.046 0.319 1861 Planarity : 0.004 0.047 2099 Dihedral : 5.032 53.691 1612 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 2.41 % 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: 0.84 (0.22), residues: 1442 helix: 2.58 (0.27), residues: 345 sheet: 1.23 (0.25), residues: 423 loop : -1.03 (0.22), residues: 674 *********************** 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 235 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 204 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 14 residues processed: 221 average time/residue: 1.2809 time to fit residues: 306.2326 Evaluate side-chains 197 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 183 time to evaluate : 1.270 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 8 residues processed: 7 average time/residue: 0.4329 time to fit residues: 5.5877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN B 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 12250 Z= 0.181 Angle : 0.597 8.470 16602 Z= 0.311 Chirality : 0.045 0.329 1861 Planarity : 0.003 0.039 2099 Dihedral : 4.966 54.631 1612 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 2.87 % 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: 0.89 (0.22), residues: 1442 helix: 2.66 (0.27), residues: 343 sheet: 1.26 (0.25), residues: 423 loop : -1.02 (0.22), residues: 676 *********************** 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 229 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 192 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 15 residues processed: 211 average time/residue: 1.2421 time to fit residues: 284.1780 Evaluate side-chains 200 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 185 time to evaluate : 1.360 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 5 average time/residue: 0.1599 time to fit residues: 3.0733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 34 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 12250 Z= 0.234 Angle : 0.632 9.652 16602 Z= 0.329 Chirality : 0.046 0.335 1861 Planarity : 0.004 0.036 2099 Dihedral : 5.120 57.404 1612 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 3.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (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: 0.77 (0.22), residues: 1442 helix: 2.51 (0.26), residues: 343 sheet: 1.20 (0.25), residues: 424 loop : -1.07 (0.22), residues: 675 *********************** 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 231 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 191 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 18 residues processed: 213 average time/residue: 1.3518 time to fit residues: 310.3495 Evaluate side-chains 199 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 181 time to evaluate : 1.314 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 11 residues processed: 8 average time/residue: 0.3421 time to fit residues: 5.2987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 80 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 137 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 N 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 12250 Z= 0.227 Angle : 0.639 10.083 16602 Z= 0.332 Chirality : 0.047 0.334 1861 Planarity : 0.004 0.037 2099 Dihedral : 5.161 59.204 1612 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 3.42 % 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: 0.74 (0.22), residues: 1442 helix: 2.46 (0.27), residues: 343 sheet: 1.15 (0.25), residues: 433 loop : -1.09 (0.22), residues: 666 *********************** 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 231 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 187 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 24 residues processed: 215 average time/residue: 1.3220 time to fit residues: 308.7053 Evaluate side-chains 203 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 179 time to evaluate : 1.324 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 19 residues processed: 6 average time/residue: 0.7710 time to fit residues: 6.9591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 7.9990 chunk 78 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 85 optimal weight: 0.0270 chunk 83 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.9244 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 12250 Z= 0.189 Angle : 0.607 10.389 16602 Z= 0.314 Chirality : 0.046 0.325 1861 Planarity : 0.003 0.036 2099 Dihedral : 5.051 59.890 1612 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 2.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.80 (0.22), residues: 1442 helix: 2.59 (0.27), residues: 343 sheet: 1.19 (0.25), residues: 432 loop : -1.09 (0.22), residues: 667 *********************** 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 225 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 187 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 19 residues processed: 214 average time/residue: 1.2797 time to fit residues: 296.5970 Evaluate side-chains 201 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 182 time to evaluate : 1.443 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 16 residues processed: 4 average time/residue: 0.1494 time to fit residues: 2.8101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 B 180 GLN N 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 12250 Z= 0.301 Angle : 0.686 11.366 16602 Z= 0.355 Chirality : 0.048 0.331 1861 Planarity : 0.004 0.039 2099 Dihedral : 5.312 56.376 1612 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 2.64 % 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: 0.59 (0.22), residues: 1442 helix: 2.29 (0.26), residues: 343 sheet: 1.06 (0.25), residues: 434 loop : -1.15 (0.22), residues: 665 *********************** 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 220 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 186 time to evaluate : 1.369 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 17 residues processed: 208 average time/residue: 1.2651 time to fit residues: 284.8863 Evaluate side-chains 196 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 179 time to evaluate : 1.386 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 4 average time/residue: 0.1607 time to fit residues: 2.9114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 2.9990 chunk 127 optimal weight: 0.3980 chunk 131 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 12250 Z= 0.175 Angle : 0.618 11.086 16602 Z= 0.319 Chirality : 0.045 0.324 1861 Planarity : 0.003 0.036 2099 Dihedral : 5.105 59.401 1612 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 1.63 % 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: 0.75 (0.22), residues: 1442 helix: 2.54 (0.27), residues: 342 sheet: 1.17 (0.25), residues: 430 loop : -1.12 (0.22), residues: 670 *********************** 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 200 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 179 time to evaluate : 1.488 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 195 average time/residue: 1.4075 time to fit residues: 296.3552 Evaluate side-chains 183 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 171 time to evaluate : 1.380 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.1443 time to fit residues: 2.0667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 120 optimal weight: 0.0970 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 12250 Z= 0.195 Angle : 0.636 11.065 16602 Z= 0.328 Chirality : 0.045 0.317 1861 Planarity : 0.003 0.036 2099 Dihedral : 5.104 59.390 1612 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 1.40 % 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: 0.72 (0.22), residues: 1442 helix: 2.48 (0.27), residues: 342 sheet: 1.14 (0.25), residues: 433 loop : -1.12 (0.22), residues: 667 ********************** 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 194 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 176 time to evaluate : 1.418 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 193 average time/residue: 1.3845 time to fit residues: 288.3033 Evaluate side-chains 185 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 173 time to evaluate : 1.393 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 1.9340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 112 optimal weight: 0.1980 chunk 47 optimal weight: 0.4980 chunk 115 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 6 optimal weight: 0.0040 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 51 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.144777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.097880 restraints weight = 18394.839| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.46 r_work: 0.3087 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 12250 Z= 0.175 Angle : 0.607 10.875 16602 Z= 0.314 Chirality : 0.045 0.317 1861 Planarity : 0.003 0.035 2099 Dihedral : 5.053 59.825 1612 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 1.24 % 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: 0.77 (0.22), residues: 1442 helix: 2.52 (0.27), residues: 342 sheet: 1.10 (0.25), residues: 445 loop : -1.06 (0.23), residues: 655 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5467.00 seconds wall clock time: 97 minutes 29.55 seconds (5849.55 seconds total)