Starting phenix.real_space_refine (version: dev) on Wed Feb 22 11:31:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kra_23003/02_2023/7kra_23003_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kra_23003/02_2023/7kra_23003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kra_23003/02_2023/7kra_23003.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kra_23003/02_2023/7kra_23003.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kra_23003/02_2023/7kra_23003_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kra_23003/02_2023/7kra_23003_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.008 sd= 1.036 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 Process input model Symmetric amino acids flipped Residue "A ASP 34": "OD1" <-> "OD2" Residue "A ARG 55": "NH1" <-> "NH2" Residue "A ASP 90": "OD1" <-> "OD2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A ASP 226": "OD1" <-> "OD2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A ASP 380": "OD1" <-> "OD2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "A GLU 458": "OE1" <-> "OE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A ARG 571": "NH1" <-> "NH2" Residue "A TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 719": "OD1" <-> "OD2" Residue "A PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 64": "NH1" <-> "NH2" Residue "B ASP 102": "OD1" <-> "OD2" Residue "B TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 69": "OD1" <-> "OD2" Residue "C PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "E PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E GLU 52": "OE1" <-> "OE2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 130": "NH1" <-> "NH2" Residue "G PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 82": "OD1" <-> "OD2" Residue "G TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 109": "OE1" <-> "OE2" Residue "G TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 39": "OE1" <-> "OE2" Residue "H ASP 45": "OD1" <-> "OD2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 95": "OD1" <-> "OD2" Residue "H GLU 101": "OE1" <-> "OE2" Residue "I TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 48": "NH1" <-> "NH2" Residue "J TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 127": "NH1" <-> "NH2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 17293 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5637 Classifications: {'peptide': 694} Link IDs: {'PTRANS': 32, 'TRANS': 661} Chain breaks: 6 Chain: "B" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2362 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 286} Chain: "C" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1522 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 6, 'TRANS': 181} Chain breaks: 3 Chain: "D" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 515 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain breaks: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "E" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1028 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain breaks: 1 Chain: "F" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 780 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "G" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1235 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 8, 'TRANS': 142} Chain: "H" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 965 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "I" Number of atoms: 1309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1309 Classifications: {'peptide': 170} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 160} Chain breaks: 6 Chain: "J" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1610 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 15, 'TRANS': 193} Chain breaks: 2 Chain: "M" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 105 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'TRANS': 20} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'UNK:plan-1': 21} Unresolved non-hydrogen planarities: 21 Chain: "N" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 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 chiralities: 3 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'X3P': 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 Time building chain proxies: 9.26, per 1000 atoms: 0.54 Number of scatterers: 17293 At special positions: 0 Unit cell: (111.743, 127.097, 194.484, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 67 16.00 P 1 15.00 O 3270 8.00 N 2814 7.00 C 11141 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 701 " - pdb=" SG CYS A 709 " distance=2.03 Simple disulfide: pdb=" SG CYS I 24 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 152 " - pdb=" SG CYS I 208 " distance=2.03 Simple disulfide: pdb=" SG CYS J 39 " - pdb=" SG CYS J 109 " distance=2.03 Simple disulfide: pdb=" SG CYS J 154 " - pdb=" SG CYS J 214 " distance=2.03 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 NAG-ASN " NAG A 801 " - " ASN A 192 " " NAG A 802 " - " ASN A 106 " " NAG A 803 " - " ASN A 73 " " NAG G 301 " - " ASN G 115 " " NAG G 302 " - " ASN G 53 " Time building additional restraints: 7.13 Conformation dependent library (CDL) restraints added in 2.5 seconds 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4110 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 24 sheets defined 29.2% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 27 through 29 No H-bonds generated for 'chain 'A' and resid 27 through 29' Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 248 through 265 Processing helix chain 'A' and resid 275 through 281 Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 727 through 756 Proline residue: A 746 - end of helix Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 18 through 21 Processing helix chain 'B' and resid 24 through 40 removed outlier: 3.961A pdb=" N LYS B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE B 36 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR B 37 " --> pdb=" O GLU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 63 Processing helix chain 'B' and resid 68 through 79 removed outlier: 4.284A pdb=" N ASP B 79 " --> pdb=" O ASN B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'B' and resid 104 through 115 removed outlier: 5.121A pdb=" N ASN B 111 " --> pdb=" O TYR B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 140 removed outlier: 3.798A pdb=" N THR B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 removed outlier: 4.302A pdb=" N THR B 156 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 176 removed outlier: 3.857A pdb=" N MET B 176 " --> pdb=" O ILE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 192 Processing helix chain 'B' and resid 199 through 213 removed outlier: 3.798A pdb=" N LEU B 207 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 236 removed outlier: 4.288A pdb=" N ARG B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 254 Processing helix chain 'B' and resid 257 through 274 Processing helix chain 'B' and resid 282 through 291 removed outlier: 3.838A pdb=" N LEU B 287 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE B 288 " --> pdb=" O THR B 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 33 Proline residue: C 14 - end of helix Processing helix chain 'C' and resid 44 through 61 Processing helix chain 'C' and resid 71 through 82 removed outlier: 4.089A pdb=" N LYS C 75 " --> pdb=" O PHE C 71 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE C 77 " --> pdb=" O ALA C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 139 Proline residue: C 128 - end of helix Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 176 through 186 removed outlier: 3.835A pdb=" N ILE C 182 " --> pdb=" O TRP C 179 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL C 184 " --> pdb=" O PHE C 181 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY C 186 " --> pdb=" O SER C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 194 Processing helix chain 'C' and resid 221 through 233 removed outlier: 3.688A pdb=" N MET C 225 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR C 233 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 250 Processing helix chain 'D' and resid 9 through 16 Processing helix chain 'D' and resid 142 through 158 removed outlier: 4.213A pdb=" N GLY D 155 " --> pdb=" O LEU D 151 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR D 156 " --> pdb=" O MET D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'E' and resid 4 through 28 Processing helix chain 'E' and resid 32 through 36 Processing helix chain 'E' and resid 46 through 65 Processing helix chain 'E' and resid 95 through 104 Processing helix chain 'E' and resid 111 through 115 Processing helix chain 'E' and resid 117 through 127 Processing helix chain 'F' and resid 17 through 31 Processing helix chain 'F' and resid 37 through 41 Processing helix chain 'F' and resid 46 through 67 removed outlier: 3.632A pdb=" N PHE F 50 " --> pdb=" O SER F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'F' and resid 93 through 104 Processing helix chain 'J' and resid 203 through 208 removed outlier: 4.187A pdb=" N LYS J 208 " --> pdb=" O ALA J 204 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 20 Processing helix chain 'N' and resid 2 through 23 Processing sheet with id= A, first strand: chain 'A' and resid 43 through 48 removed outlier: 6.734A pdb=" N LEU A 59 " --> pdb=" O GLU A 44 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL A 46 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU A 57 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 81 " --> pdb=" O SER A 71 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 103 through 105 Processing sheet with id= C, first strand: chain 'A' and resid 146 through 148 Processing sheet with id= D, first strand: chain 'A' and resid 175 through 180 removed outlier: 3.626A pdb=" N LYS A 175 " --> pdb=" O ASN A 190 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL A 188 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE A 179 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA A 186 " --> pdb=" O PHE A 179 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N SER A 200 " --> pdb=" O PRO A 208 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 219 through 226 removed outlier: 7.042A pdb=" N LEU A 305 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR A 222 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE A 303 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL A 224 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE A 301 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TRP A 324 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASP A 315 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU A 322 " --> pdb=" O ASP A 315 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 333 through 338 removed outlier: 6.899A pdb=" N PHE A 349 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N MET A 336 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL A 347 " --> pdb=" O MET A 336 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TRP A 338 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLU A 345 " --> pdb=" O TRP A 338 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N HIS A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLU A 359 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE A 367 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 400 through 405 Processing sheet with id= H, first strand: chain 'A' and resid 426 through 428 removed outlier: 3.886A pdb=" N ILE A 426 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 520 through 523 removed outlier: 3.980A pdb=" N ALA A 462 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA A 498 " --> pdb=" O MET A 460 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N MET A 460 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 534 through 537 removed outlier: 3.713A pdb=" N SER A 548 " --> pdb=" O GLU A 554 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 630 through 633 Processing sheet with id= L, first strand: chain 'A' and resid 686 through 691 Processing sheet with id= M, first strand: chain 'G' and resid 26 through 28 Processing sheet with id= N, first strand: chain 'G' and resid 61 through 64 removed outlier: 3.533A pdb=" N PHE G 46 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR G 89 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU G 107 " --> pdb=" O PHE G 123 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA G 122 " --> pdb=" O MET G 146 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET G 146 " --> pdb=" O ALA G 122 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLN G 144 " --> pdb=" O LYS G 124 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 81 through 85 removed outlier: 3.760A pdb=" N ASP H 19 " --> pdb=" O ILE H 40 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N TYR H 25 " --> pdb=" O PRO H 34 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 68 through 70 Processing sheet with id= Q, first strand: chain 'H' and resid 117 through 121 removed outlier: 3.649A pdb=" N THR H 117 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 7 through 9 Processing sheet with id= S, first strand: chain 'I' and resid 39 through 41 Processing sheet with id= T, first strand: chain 'I' and resid 208 through 212 Processing sheet with id= U, first strand: chain 'J' and resid 20 through 22 Processing sheet with id= V, first strand: chain 'J' and resid 65 through 69 removed outlier: 6.676A pdb=" N TRP J 56 " --> pdb=" O LEU J 68 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY J 105 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL J 124 " --> pdb=" O GLY J 105 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N CYS J 109 " --> pdb=" O GLY J 120 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLY J 120 " --> pdb=" O CYS J 109 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 134 through 138 removed outlier: 3.866A pdb=" N VAL J 153 " --> pdb=" O PHE J 138 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER J 194 " --> pdb=" O THR J 184 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 164 through 170 removed outlier: 3.623A pdb=" N LYS J 165 " --> pdb=" O THR J 217 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR J 217 " --> pdb=" O LYS J 165 " (cutoff:3.500A) 650 hydrogen bonds defined for protein. 1791 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: 5.34 Time building geometry restraints manager: 7.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2848 1.31 - 1.44: 4736 1.44 - 1.56: 9964 1.56 - 1.69: 5 1.69 - 1.81: 111 Bond restraints: 17664 Sorted by residual: bond pdb=" C31 X3P C 301 " pdb=" O31 X3P C 301 " ideal model delta sigma weight residual 1.332 1.429 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C21 X3P C 301 " pdb=" O22 X3P C 301 " ideal model delta sigma weight residual 1.280 1.184 0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C11 X3P C 301 " pdb=" C12 X3P C 301 " ideal model delta sigma weight residual 1.516 1.574 -0.058 2.00e-02 2.50e+03 8.40e+00 bond pdb=" N LEU H 74 " pdb=" CA LEU H 74 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.15e+00 bond pdb=" N X3P C 301 " pdb=" C15 X3P C 301 " ideal model delta sigma weight residual 1.491 1.443 0.048 2.00e-02 2.50e+03 5.78e+00 ... (remaining 17659 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.51: 304 105.51 - 112.71: 9298 112.71 - 119.92: 6305 119.92 - 127.13: 7831 127.13 - 134.34: 218 Bond angle restraints: 23956 Sorted by residual: angle pdb=" N TRP A 35 " pdb=" CA TRP A 35 " pdb=" CB TRP A 35 " ideal model delta sigma weight residual 111.51 104.18 7.33 1.48e+00 4.57e-01 2.45e+01 angle pdb=" N LYS H 73 " pdb=" CA LYS H 73 " pdb=" C LYS H 73 " ideal model delta sigma weight residual 110.65 116.37 -5.72 1.26e+00 6.30e-01 2.06e+01 angle pdb=" C22 X3P C 301 " pdb=" C21 X3P C 301 " pdb=" O21 X3P C 301 " ideal model delta sigma weight residual 108.34 120.14 -11.80 3.00e+00 1.11e-01 1.55e+01 angle pdb=" C PRO D 166 " pdb=" N ASN D 167 " pdb=" CA ASN D 167 " ideal model delta sigma weight residual 124.82 131.75 -6.93 1.78e+00 3.16e-01 1.52e+01 angle pdb=" O13 X3P C 301 " pdb=" P X3P C 301 " pdb=" O14 X3P C 301 " ideal model delta sigma weight residual 120.95 109.62 11.33 3.00e+00 1.11e-01 1.43e+01 ... (remaining 23951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.61: 9757 22.61 - 45.22: 692 45.22 - 67.83: 55 67.83 - 90.44: 17 90.44 - 113.05: 1 Dihedral angle restraints: 10522 sinusoidal: 4183 harmonic: 6339 Sorted by residual: dihedral pdb=" CB CYS J 39 " pdb=" SG CYS J 39 " pdb=" SG CYS J 109 " pdb=" CB CYS J 109 " ideal model delta sinusoidal sigma weight residual 93.00 167.19 -74.19 1 1.00e+01 1.00e-02 6.98e+01 dihedral pdb=" C1 NAG A 801 " pdb=" C2 NAG A 801 " pdb=" C3 NAG A 801 " pdb=" C4 NAG A 801 " ideal model delta sinusoidal sigma weight residual -50.00 63.05 -113.05 1 2.00e+01 2.50e-03 3.34e+01 dihedral pdb=" CA ASP A 34 " pdb=" C ASP A 34 " pdb=" N TRP A 35 " pdb=" CA TRP A 35 " ideal model delta harmonic sigma weight residual -180.00 -151.37 -28.63 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 10519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 2679 0.124 - 0.249: 57 0.249 - 0.373: 0 0.373 - 0.498: 0 0.498 - 0.622: 1 Chirality restraints: 2737 Sorted by residual: chirality pdb=" C1 NAG G 301 " pdb=" ND2 ASN G 115 " pdb=" C2 NAG G 301 " pdb=" O5 NAG G 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.68e+00 chirality pdb=" C1 NAG A 803 " pdb=" ND2 ASN A 73 " pdb=" C2 NAG A 803 " pdb=" O5 NAG A 803 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.51e-01 chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 106 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.12e-01 ... (remaining 2734 not shown) Planarity restraints: 3012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 166 " 0.012 2.00e-02 2.50e+03 2.50e-02 1.56e+01 pdb=" CG TRP B 166 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP B 166 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 TRP B 166 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 166 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP B 166 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 166 " 0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 166 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 166 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 166 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 35 " 0.023 2.00e-02 2.50e+03 1.92e-02 9.25e+00 pdb=" CG TRP A 35 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP A 35 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 35 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 35 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 35 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 35 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 35 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 35 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 35 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 72 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.67e+00 pdb=" C GLY H 72 " 0.048 2.00e-02 2.50e+03 pdb=" O GLY H 72 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS H 73 " -0.016 2.00e-02 2.50e+03 ... (remaining 3009 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1030 2.73 - 3.27: 17291 3.27 - 3.81: 26214 3.81 - 4.36: 31588 4.36 - 4.90: 56055 Nonbonded interactions: 132178 Sorted by model distance: nonbonded pdb=" O THR B 12 " pdb=" OG1 THR B 16 " model vdw 2.182 2.440 nonbonded pdb=" OD2 ASP J 190 " pdb=" OG1 THR J 192 " model vdw 2.187 2.440 nonbonded pdb=" OE2 GLU J 125 " pdb=" OH TYR J 193 " model vdw 2.205 2.440 nonbonded pdb=" O THR B 156 " pdb=" OH TYR C 52 " model vdw 2.220 2.440 nonbonded pdb=" OH TYR J 206 " pdb=" NH2 ARG J 231 " model vdw 2.229 2.520 ... (remaining 132173 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 'M' selection = (chain 'N' and resid 4 through 24) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 67 5.16 5 C 11141 2.51 5 N 2814 2.21 5 O 3270 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 5.100 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: 24.530 Check model and map are aligned: 0.280 Process input model: 45.030 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.160 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 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 0.097 17664 Z= 0.316 Angle : 0.817 11.799 23956 Z= 0.431 Chirality : 0.048 0.622 2737 Planarity : 0.005 0.065 3007 Dihedral : 15.009 113.053 6397 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -2.08 (0.17), residues: 2061 helix: -0.33 (0.20), residues: 579 sheet: -0.30 (0.22), residues: 536 loop : -2.78 (0.17), residues: 946 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 2.432 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 238 average time/residue: 0.3232 time to fit residues: 113.1783 Evaluate side-chains 188 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 1.954 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4945 time to fit residues: 3.4022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 107 optimal weight: 0.0040 chunk 85 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 145 GLN A 639 ASN C 51 GLN H 56 GLN I 212 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 17664 Z= 0.204 Angle : 0.614 10.636 23956 Z= 0.320 Chirality : 0.044 0.501 2737 Planarity : 0.004 0.048 3007 Dihedral : 6.978 110.833 2341 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -1.62 (0.18), residues: 2061 helix: 0.39 (0.21), residues: 580 sheet: -0.02 (0.23), residues: 522 loop : -2.72 (0.17), residues: 959 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 200 time to evaluate : 2.271 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 14 residues processed: 207 average time/residue: 0.3170 time to fit residues: 97.5887 Evaluate side-chains 194 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 180 time to evaluate : 1.965 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1535 time to fit residues: 6.6558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 170 optimal weight: 0.9980 chunk 190 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 693 ASN A 717 GLN B 145 GLN E 86 GLN E 103 ASN H 67 ASN ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.086 17664 Z= 0.496 Angle : 0.726 10.624 23956 Z= 0.383 Chirality : 0.049 0.574 2737 Planarity : 0.005 0.056 3007 Dihedral : 7.326 113.839 2341 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -1.73 (0.18), residues: 2061 helix: 0.42 (0.21), residues: 581 sheet: -0.27 (0.22), residues: 543 loop : -2.81 (0.18), residues: 937 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 185 time to evaluate : 1.979 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 199 average time/residue: 0.3350 time to fit residues: 100.2857 Evaluate side-chains 186 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 172 time to evaluate : 2.300 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1704 time to fit residues: 7.5685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 189 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 128 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 17664 Z= 0.232 Angle : 0.611 11.551 23956 Z= 0.320 Chirality : 0.044 0.445 2737 Planarity : 0.004 0.048 3007 Dihedral : 6.894 111.128 2341 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.46 (0.18), residues: 2061 helix: 0.72 (0.22), residues: 575 sheet: -0.10 (0.23), residues: 536 loop : -2.67 (0.18), residues: 950 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 187 time to evaluate : 2.241 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 196 average time/residue: 0.3183 time to fit residues: 94.3140 Evaluate side-chains 185 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 176 time to evaluate : 2.349 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1669 time to fit residues: 5.9278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 169 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 chunk 140 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 51 optimal weight: 0.0870 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS I 5 GLN ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 17664 Z= 0.231 Angle : 0.601 11.443 23956 Z= 0.313 Chirality : 0.044 0.503 2737 Planarity : 0.004 0.052 3007 Dihedral : 6.708 111.131 2341 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.29 (0.18), residues: 2061 helix: 0.88 (0.22), residues: 576 sheet: 0.03 (0.23), residues: 536 loop : -2.61 (0.18), residues: 949 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 183 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 194 average time/residue: 0.3207 time to fit residues: 93.5054 Evaluate side-chains 189 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 2.145 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2000 time to fit residues: 8.5085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 68 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 chunk 107 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 17664 Z= 0.349 Angle : 0.654 11.768 23956 Z= 0.342 Chirality : 0.046 0.520 2737 Planarity : 0.004 0.055 3007 Dihedral : 6.875 112.715 2341 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.35 (0.18), residues: 2061 helix: 0.79 (0.22), residues: 577 sheet: 0.01 (0.23), residues: 538 loop : -2.64 (0.18), residues: 946 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 2.130 Fit side-chains outliers start: 31 outliers final: 17 residues processed: 197 average time/residue: 0.3065 time to fit residues: 92.3083 Evaluate side-chains 188 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 171 time to evaluate : 2.130 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1635 time to fit residues: 7.8762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 196 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 116 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 171 optimal weight: 0.0170 chunk 113 optimal weight: 0.0040 chunk 203 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 overall best weight: 0.4230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 17664 Z= 0.163 Angle : 0.589 12.491 23956 Z= 0.304 Chirality : 0.043 0.361 2737 Planarity : 0.004 0.048 3007 Dihedral : 6.451 109.745 2341 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -1.10 (0.19), residues: 2061 helix: 1.06 (0.22), residues: 571 sheet: 0.17 (0.23), residues: 541 loop : -2.52 (0.19), residues: 949 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 187 time to evaluate : 2.069 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 194 average time/residue: 0.3145 time to fit residues: 92.6538 Evaluate side-chains 185 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 176 time to evaluate : 2.693 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2219 time to fit residues: 6.2646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 125 optimal weight: 0.0170 chunk 81 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 chunk 184 optimal weight: 1.9990 overall best weight: 1.2822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN F 82 HIS ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 17664 Z= 0.290 Angle : 0.622 12.055 23956 Z= 0.324 Chirality : 0.044 0.393 2737 Planarity : 0.004 0.047 3007 Dihedral : 6.558 111.975 2341 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -1.11 (0.19), residues: 2061 helix: 1.00 (0.22), residues: 577 sheet: 0.19 (0.23), residues: 538 loop : -2.53 (0.19), residues: 946 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 176 time to evaluate : 2.210 Fit side-chains outliers start: 18 outliers final: 13 residues processed: 183 average time/residue: 0.3234 time to fit residues: 89.7101 Evaluate side-chains 186 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 173 time to evaluate : 2.089 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2013 time to fit residues: 7.4305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 194 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 171 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 188 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 17664 Z= 0.302 Angle : 0.640 12.699 23956 Z= 0.332 Chirality : 0.045 0.414 2737 Planarity : 0.004 0.047 3007 Dihedral : 6.660 112.227 2341 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -1.14 (0.18), residues: 2061 helix: 0.95 (0.22), residues: 578 sheet: 0.17 (0.23), residues: 538 loop : -2.53 (0.19), residues: 945 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 180 time to evaluate : 2.115 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 186 average time/residue: 0.3298 time to fit residues: 94.2292 Evaluate side-chains 182 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 174 time to evaluate : 2.226 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1526 time to fit residues: 5.0874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 200 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 139 optimal weight: 0.7980 chunk 210 optimal weight: 20.0000 chunk 193 optimal weight: 0.6980 chunk 167 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 ASN E 79 ASN E 100 ASN F 82 HIS ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 17664 Z= 0.214 Angle : 0.609 12.626 23956 Z= 0.315 Chirality : 0.043 0.409 2737 Planarity : 0.004 0.055 3007 Dihedral : 6.475 110.912 2341 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -1.03 (0.19), residues: 2061 helix: 1.05 (0.22), residues: 576 sheet: 0.28 (0.23), residues: 540 loop : -2.49 (0.19), residues: 945 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 181 time to evaluate : 2.233 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 182 average time/residue: 0.3187 time to fit residues: 88.3598 Evaluate side-chains 178 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 173 time to evaluate : 2.199 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1941 time to fit residues: 4.6467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 167 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 147 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.123970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.083758 restraints weight = 36890.799| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.05 r_work: 0.3299 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 17664 Z= 0.209 Angle : 0.611 13.569 23956 Z= 0.315 Chirality : 0.043 0.414 2737 Planarity : 0.004 0.056 3007 Dihedral : 6.405 111.139 2341 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -0.95 (0.19), residues: 2061 helix: 1.18 (0.22), residues: 571 sheet: 0.33 (0.23), residues: 540 loop : -2.47 (0.19), residues: 950 =============================================================================== Job complete usr+sys time: 3901.86 seconds wall clock time: 71 minutes 48.77 seconds (4308.77 seconds total)