Starting phenix.real_space_refine on Wed Feb 4 01:15:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pzv_72083/02_2026/9pzv_72083.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pzv_72083/02_2026/9pzv_72083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pzv_72083/02_2026/9pzv_72083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pzv_72083/02_2026/9pzv_72083.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pzv_72083/02_2026/9pzv_72083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pzv_72083/02_2026/9pzv_72083.map" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 28 5.16 5 C 5118 2.51 5 N 1374 2.21 5 O 1549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8069 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2536 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 446 Unresolved non-hydrogen dihedrals: 306 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 11, 'GLN:plan1': 7, 'TRP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 16} Unresolved non-hydrogen planarities: 233 Chain: "B" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2399 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 11, 'TRANS': 323} Chain breaks: 3 Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'HIS:plan': 3, 'ASP:plan': 5, 'GLU:plan': 10, 'ARG:plan': 6, 'ASN:plan1': 1, 'GLN:plan1': 5, 'PHE:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 143 Chain: "H" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 810 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'PHE:plan': 1, 'ASP:plan': 4, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "I" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 773 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 108} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 4, 'ARG:plan': 2, 'ASN:plan1': 5, 'GLU:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "J" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 747 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "K" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 650 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 93} Chain breaks: 2 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 2, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.61, per 1000 atoms: 0.20 Number of scatterers: 8069 At special positions: 0 Unit cell: (111.52, 133.824, 85.034, 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 28 16.00 O 1549 8.00 N 1374 7.00 C 5118 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.02 Simple disulfide: pdb=" SG CYS H 42 " - pdb=" SG CYS H 116 " distance=2.03 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 114 " distance=2.04 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 115 " distance=2.04 Simple disulfide: pdb=" SG CYS K 43 " - pdb=" SG CYS K 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A1001 " - " ASN A 61 " " NAG A1002 " - " ASN A 203 " " NAG A1003 " - " ASN A 239 " " NAG A1004 " - " ASN A 300 " " NAG A1005 " - " ASN A 350 " " NAG A1006 " - " ASN A 368 " " NAG B1501 " - " ASN B 75 " " NAG B1502 " - " ASN B 340 " " NAG B1503 " - " ASN B 380 " " NAG C 1 " - " ASN A 276 " Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 315.8 milliseconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2116 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 15 sheets defined 23.7% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 35 through 49 Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.582A pdb=" N MET A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 78 " --> pdb=" O MET A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.593A pdb=" N TYR A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 Processing helix chain 'A' and resid 170 through 188 removed outlier: 3.620A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 224 through 239 Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.880A pdb=" N ARG A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 298 removed outlier: 3.510A pdb=" N GLU A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.843A pdb=" N GLN B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 150 through 165 removed outlier: 3.643A pdb=" N VAL B 157 " --> pdb=" O GLN B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 192 removed outlier: 3.560A pdb=" N PHE B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 191 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 232 through 245 removed outlier: 4.523A pdb=" N LEU B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 241 " --> pdb=" O VAL B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 310 removed outlier: 4.150A pdb=" N ASP B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 301 " --> pdb=" O GLY B 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 111 Processing helix chain 'I' and resid 105 through 109 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 65 removed outlier: 3.626A pdb=" N THR A 63 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N LEU A 91 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLY A 30 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 196 removed outlier: 5.949A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 270 removed outlier: 3.848A pdb=" N GLN A 270 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 352 " --> pdb=" O GLN A 270 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 365 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLN A 357 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 74 removed outlier: 6.949A pdb=" N ILE B 36 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N LEU B 72 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B 38 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N MET B 74 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B 40 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL B 99 " --> pdb=" O ASN B 35 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 37 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 125 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE B 124 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 203 through 204 removed outlier: 9.204A pdb=" N ILE B 204 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 172 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N SER B 171 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N TYR B 230 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL B 173 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE B 277 " --> pdb=" O TRP B 255 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 279 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU B 361 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LYS B 377 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 363 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS B 377 " --> pdb=" O SER B 384 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B 379 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 23 through 26 removed outlier: 3.517A pdb=" N SER H 45 " --> pdb=" O GLN H 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 30 through 31 removed outlier: 7.729A pdb=" N GLU H 30 " --> pdb=" O THR H 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'H' and resid 38 through 40 removed outlier: 3.712A pdb=" N VAL H 38 " --> pdb=" O PHE H 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 78 through 80 removed outlier: 4.040A pdb=" N TRP H 70 " --> pdb=" O SER H 79 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA H 69 " --> pdb=" O TRP H 56 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N TYR H 53 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU H 119 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR H 115 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N CYS H 116 " --> pdb=" O TYR H 131 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N TYR H 131 " --> pdb=" O CYS H 116 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ARG H 118 " --> pdb=" O PHE H 129 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N PHE H 129 " --> pdb=" O ARG H 118 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY H 120 " --> pdb=" O ALA H 127 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 25 through 27 removed outlier: 3.810A pdb=" N THR I 25 " --> pdb=" O LYS I 44 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS I 44 " --> pdb=" O THR I 25 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG I 42 " --> pdb=" O SER I 27 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL I 39 " --> pdb=" O ILE I 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 79 through 80 removed outlier: 3.786A pdb=" N ILE I 79 " --> pdb=" O TYR I 75 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR I 75 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU I 72 " --> pdb=" O GLN I 63 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLN I 63 " --> pdb=" O LEU I 72 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE I 74 " --> pdb=" O TRP I 61 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR I 113 " --> pdb=" O TYR I 62 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL I 111 " --> pdb=" O GLN I 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 23 through 25 removed outlier: 3.533A pdb=" N GLN J 24 " --> pdb=" O LYS J 42 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL J 37 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU J 102 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE J 39 " --> pdb=" O MET J 100 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET J 100 " --> pdb=" O ILE J 39 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR J 97 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 77 through 79 removed outlier: 4.161A pdb=" N GLY J 68 " --> pdb=" O TRP J 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA J 134 " --> pdb=" O TYR J 113 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 24 through 27 removed outlier: 3.511A pdb=" N THR K 25 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER K 27 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER K 42 " --> pdb=" O SER K 27 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER K 89 " --> pdb=" O SER K 96 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN K 98 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER K 87 " --> pdb=" O ASN K 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 77 through 78 removed outlier: 6.574A pdb=" N TRP K 59 " --> pdb=" O LEU K 71 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR K 73 " --> pdb=" O MET K 57 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N MET K 57 " --> pdb=" O TYR K 73 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE K 111 " --> pdb=" O TYR K 60 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET K 109 " --> pdb=" O GLN K 62 " (cutoff:3.500A) 269 hydrogen bonds defined for protein. 756 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: 1.14 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2627 1.34 - 1.46: 1641 1.46 - 1.58: 3936 1.58 - 1.70: 0 1.70 - 1.82: 43 Bond restraints: 8247 Sorted by residual: bond pdb=" N ILE B 151 " pdb=" CA ILE B 151 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.17e-02 7.31e+03 8.92e+00 bond pdb=" N SER B 150 " pdb=" CA SER B 150 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.16e-02 7.43e+03 8.55e+00 bond pdb=" N GLN B 152 " pdb=" CA GLN B 152 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 6.01e+00 bond pdb=" N MET I 24 " pdb=" CA MET I 24 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.23e-02 6.61e+03 5.79e+00 bond pdb=" N GLU B 371 " pdb=" CA GLU B 371 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.23e-02 6.61e+03 5.53e+00 ... (remaining 8242 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 10862 1.23 - 2.45: 351 2.45 - 3.68: 82 3.68 - 4.91: 14 4.91 - 6.13: 3 Bond angle restraints: 11312 Sorted by residual: angle pdb=" N VAL B 375 " pdb=" CA VAL B 375 " pdb=" C VAL B 375 " ideal model delta sigma weight residual 113.53 109.66 3.87 9.80e-01 1.04e+00 1.56e+01 angle pdb=" CA SER B 150 " pdb=" C SER B 150 " pdb=" O SER B 150 " ideal model delta sigma weight residual 121.89 118.26 3.63 1.27e+00 6.20e-01 8.18e+00 angle pdb=" CA ILE B 151 " pdb=" C ILE B 151 " pdb=" O ILE B 151 " ideal model delta sigma weight residual 121.17 118.15 3.02 1.06e+00 8.90e-01 8.13e+00 angle pdb=" CA LEU B 383 " pdb=" C LEU B 383 " pdb=" O LEU B 383 " ideal model delta sigma weight residual 121.47 118.53 2.94 1.15e+00 7.56e-01 6.54e+00 angle pdb=" CA GLU B 371 " pdb=" C GLU B 371 " pdb=" O GLU B 371 " ideal model delta sigma weight residual 120.89 118.09 2.80 1.10e+00 8.26e-01 6.49e+00 ... (remaining 11307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.53: 4709 22.53 - 45.06: 133 45.06 - 67.58: 18 67.58 - 90.11: 1 90.11 - 112.64: 25 Dihedral angle restraints: 4886 sinusoidal: 1595 harmonic: 3291 Sorted by residual: dihedral pdb=" CA ASN A 70 " pdb=" C ASN A 70 " pdb=" N ALA A 71 " pdb=" CA ALA A 71 " ideal model delta harmonic sigma weight residual -180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" C1 NAG C 1 " pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " pdb=" C6 NAG C 1 " ideal model delta sinusoidal sigma weight residual 171.16 -76.20 -112.64 1 3.00e+01 1.11e-03 1.48e+01 dihedral pdb=" C1 NAG C 1 " pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " pdb=" C4 NAG C 1 " ideal model delta sinusoidal sigma weight residual -64.11 48.52 -112.63 1 3.00e+01 1.11e-03 1.48e+01 ... (remaining 4883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.225: 1355 0.225 - 0.451: 1 0.451 - 0.676: 0 0.676 - 0.901: 0 0.901 - 1.126: 1 Chirality restraints: 1357 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.31e+01 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 276 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.27 -1.13 2.00e-01 2.50e+01 3.17e+01 chirality pdb=" C1 NAG A1003 " pdb=" ND2 ASN A 239 " pdb=" C2 NAG A1003 " pdb=" O5 NAG A1003 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 1354 not shown) Planarity restraints: 1457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.250 2.00e-02 2.50e+03 2.13e-01 5.70e+02 pdb=" C7 NAG C 1 " 0.054 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.031 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.355 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " -0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1501 " 0.094 2.00e-02 2.50e+03 7.72e-02 7.46e+01 pdb=" C7 NAG B1501 " -0.029 2.00e-02 2.50e+03 pdb=" C8 NAG B1501 " 0.072 2.00e-02 2.50e+03 pdb=" N2 NAG B1501 " -0.121 2.00e-02 2.50e+03 pdb=" O7 NAG B1501 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 277 " 0.013 2.00e-02 2.50e+03 2.50e-02 6.25e+00 pdb=" C GLU A 277 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU A 277 " 0.016 2.00e-02 2.50e+03 pdb=" N SER A 278 " 0.015 2.00e-02 2.50e+03 ... (remaining 1454 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1858 2.79 - 3.32: 7212 3.32 - 3.84: 12316 3.84 - 4.37: 12747 4.37 - 4.90: 23183 Nonbonded interactions: 57316 Sorted by model distance: nonbonded pdb=" O TYR K 51 " pdb=" OG1 THR K 54 " model vdw 2.259 3.040 nonbonded pdb=" N LEU B 34 " pdb=" O ASP B 66 " model vdw 2.272 3.120 nonbonded pdb=" N ASN B 75 " pdb=" OD1 ASN B 75 " model vdw 2.302 3.120 nonbonded pdb=" OG1 THR J 124 " pdb=" OE1 GLU J 126 " model vdw 2.306 3.040 nonbonded pdb=" OD1 ASN A 203 " pdb=" OG1 THR A 205 " model vdw 2.314 3.040 ... (remaining 57311 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 3.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.660 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5251 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 : 0.003 0.050 8263 Z= 0.168 Angle : 0.578 9.223 11355 Z= 0.316 Chirality : 0.053 1.126 1357 Planarity : 0.007 0.213 1447 Dihedral : 14.298 112.640 2755 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.63 % Allowed : 8.61 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.27), residues: 1117 helix: 0.98 (0.35), residues: 252 sheet: -0.81 (0.31), residues: 320 loop : -1.34 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 125 TYR 0.011 0.001 TYR J 114 PHE 0.009 0.001 PHE A 42 TRP 0.008 0.001 TRP B 378 HIS 0.001 0.000 HIS K 100 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8247) covalent geometry : angle 0.55661 (11312) SS BOND : bond 0.00561 ( 5) SS BOND : angle 0.61038 ( 10) hydrogen bonds : bond 0.24147 ( 269) hydrogen bonds : angle 8.17712 ( 756) link_BETA1-4 : bond 0.00491 ( 1) link_BETA1-4 : angle 0.56159 ( 3) link_NAG-ASN : bond 0.00523 ( 10) link_NAG-ASN : angle 3.10761 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 MET cc_start: 0.9455 (mmm) cc_final: 0.9186 (mmm) REVERT: A 240 MET cc_start: 0.8090 (mtp) cc_final: 0.7880 (mmt) REVERT: A 248 LEU cc_start: 0.8424 (mt) cc_final: 0.8214 (mt) REVERT: A 354 MET cc_start: 0.8778 (mmm) cc_final: 0.8524 (mmt) REVERT: B 74 MET cc_start: 0.9026 (ttp) cc_final: 0.8727 (ttt) outliers start: 11 outliers final: 3 residues processed: 137 average time/residue: 0.0649 time to fit residues: 12.7022 Evaluate side-chains 85 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 383 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 0.6980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 293 HIS A 311 ASN A 371 HIS ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN K 66 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.065969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.057437 restraints weight = 66470.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.058330 restraints weight = 51190.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.058701 restraints weight = 42705.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.059079 restraints weight = 37651.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.059464 restraints weight = 34390.038| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8263 Z= 0.132 Angle : 0.598 10.061 11355 Z= 0.303 Chirality : 0.046 0.348 1357 Planarity : 0.004 0.045 1447 Dihedral : 12.256 94.751 1435 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.41 % Allowed : 12.76 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.26), residues: 1117 helix: 0.79 (0.34), residues: 256 sheet: -0.59 (0.31), residues: 306 loop : -1.53 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 181 TYR 0.018 0.001 TYR A 232 PHE 0.012 0.001 PHE A 42 TRP 0.016 0.001 TRP B 390 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8247) covalent geometry : angle 0.57589 (11312) SS BOND : bond 0.00920 ( 5) SS BOND : angle 1.60503 ( 10) hydrogen bonds : bond 0.04079 ( 269) hydrogen bonds : angle 5.74978 ( 756) link_BETA1-4 : bond 0.00190 ( 1) link_BETA1-4 : angle 2.37933 ( 3) link_NAG-ASN : bond 0.00605 ( 10) link_NAG-ASN : angle 2.96767 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 MET cc_start: 0.8820 (mmm) cc_final: 0.8571 (mmm) REVERT: B 181 ARG cc_start: 0.8613 (mmm160) cc_final: 0.7992 (tpm170) REVERT: B 246 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7213 (pp) REVERT: B 306 MET cc_start: 0.8049 (tpt) cc_final: 0.7701 (tpt) REVERT: H 103 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: I 64 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7440 (pp30) REVERT: J 123 ILE cc_start: 0.8230 (mm) cc_final: 0.7898 (mp) outliers start: 23 outliers final: 12 residues processed: 109 average time/residue: 0.0590 time to fit residues: 9.4729 Evaluate side-chains 93 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain H residue 103 PHE Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain K residue 56 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 171 HIS ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 63 GLN ** 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 = 0.3511 r_free = 0.3511 target = 0.061455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.053772 restraints weight = 76613.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.054353 restraints weight = 58698.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.055068 restraints weight = 48548.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.055481 restraints weight = 40997.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.055832 restraints weight = 36022.260| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8263 Z= 0.279 Angle : 0.794 10.128 11355 Z= 0.406 Chirality : 0.049 0.312 1357 Planarity : 0.005 0.067 1447 Dihedral : 11.266 105.596 1435 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.45 % Allowed : 16.91 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.24), residues: 1117 helix: 0.07 (0.32), residues: 250 sheet: -0.98 (0.30), residues: 293 loop : -1.95 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 125 TYR 0.026 0.002 TYR J 114 PHE 0.025 0.002 PHE A 42 TRP 0.022 0.002 TRP J 130 HIS 0.007 0.002 HIS K 100 Details of bonding type rmsd covalent geometry : bond 0.00582 ( 8247) covalent geometry : angle 0.77237 (11312) SS BOND : bond 0.01374 ( 5) SS BOND : angle 3.41003 ( 10) hydrogen bonds : bond 0.04855 ( 269) hydrogen bonds : angle 6.18962 ( 756) link_BETA1-4 : bond 0.00164 ( 1) link_BETA1-4 : angle 3.16094 ( 3) link_NAG-ASN : bond 0.00607 ( 10) link_NAG-ASN : angle 2.93940 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 MET cc_start: 0.8981 (mmm) cc_final: 0.8777 (mmp) REVERT: B 74 MET cc_start: 0.8221 (ttt) cc_final: 0.7792 (tmm) REVERT: B 306 MET cc_start: 0.7954 (tpt) cc_final: 0.7577 (tpt) REVERT: H 103 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8313 (m-80) REVERT: J 46 TYR cc_start: 0.7939 (p90) cc_final: 0.7730 (p90) REVERT: J 123 ILE cc_start: 0.8478 (mm) cc_final: 0.8128 (mp) outliers start: 30 outliers final: 20 residues processed: 92 average time/residue: 0.0517 time to fit residues: 7.2938 Evaluate side-chains 87 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain H residue 103 PHE Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 96 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 63 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS A 358 ASN ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 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 = 0.3509 r_free = 0.3509 target = 0.061115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.053389 restraints weight = 78470.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.054216 restraints weight = 58977.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.054669 restraints weight = 47205.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.055144 restraints weight = 40816.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.055394 restraints weight = 35681.787| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8263 Z= 0.218 Angle : 0.683 8.721 11355 Z= 0.351 Chirality : 0.047 0.332 1357 Planarity : 0.004 0.073 1447 Dihedral : 10.483 103.431 1433 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.75 % Allowed : 17.80 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.24), residues: 1117 helix: 0.26 (0.33), residues: 249 sheet: -1.15 (0.30), residues: 292 loop : -2.01 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 181 TYR 0.020 0.002 TYR J 114 PHE 0.016 0.002 PHE A 42 TRP 0.028 0.002 TRP J 130 HIS 0.005 0.001 HIS K 100 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 8247) covalent geometry : angle 0.66183 (11312) SS BOND : bond 0.01149 ( 5) SS BOND : angle 2.74938 ( 10) hydrogen bonds : bond 0.04086 ( 269) hydrogen bonds : angle 5.91855 ( 756) link_BETA1-4 : bond 0.00217 ( 1) link_BETA1-4 : angle 2.99412 ( 3) link_NAG-ASN : bond 0.00545 ( 10) link_NAG-ASN : angle 2.82212 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 HIS cc_start: 0.8739 (OUTLIER) cc_final: 0.8487 (m90) REVERT: A 315 TRP cc_start: 0.8376 (OUTLIER) cc_final: 0.8168 (t60) REVERT: B 181 ARG cc_start: 0.8549 (mmm160) cc_final: 0.7930 (tpm170) REVERT: B 306 MET cc_start: 0.7910 (tpt) cc_final: 0.7696 (tpt) REVERT: J 46 TYR cc_start: 0.7618 (p90) cc_final: 0.7348 (p90) outliers start: 32 outliers final: 20 residues processed: 93 average time/residue: 0.0544 time to fit residues: 7.8346 Evaluate side-chains 85 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 312 TYR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 64 optimal weight: 0.0050 chunk 68 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 overall best weight: 1.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.061210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.053465 restraints weight = 77157.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.054319 restraints weight = 58479.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.054940 restraints weight = 46385.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.055291 restraints weight = 38874.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.055514 restraints weight = 34282.890| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8263 Z= 0.160 Angle : 0.624 9.316 11355 Z= 0.322 Chirality : 0.045 0.346 1357 Planarity : 0.004 0.038 1447 Dihedral : 10.122 102.269 1433 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.71 % Allowed : 19.88 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.25), residues: 1117 helix: 0.55 (0.33), residues: 247 sheet: -1.07 (0.30), residues: 296 loop : -2.01 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 181 TYR 0.014 0.001 TYR J 114 PHE 0.013 0.002 PHE A 42 TRP 0.026 0.002 TRP J 130 HIS 0.013 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8247) covalent geometry : angle 0.60486 (11312) SS BOND : bond 0.01069 ( 5) SS BOND : angle 2.17184 ( 10) hydrogen bonds : bond 0.03674 ( 269) hydrogen bonds : angle 5.68689 ( 756) link_BETA1-4 : bond 0.00198 ( 1) link_BETA1-4 : angle 2.82138 ( 3) link_NAG-ASN : bond 0.00502 ( 10) link_NAG-ASN : angle 2.67042 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 181 ARG cc_start: 0.8495 (mmm160) cc_final: 0.7661 (tpm170) REVERT: B 306 MET cc_start: 0.7868 (tpt) cc_final: 0.7506 (tpt) REVERT: B 380 ASN cc_start: 0.7363 (OUTLIER) cc_final: 0.7135 (m-40) REVERT: J 46 TYR cc_start: 0.7730 (p90) cc_final: 0.7489 (p90) outliers start: 25 outliers final: 21 residues processed: 87 average time/residue: 0.0579 time to fit residues: 7.6556 Evaluate side-chains 88 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 312 TYR Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 44 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 79 optimal weight: 0.0040 chunk 74 optimal weight: 7.9990 chunk 86 optimal weight: 0.0000 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.062212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.054425 restraints weight = 75516.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.055241 restraints weight = 57393.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.055843 restraints weight = 46060.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.056244 restraints weight = 38911.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.056599 restraints weight = 34194.754| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8263 Z= 0.105 Angle : 0.569 9.514 11355 Z= 0.290 Chirality : 0.044 0.352 1357 Planarity : 0.004 0.037 1447 Dihedral : 9.437 97.727 1433 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.86 % Allowed : 20.33 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.25), residues: 1117 helix: 0.80 (0.34), residues: 254 sheet: -1.05 (0.31), residues: 295 loop : -1.83 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 125 TYR 0.009 0.001 TYR H 114 PHE 0.007 0.001 PHE A 42 TRP 0.031 0.002 TRP J 130 HIS 0.003 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8247) covalent geometry : angle 0.55136 (11312) SS BOND : bond 0.00765 ( 5) SS BOND : angle 1.50124 ( 10) hydrogen bonds : bond 0.02984 ( 269) hydrogen bonds : angle 5.27904 ( 756) link_BETA1-4 : bond 0.00033 ( 1) link_BETA1-4 : angle 2.83907 ( 3) link_NAG-ASN : bond 0.00522 ( 10) link_NAG-ASN : angle 2.54966 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 MET cc_start: 0.8289 (mmm) cc_final: 0.7947 (mmm) REVERT: B 306 MET cc_start: 0.7930 (tpt) cc_final: 0.7698 (tpt) REVERT: B 380 ASN cc_start: 0.7407 (OUTLIER) cc_final: 0.7191 (m-40) REVERT: I 64 GLN cc_start: 0.7938 (tm-30) cc_final: 0.6917 (pp30) outliers start: 26 outliers final: 19 residues processed: 95 average time/residue: 0.0512 time to fit residues: 7.5986 Evaluate side-chains 91 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 312 TYR Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.062217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.054390 restraints weight = 76413.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.055224 restraints weight = 58016.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.055720 restraints weight = 46529.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.056264 restraints weight = 39576.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.056510 restraints weight = 34327.590| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8263 Z= 0.106 Angle : 0.581 9.536 11355 Z= 0.293 Chirality : 0.045 0.352 1357 Planarity : 0.004 0.064 1447 Dihedral : 9.058 94.899 1433 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.41 % Allowed : 21.81 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.25), residues: 1117 helix: 0.90 (0.33), residues: 259 sheet: -0.92 (0.31), residues: 299 loop : -1.78 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 181 TYR 0.008 0.001 TYR J 114 PHE 0.007 0.001 PHE A 42 TRP 0.017 0.001 TRP B 390 HIS 0.003 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 8247) covalent geometry : angle 0.56368 (11312) SS BOND : bond 0.00666 ( 5) SS BOND : angle 1.41151 ( 10) hydrogen bonds : bond 0.02921 ( 269) hydrogen bonds : angle 5.11189 ( 756) link_BETA1-4 : bond 0.00273 ( 1) link_BETA1-4 : angle 2.64124 ( 3) link_NAG-ASN : bond 0.00518 ( 10) link_NAG-ASN : angle 2.55942 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: A 354 MET cc_start: 0.8501 (mmm) cc_final: 0.8287 (mmm) REVERT: B 181 ARG cc_start: 0.8542 (mmm160) cc_final: 0.7661 (tpm170) REVERT: B 306 MET cc_start: 0.7823 (tpt) cc_final: 0.7486 (tpt) REVERT: I 64 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7500 (pp30) outliers start: 23 outliers final: 20 residues processed: 87 average time/residue: 0.0601 time to fit residues: 8.0835 Evaluate side-chains 90 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 312 TYR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 68 optimal weight: 0.0270 chunk 57 optimal weight: 0.7980 chunk 104 optimal weight: 8.9990 chunk 51 optimal weight: 0.0670 chunk 46 optimal weight: 10.0000 chunk 92 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.062520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.054504 restraints weight = 70704.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.055391 restraints weight = 53054.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.055748 restraints weight = 43349.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.056135 restraints weight = 37752.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.056397 restraints weight = 33524.348| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 8263 Z= 0.096 Angle : 0.567 9.501 11355 Z= 0.283 Chirality : 0.045 0.354 1357 Planarity : 0.004 0.055 1447 Dihedral : 8.407 89.527 1430 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.97 % Allowed : 21.96 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.26), residues: 1117 helix: 1.01 (0.33), residues: 259 sheet: -0.70 (0.31), residues: 299 loop : -1.69 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 181 TYR 0.007 0.001 TYR A 232 PHE 0.006 0.001 PHE I 126 TRP 0.023 0.001 TRP B 390 HIS 0.004 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 8247) covalent geometry : angle 0.54997 (11312) SS BOND : bond 0.00380 ( 5) SS BOND : angle 1.07902 ( 10) hydrogen bonds : bond 0.02714 ( 269) hydrogen bonds : angle 4.88036 ( 756) link_BETA1-4 : bond 0.00247 ( 1) link_BETA1-4 : angle 2.65199 ( 3) link_NAG-ASN : bond 0.00566 ( 10) link_NAG-ASN : angle 2.55204 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 HIS cc_start: 0.9341 (m90) cc_final: 0.9085 (t70) REVERT: A 253 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7394 (mp0) REVERT: B 74 MET cc_start: 0.8328 (ttt) cc_final: 0.7844 (tmm) REVERT: B 78 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6737 (t70) REVERT: B 181 ARG cc_start: 0.8530 (mmm160) cc_final: 0.7721 (tpm170) REVERT: B 306 MET cc_start: 0.7725 (tpt) cc_final: 0.7457 (tpt) REVERT: B 380 ASN cc_start: 0.7472 (OUTLIER) cc_final: 0.7198 (m-40) REVERT: I 64 GLN cc_start: 0.7705 (tm-30) cc_final: 0.7115 (pp30) REVERT: J 116 THR cc_start: 0.8044 (m) cc_final: 0.7563 (p) outliers start: 20 outliers final: 14 residues processed: 92 average time/residue: 0.0611 time to fit residues: 8.7016 Evaluate side-chains 87 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 312 TYR Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain K residue 56 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 8.9990 chunk 100 optimal weight: 0.0370 chunk 87 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 27 optimal weight: 0.0010 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.0068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.061717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.053734 restraints weight = 69760.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.054578 restraints weight = 53054.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.054929 restraints weight = 43894.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.055324 restraints weight = 38383.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 14)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.055597 restraints weight = 34330.095| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 8263 Z= 0.109 Angle : 0.580 9.278 11355 Z= 0.288 Chirality : 0.045 0.348 1357 Planarity : 0.004 0.051 1447 Dihedral : 8.239 87.356 1430 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.82 % Allowed : 23.00 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.26), residues: 1117 helix: 1.11 (0.33), residues: 259 sheet: -0.66 (0.31), residues: 297 loop : -1.67 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 181 TYR 0.010 0.001 TYR J 114 PHE 0.011 0.001 PHE A 137 TRP 0.021 0.001 TRP B 390 HIS 0.002 0.001 HIS K 100 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8247) covalent geometry : angle 0.56308 (11312) SS BOND : bond 0.00606 ( 5) SS BOND : angle 1.34379 ( 10) hydrogen bonds : bond 0.02826 ( 269) hydrogen bonds : angle 4.87271 ( 756) link_BETA1-4 : bond 0.00229 ( 1) link_BETA1-4 : angle 2.25294 ( 3) link_NAG-ASN : bond 0.00514 ( 10) link_NAG-ASN : angle 2.57320 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.7617 (mmp) cc_final: 0.7273 (mmp) REVERT: A 146 HIS cc_start: 0.9342 (m90) cc_final: 0.9094 (t70) REVERT: A 253 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: B 78 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.6774 (t70) REVERT: B 181 ARG cc_start: 0.8523 (mmm160) cc_final: 0.7982 (tpm170) REVERT: B 306 MET cc_start: 0.7933 (tpt) cc_final: 0.7638 (tpt) REVERT: B 380 ASN cc_start: 0.7599 (OUTLIER) cc_final: 0.7328 (m-40) REVERT: I 64 GLN cc_start: 0.7743 (tm-30) cc_final: 0.7156 (pp30) outliers start: 19 outliers final: 14 residues processed: 88 average time/residue: 0.0590 time to fit residues: 8.1790 Evaluate side-chains 88 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 312 TYR Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain K residue 56 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 78 optimal weight: 0.0050 chunk 75 optimal weight: 1.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.061670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.053682 restraints weight = 69580.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.054509 restraints weight = 51770.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.054864 restraints weight = 42130.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.055292 restraints weight = 36957.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.055292 restraints weight = 32191.741| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 8263 Z= 0.103 Angle : 0.572 9.198 11355 Z= 0.285 Chirality : 0.045 0.346 1357 Planarity : 0.004 0.046 1447 Dihedral : 8.083 85.049 1430 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.41 % Allowed : 22.26 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.25), residues: 1117 helix: 1.14 (0.33), residues: 259 sheet: -0.67 (0.31), residues: 299 loop : -1.67 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 181 TYR 0.009 0.001 TYR J 129 PHE 0.007 0.001 PHE A 42 TRP 0.021 0.001 TRP B 390 HIS 0.002 0.000 HIS K 100 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8247) covalent geometry : angle 0.55515 (11312) SS BOND : bond 0.00513 ( 5) SS BOND : angle 1.27295 ( 10) hydrogen bonds : bond 0.02698 ( 269) hydrogen bonds : angle 4.83025 ( 756) link_BETA1-4 : bond 0.00375 ( 1) link_BETA1-4 : angle 2.24617 ( 3) link_NAG-ASN : bond 0.00495 ( 10) link_NAG-ASN : angle 2.58343 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 HIS cc_start: 0.9314 (m90) cc_final: 0.9023 (t70) REVERT: A 253 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: B 78 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6712 (t70) REVERT: B 181 ARG cc_start: 0.8497 (mmm160) cc_final: 0.7966 (tpm170) REVERT: B 306 MET cc_start: 0.7966 (tpt) cc_final: 0.7660 (tpt) REVERT: B 380 ASN cc_start: 0.7599 (OUTLIER) cc_final: 0.7321 (m-40) REVERT: I 64 GLN cc_start: 0.7712 (tm-30) cc_final: 0.7124 (pp30) outliers start: 23 outliers final: 17 residues processed: 92 average time/residue: 0.0568 time to fit residues: 8.0960 Evaluate side-chains 92 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 312 TYR Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain K residue 56 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 96 optimal weight: 0.0170 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 0.0670 chunk 48 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 21 optimal weight: 0.4980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.062317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.054649 restraints weight = 75894.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.055514 restraints weight = 57113.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.056008 restraints weight = 45470.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.056480 restraints weight = 39103.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.056793 restraints weight = 34112.090| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8263 Z= 0.104 Angle : 0.588 9.173 11355 Z= 0.290 Chirality : 0.045 0.344 1357 Planarity : 0.004 0.044 1447 Dihedral : 7.779 80.757 1430 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.41 % Allowed : 22.26 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.26), residues: 1117 helix: 1.20 (0.33), residues: 259 sheet: -0.64 (0.31), residues: 301 loop : -1.62 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 181 TYR 0.009 0.001 TYR J 114 PHE 0.009 0.001 PHE A 137 TRP 0.020 0.001 TRP B 390 HIS 0.002 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8247) covalent geometry : angle 0.56556 (11312) SS BOND : bond 0.00655 ( 5) SS BOND : angle 3.05257 ( 10) hydrogen bonds : bond 0.02779 ( 269) hydrogen bonds : angle 4.83084 ( 756) link_BETA1-4 : bond 0.00440 ( 1) link_BETA1-4 : angle 2.18885 ( 3) link_NAG-ASN : bond 0.00509 ( 10) link_NAG-ASN : angle 2.60767 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1251.44 seconds wall clock time: 22 minutes 14.34 seconds (1334.34 seconds total)