Starting phenix.real_space_refine on Fri Sep 11 14:41:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6jmr_9850/09_2026/6jmr_9850.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jmr_9850/09_2026/6jmr_9850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6jmr_9850/09_2026/6jmr_9850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jmr_9850/09_2026/6jmr_9850.map" model { file = "/net/cci-nas-00/data/ceres_data/6jmr_9850/09_2026/6jmr_9850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jmr_9850/09_2026/6jmr_9850.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6jmr_9850/09_2026/6jmr_9850.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6jmr_9850/09_2026/6jmr_9850.cif" } resolution = 4.1 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 32 5.16 5 C 6190 2.51 5 N 1643 2.21 5 O 1944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9809 Number of models: 1 Model: "" Number of chains: 12 Chain: "E" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1646 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain breaks: 1 Chain: "F" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1694 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 11, 'TRANS': 206} Chain: "B" Number of atoms: 3276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3276 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 400} Chain: "C" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 212 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 3, 'TRANS': 26} Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 140 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 16} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 340 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 47} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 834 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 11, 'TRANS': 105} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 162 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "D" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 486 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 3, 'TRANS': 67} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 949 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 119} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.02, per 1000 atoms: 0.21 Number of scatterers: 9809 At special positions: 0 Unit cell: (84.93, 137.08, 140.06, 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 32 16.00 O 1944 8.00 N 1643 7.00 C 6190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS E 146 " - pdb=" SG CYS E 201 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 94 " distance=2.03 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 199 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 200 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 94 " distance=2.04 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 200 " distance=2.02 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 A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN B 381 " " NAG B 703 " - " ASN B 424 " " NAG B 704 " - " ASN B 506 " " NAG B 705 " - " ASN B 365 " TRANS " UNK C 31 " - " THR C 30 " " UNK C 50 " - " GLY C 49 " " UNK C 98 " - " ARG C 97 " " UNK D 24 " - " CYS D 23 " " UNK D 95 " - " CYS D 94 " Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 286.1 milliseconds 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2398 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 27 sheets defined 14.1% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'E' and resid 28 through 32 removed outlier: 4.237A pdb=" N THR E 31 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.860A pdb=" N THR E 90 " --> pdb=" O ASP E 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 132 Processing helix chain 'F' and resid 188 through 193 Processing helix chain 'B' and resid 229 through 234 removed outlier: 3.587A pdb=" N GLN B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'B' and resid 246 through 252 removed outlier: 4.056A pdb=" N TYR B 250 " --> pdb=" O GLY B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 removed outlier: 3.800A pdb=" N SER B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 340 removed outlier: 4.044A pdb=" N VAL B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP B 332 " --> pdb=" O THR B 328 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE B 336 " --> pdb=" O ASP B 332 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 370 removed outlier: 3.663A pdb=" N PHE B 359 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TRP B 363 " --> pdb=" O PHE B 359 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 367 " --> pdb=" O TRP B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 Processing helix chain 'B' and resid 414 through 426 removed outlier: 3.814A pdb=" N THR B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 460 removed outlier: 3.598A pdb=" N THR B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 496 removed outlier: 4.137A pdb=" N PHE B 496 " --> pdb=" O GLU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 513 Processing helix chain 'B' and resid 519 through 524 Processing helix chain 'B' and resid 526 through 533 removed outlier: 3.676A pdb=" N GLU B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 539 removed outlier: 3.622A pdb=" N HIS B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing helix chain 'C' and resid 63 through 67 removed outlier: 3.702A pdb=" N LEU C 67 " --> pdb=" O UNK C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.903A pdb=" N ASP C 89 " --> pdb=" O GLN C 86 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR C 90 " --> pdb=" O THR C 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 86 through 90' Processing helix chain 'D' and resid 127 through 133 removed outlier: 3.566A pdb=" N SER D 133 " --> pdb=" O GLU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 194 Processing sheet with id=AA1, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.736A pdb=" N VAL E 12 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA E 96 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS E 35 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.736A pdb=" N VAL E 12 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG E 97 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR E 107 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 126 through 130 removed outlier: 3.590A pdb=" N LEU E 130 " --> pdb=" O GLY E 145 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY E 145 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N THR E 143 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL E 189 " --> pdb=" O THR E 143 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N GLY E 145 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL E 187 " --> pdb=" O GLY E 145 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LEU E 147 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N SER E 185 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LYS E 149 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU E 183 " --> pdb=" O LYS E 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 126 through 130 removed outlier: 3.590A pdb=" N LEU E 130 " --> pdb=" O GLY E 145 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY E 145 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N THR E 143 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL E 189 " --> pdb=" O THR E 143 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N GLY E 145 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL E 187 " --> pdb=" O GLY E 145 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LEU E 147 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N SER E 185 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LYS E 149 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU E 183 " --> pdb=" O LYS E 149 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL E 175 " --> pdb=" O THR E 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 157 through 160 removed outlier: 4.155A pdb=" N VAL E 199 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL E 212 " --> pdb=" O VAL E 203 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS E 205 " --> pdb=" O THR E 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.701A pdb=" N VAL F 19 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE F 77 " --> pdb=" O CYS F 23 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 10 through 12 removed outlier: 5.593A pdb=" N LEU F 11 " --> pdb=" O GLU F 110 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN F 95 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU F 39 " --> pdb=" O PHE F 55 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE F 55 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TRP F 41 " --> pdb=" O LEU F 53 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 119 through 123 removed outlier: 5.949A pdb=" N TYR F 178 " --> pdb=" O ASN F 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 134 through 135 Processing sheet with id=AB2, first strand: chain 'F' and resid 158 through 160 removed outlier: 4.443A pdb=" N TRP F 153 " --> pdb=" O ARG F 160 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 259 through 261 removed outlier: 8.581A pdb=" N GLN B 346 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU B 306 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE B 345 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N GLY B 379 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N THR B 401 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA B 378 " --> pdb=" O THR B 401 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 265 through 267 removed outlier: 6.846A pdb=" N GLN B 279 " --> pdb=" O LYS B 266 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 431 through 433 Processing sheet with id=AB6, first strand: chain 'B' and resid 540 through 542 removed outlier: 3.501A pdb=" N VAL B 566 " --> pdb=" O LEU B 622 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 592 through 593 Processing sheet with id=AB8, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.506A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.513A pdb=" N TYR C 94 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 18 through 19 removed outlier: 3.801A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET C 82 " --> pdb=" O LEU C 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 125 through 129 removed outlier: 3.881A pdb=" N GLY C 144 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LYS C 148 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU C 182 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR C 150 " --> pdb=" O TYR C 180 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 125 through 129 removed outlier: 3.881A pdb=" N GLY C 144 " --> pdb=" O LEU C 129 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 156 through 157 removed outlier: 3.622A pdb=" N THR C 156 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA C 203 " --> pdb=" O THR C 156 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 4 through 6 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 4 through 6 current: chain 'D' and resid 20 through 25 removed outlier: 3.919A pdb=" N ASP D 76 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 10 through 14 removed outlier: 5.830A pdb=" N LEU D 11 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LYS D 113 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL D 13 " --> pdb=" O LYS D 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 51 through 54 removed outlier: 6.600A pdb=" N TRP D 41 " --> pdb=" O LEU D 53 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 122 through 124 removed outlier: 3.705A pdb=" N SER D 122 " --> pdb=" O PHE D 141 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 139 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N SER D 137 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU D 187 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N VAL D 139 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU D 185 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N PHE D 141 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N SER D 183 " --> pdb=" O PHE D 141 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASN D 143 " --> pdb=" O MET D 181 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N MET D 181 " --> pdb=" O ASN D 143 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE D 145 " --> pdb=" O TYR D 179 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 159 through 161 removed outlier: 3.836A pdb=" N TRP D 154 " --> pdb=" O ARG D 161 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS D 200 " --> pdb=" O LYS D 213 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS D 213 " --> pdb=" O CYS D 200 " (cutoff:3.500A) 260 hydrogen bonds defined for protein. 633 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: 1.06 Time building geometry restraints manager: 1.07 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: 3125 1.34 - 1.46: 2269 1.46 - 1.58: 4587 1.58 - 1.70: 1 1.70 - 1.81: 46 Bond restraints: 10028 Sorted by residual: bond pdb=" C TYR D 146 " pdb=" N PRO D 147 " ideal model delta sigma weight residual 1.332 1.381 -0.049 1.12e-02 7.97e+03 1.90e+01 bond pdb=" C THR B 459 " pdb=" N LEU B 460 " ideal model delta sigma weight residual 1.329 1.250 0.079 1.86e-02 2.89e+03 1.79e+01 bond pdb=" C GLU E 154 " pdb=" N PRO E 155 " ideal model delta sigma weight residual 1.334 1.406 -0.072 2.34e-02 1.83e+03 9.47e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 7.99e+00 bond pdb=" C GLU C 153 " pdb=" N PRO C 154 " ideal model delta sigma weight residual 1.334 1.365 -0.031 1.11e-02 8.12e+03 7.62e+00 ... (remaining 10023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 13004 2.25 - 4.50: 569 4.50 - 6.75: 61 6.75 - 9.00: 12 9.00 - 11.25: 6 Bond angle restraints: 13652 Sorted by residual: angle pdb=" C VAL E 99 " pdb=" N TYR E 100 " pdb=" CA TYR E 100 " ideal model delta sigma weight residual 120.82 130.62 -9.80 1.50e+00 4.44e-01 4.27e+01 angle pdb=" N PRO E 155 " pdb=" CA PRO E 155 " pdb=" C PRO E 155 " ideal model delta sigma weight residual 112.47 123.04 -10.57 2.06e+00 2.36e-01 2.63e+01 angle pdb=" C LYS B 354 " pdb=" N ASP B 355 " pdb=" CA ASP B 355 " ideal model delta sigma weight residual 122.82 129.76 -6.94 1.42e+00 4.96e-01 2.39e+01 angle pdb=" N VAL E 99 " pdb=" CA VAL E 99 " pdb=" C VAL E 99 " ideal model delta sigma weight residual 109.55 103.30 6.25 1.38e+00 5.25e-01 2.05e+01 angle pdb=" C SER D 7 " pdb=" N PRO D 8 " pdb=" CA PRO D 8 " ideal model delta sigma weight residual 119.84 114.83 5.01 1.25e+00 6.40e-01 1.61e+01 ... (remaining 13647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.59: 5190 15.59 - 31.18: 646 31.18 - 46.77: 113 46.77 - 62.36: 19 62.36 - 77.95: 9 Dihedral angle restraints: 5977 sinusoidal: 2258 harmonic: 3719 Sorted by residual: dihedral pdb=" CA PHE C 151 " pdb=" C PHE C 151 " pdb=" N PRO C 152 " pdb=" CA PRO C 152 " ideal model delta harmonic sigma weight residual 180.00 128.39 51.61 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" CA TRP B 557 " pdb=" C TRP B 557 " pdb=" N ASP B 558 " pdb=" CA ASP B 558 " ideal model delta harmonic sigma weight residual 180.00 -138.75 -41.25 0 5.00e+00 4.00e-02 6.81e+01 dihedral pdb=" CA THR F 102 " pdb=" C THR F 102 " pdb=" N PHE F 103 " pdb=" CA PHE F 103 " ideal model delta harmonic sigma weight residual 180.00 143.79 36.21 0 5.00e+00 4.00e-02 5.24e+01 ... (remaining 5974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1205 0.061 - 0.122: 309 0.122 - 0.183: 51 0.183 - 0.245: 2 0.245 - 0.306: 5 Chirality restraints: 1572 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 9.44e+00 chirality pdb=" C1 NAG B 705 " pdb=" ND2 ASN B 365 " pdb=" C2 NAG B 705 " pdb=" O5 NAG B 705 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" C1 NAG B 703 " pdb=" ND2 ASN B 424 " pdb=" C2 NAG B 703 " pdb=" O5 NAG B 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1569 not shown) Planarity restraints: 1750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 151 " 0.085 5.00e-02 4.00e+02 1.29e-01 2.66e+01 pdb=" N PRO C 152 " -0.223 5.00e-02 4.00e+02 pdb=" CA PRO C 152 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO C 152 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 8 " -0.061 5.00e-02 4.00e+02 9.30e-02 1.38e+01 pdb=" N PRO C 9 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO C 9 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 9 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 154 " -0.050 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO E 155 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO E 155 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 155 " -0.042 5.00e-02 4.00e+02 ... (remaining 1747 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1971 2.77 - 3.30: 8690 3.30 - 3.84: 16307 3.84 - 4.37: 17584 4.37 - 4.90: 30918 Nonbonded interactions: 75470 Sorted by model distance: nonbonded pdb=" OG SER F 7 " pdb=" OG1 THR F 22 " model vdw 2.239 3.040 nonbonded pdb=" O PHE F 55 " pdb=" OG1 THR F 59 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR B 468 " pdb=" O PRO B 487 " model vdw 2.265 3.040 nonbonded pdb=" O ASP B 271 " pdb=" OG1 THR B 275 " model vdw 2.295 3.040 nonbonded pdb=" O GLY B 462 " pdb=" NH2 ARG B 530 " model vdw 2.296 3.120 ... (remaining 75465 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: 0.410 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: 0.040 Set scattering table: 0.020 Process input model: 8.570 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 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 : 0.007 0.079 10046 Z= 0.320 Angle : 1.073 12.457 13698 Z= 0.595 Chirality : 0.056 0.306 1572 Planarity : 0.008 0.129 1741 Dihedral : 14.056 77.952 3540 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.10 % Favored : 92.82 % Rotamer: Outliers : 0.56 % Allowed : 9.55 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.35 % 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: -4.05 (0.20), residues: 1197 helix: -3.64 (0.26), residues: 142 sheet: -2.18 (0.23), residues: 387 loop : -2.82 (0.19), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 211 TYR 0.023 0.003 TYR F 42 PHE 0.020 0.003 PHE B 551 TRP 0.026 0.002 TRP E 47 HIS 0.010 0.003 HIS B 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.32 (10028) covalent geometry : angle 1.05773 / 0.59 (13652) SS BOND : bond 0.00725 / 0.33 ( 8) SS BOND : angle 1.22626 / 0.98 ( 16) hydrogen bonds : bond 0.29337 / 20.58 ( 245) hydrogen bonds : angle 10.78227 / 7.61 ( 633) link_BETA1-4 : bond 0.02632 / 1.39 ( 1) link_BETA1-4 : angle 3.56857 / 1.90 ( 3) link_NAG-ASN : bond 0.00814 / 0.41 ( 4) link_NAG-ASN : angle 5.96459 / 3.65 ( 12) link_TRANS : bond 0.00344 / 0.21 ( 5) link_TRANS : angle 0.82220 / 0.54 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 241 time to evaluate : 0.378 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 LYS cc_start: 0.7338 (mppt) cc_final: 0.7059 (mptt) REVERT: E 89 ASP cc_start: 0.7289 (m-30) cc_final: 0.6870 (m-30) REVERT: E 177 GLN cc_start: 0.8448 (tt0) cc_final: 0.7915 (pm20) REVERT: F 41 TRP cc_start: 0.8218 (m100) cc_final: 0.7938 (m100) REVERT: F 45 LYS cc_start: 0.8866 (mttt) cc_final: 0.8394 (mmtm) REVERT: F 100 TYR cc_start: 0.7287 (t80) cc_final: 0.6722 (t80) REVERT: F 150 ASN cc_start: 0.8746 (t0) cc_final: 0.8363 (t0) REVERT: B 283 ASN cc_start: 0.8329 (m-40) cc_final: 0.7968 (t0) REVERT: B 300 LYS cc_start: 0.8981 (mttm) cc_final: 0.8636 (mmmt) REVERT: B 387 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8348 (tp40) REVERT: B 413 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6841 (mm-30) REVERT: B 422 TYR cc_start: 0.8092 (t80) cc_final: 0.7450 (t80) REVERT: B 579 GLN cc_start: 0.8417 (tm-30) cc_final: 0.7516 (tm-30) REVERT: C 2 VAL cc_start: 0.6445 (OUTLIER) cc_final: 0.6041 (m) REVERT: C 16 GLN cc_start: 0.8243 (mm-40) cc_final: 0.8026 (mm-40) REVERT: C 72 ASP cc_start: 0.8682 (t0) cc_final: 0.8016 (t0) REVERT: C 175 LEU cc_start: 0.8673 (tp) cc_final: 0.8442 (tp) REVERT: C 201 ASN cc_start: 0.6727 (m-40) cc_final: 0.6112 (m110) REVERT: C 212 ASP cc_start: 0.8637 (m-30) cc_final: 0.8296 (m-30) REVERT: C 213 LYS cc_start: 0.8016 (mmtt) cc_final: 0.7637 (tttm) REVERT: D 48 GLN cc_start: 0.8657 (mp-120) cc_final: 0.8420 (mp10) REVERT: D 79 LEU cc_start: 0.8940 (tp) cc_final: 0.8738 (tp) REVERT: D 190 ASP cc_start: 0.8152 (t0) cc_final: 0.7950 (t0) outliers start: 6 outliers final: 3 residues processed: 247 average time/residue: 0.1061 time to fit residues: 35.5588 Evaluate side-chains 147 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 143 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.0970 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN F 95 GLN F 150 ASN B 216 GLN B 322 GLN B 395 ASN ** B 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.105232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.085508 restraints weight = 26283.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.087786 restraints weight = 16362.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.089412 restraints weight = 11798.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.090493 restraints weight = 9272.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.091246 restraints weight = 7799.573| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10046 Z= 0.170 Angle : 0.763 10.552 13698 Z= 0.383 Chirality : 0.047 0.225 1572 Planarity : 0.006 0.105 1741 Dihedral : 6.616 42.957 1359 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.18 % 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: -3.32 (0.21), residues: 1197 helix: -2.54 (0.34), residues: 146 sheet: -1.90 (0.23), residues: 403 loop : -2.32 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 439 TYR 0.025 0.002 TYR E 94 PHE 0.026 0.002 PHE F 103 TRP 0.012 0.001 TRP F 41 HIS 0.005 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (10028) covalent geometry : angle 0.75054 / 0.38 (13652) SS BOND : bond 0.00585 / 0.31 ( 8) SS BOND : angle 1.49217 / 0.96 ( 16) hydrogen bonds : bond 0.04722 / 3.18 ( 245) hydrogen bonds : angle 7.46580 / 5.31 ( 633) link_BETA1-4 : bond 0.00232 / 0.12 ( 1) link_BETA1-4 : angle 1.43976 / 0.75 ( 3) link_NAG-ASN : bond 0.00809 / 0.41 ( 4) link_NAG-ASN : angle 4.52397 / 2.71 ( 12) link_TRANS : bond 0.00070 / 0.04 ( 5) link_TRANS : angle 0.51164 / 0.37 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.379 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: symmetry clash REVERT: E 81 LYS cc_start: 0.7609 (mppt) cc_final: 0.7390 (mmtp) REVERT: E 86 GLN cc_start: 0.7801 (mp10) cc_final: 0.7438 (mp10) REVERT: E 89 ASP cc_start: 0.7315 (m-30) cc_final: 0.6092 (p0) REVERT: E 154 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8251 (tm-30) REVERT: F 175 ASP cc_start: 0.8370 (p0) cc_final: 0.7629 (p0) REVERT: B 283 ASN cc_start: 0.8050 (m-40) cc_final: 0.7804 (t0) REVERT: B 300 LYS cc_start: 0.8804 (mttm) cc_final: 0.8551 (mmmt) REVERT: B 472 ILE cc_start: 0.9445 (mt) cc_final: 0.9213 (mp) REVERT: C 77 GLN cc_start: 0.8458 (pm20) cc_final: 0.8116 (pm20) REVERT: C 201 ASN cc_start: 0.6179 (m-40) cc_final: 0.5496 (m110) REVERT: D 89 LEU cc_start: 0.6766 (pt) cc_final: 0.6261 (tt) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1005 time to fit residues: 30.2475 Evaluate side-chains 138 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 0.5980 chunk 17 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 93 optimal weight: 0.0370 chunk 45 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.5264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 13 GLN E 202 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 GLN C 16 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.105221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.086058 restraints weight = 26936.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.088197 restraints weight = 17553.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.089650 restraints weight = 12950.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.090593 restraints weight = 10411.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.091323 restraints weight = 8951.882| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10046 Z= 0.188 Angle : 0.740 10.076 13698 Z= 0.372 Chirality : 0.047 0.197 1572 Planarity : 0.006 0.098 1741 Dihedral : 6.364 41.142 1359 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.18 % 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: -2.99 (0.22), residues: 1197 helix: -2.03 (0.35), residues: 148 sheet: -1.61 (0.25), residues: 394 loop : -2.22 (0.21), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 92 TYR 0.024 0.002 TYR E 94 PHE 0.018 0.002 PHE E 80 TRP 0.041 0.002 TRP E 194 HIS 0.006 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (10028) covalent geometry : angle 0.73053 / 0.37 (13652) SS BOND : bond 0.00518 / 0.28 ( 8) SS BOND : angle 1.03731 / 0.61 ( 16) hydrogen bonds : bond 0.04203 / 2.85 ( 245) hydrogen bonds : angle 7.03448 / 4.95 ( 633) link_BETA1-4 : bond 0.00005 / 0.00 ( 1) link_BETA1-4 : angle 1.20914 / 0.64 ( 3) link_NAG-ASN : bond 0.00546 / 0.27 ( 4) link_NAG-ASN : angle 4.08094 / 2.44 ( 12) link_TRANS : bond 0.00106 / 0.05 ( 5) link_TRANS : angle 0.38216 / 0.29 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.393 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: symmetry clash REVERT: E 89 ASP cc_start: 0.7375 (m-30) cc_final: 0.6919 (m-30) REVERT: E 154 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8340 (tm-30) REVERT: E 181 TYR cc_start: 0.7814 (m-10) cc_final: 0.7552 (m-10) REVERT: F 175 ASP cc_start: 0.8423 (p0) cc_final: 0.7817 (p0) REVERT: F 189 ASP cc_start: 0.8362 (p0) cc_final: 0.7438 (p0) REVERT: B 300 LYS cc_start: 0.8770 (mttm) cc_final: 0.8504 (mmmt) REVERT: C 77 GLN cc_start: 0.8585 (pm20) cc_final: 0.8291 (pm20) REVERT: C 213 LYS cc_start: 0.7827 (mmtt) cc_final: 0.7217 (mmmt) REVERT: D 48 GLN cc_start: 0.8933 (mp10) cc_final: 0.8643 (mp10) REVERT: D 181 MET cc_start: 0.8187 (tpt) cc_final: 0.7983 (tpp) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.0887 time to fit residues: 24.1064 Evaluate side-chains 142 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 73 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 13 optimal weight: 0.0470 chunk 52 optimal weight: 0.0570 chunk 35 optimal weight: 0.1980 chunk 78 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 129 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 = 0.3737 r_free = 0.3737 target = 0.107455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.088239 restraints weight = 26604.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.090648 restraints weight = 16284.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.092274 restraints weight = 11508.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.093424 restraints weight = 8972.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.094204 restraints weight = 7484.839| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10046 Z= 0.128 Angle : 0.676 10.013 13698 Z= 0.337 Chirality : 0.045 0.240 1572 Planarity : 0.005 0.090 1741 Dihedral : 5.895 41.305 1359 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.09 % 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: -2.70 (0.22), residues: 1197 helix: -1.66 (0.38), residues: 147 sheet: -1.42 (0.26), residues: 376 loop : -2.06 (0.21), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 92 TYR 0.017 0.002 TYR F 42 PHE 0.012 0.001 PHE E 152 TRP 0.009 0.001 TRP B 219 HIS 0.003 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (10028) covalent geometry : angle 0.66499 / 0.33 (13652) SS BOND : bond 0.00621 / 0.34 ( 8) SS BOND : angle 1.07707 / 0.62 ( 16) hydrogen bonds : bond 0.03614 / 2.45 ( 245) hydrogen bonds : angle 6.62232 / 4.67 ( 633) link_BETA1-4 : bond 0.00248 / 0.13 ( 1) link_BETA1-4 : angle 1.23023 / 0.64 ( 3) link_NAG-ASN : bond 0.00829 / 0.42 ( 4) link_NAG-ASN : angle 4.04871 / 2.41 ( 12) link_TRANS : bond 0.00070 / 0.04 ( 5) link_TRANS : angle 0.44998 / 0.32 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.435 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: symmetry clash revert: symmetry clash REVERT: E 154 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8248 (tm-30) REVERT: E 181 TYR cc_start: 0.7789 (m-10) cc_final: 0.7544 (m-10) REVERT: F 175 ASP cc_start: 0.8520 (p0) cc_final: 0.7985 (p0) REVERT: B 300 LYS cc_start: 0.8704 (mttm) cc_final: 0.8472 (mmmt) REVERT: B 471 GLU cc_start: 0.8643 (pm20) cc_final: 0.8199 (pm20) REVERT: C 48 LEU cc_start: 0.7917 (pp) cc_final: 0.7214 (mt) REVERT: C 77 GLN cc_start: 0.8460 (pm20) cc_final: 0.8129 (pm20) REVERT: C 213 LYS cc_start: 0.7925 (mmtt) cc_final: 0.7312 (mmmt) REVERT: D 48 GLN cc_start: 0.8814 (mp10) cc_final: 0.8510 (mp10) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.0898 time to fit residues: 25.0083 Evaluate side-chains 138 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 98 ASN ** F 6 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 = 0.3618 r_free = 0.3618 target = 0.100213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.080447 restraints weight = 27254.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.082485 restraints weight = 17905.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.083916 restraints weight = 13309.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.084897 restraints weight = 10744.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.085514 restraints weight = 9208.450| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 10046 Z= 0.300 Angle : 0.839 10.133 13698 Z= 0.418 Chirality : 0.051 0.218 1572 Planarity : 0.006 0.097 1741 Dihedral : 6.404 38.582 1359 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.18 % 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: -2.76 (0.22), residues: 1197 helix: -1.50 (0.39), residues: 143 sheet: -1.62 (0.25), residues: 380 loop : -2.04 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 92 TYR 0.020 0.003 TYR D 55 PHE 0.033 0.003 PHE B 544 TRP 0.019 0.002 TRP E 47 HIS 0.007 0.002 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.30 (10028) covalent geometry : angle 0.83072 / 0.42 (13652) SS BOND : bond 0.00537 / 0.27 ( 8) SS BOND : angle 1.19275 / 0.78 ( 16) hydrogen bonds : bond 0.04044 / 2.75 ( 245) hydrogen bonds : angle 6.65467 / 4.65 ( 633) link_BETA1-4 : bond 0.00475 / 0.25 ( 1) link_BETA1-4 : angle 0.86139 / 0.50 ( 3) link_NAG-ASN : bond 0.00443 / 0.22 ( 4) link_NAG-ASN : angle 4.02494 / 2.38 ( 12) link_TRANS : bond 0.00192 / 0.11 ( 5) link_TRANS : angle 0.40536 / 0.33 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 181 TYR cc_start: 0.7439 (m-10) cc_final: 0.7167 (m-10) REVERT: F 170 ASP cc_start: 0.8745 (p0) cc_final: 0.8527 (p0) REVERT: F 193 ARG cc_start: 0.7217 (mtm180) cc_final: 0.6868 (mtm180) REVERT: B 300 LYS cc_start: 0.8692 (mttm) cc_final: 0.8429 (mmmm) REVERT: B 471 GLU cc_start: 0.8218 (pm20) cc_final: 0.7772 (pm20) REVERT: B 534 ARG cc_start: 0.7575 (mmm-85) cc_final: 0.7329 (mmm160) REVERT: C 77 GLN cc_start: 0.9045 (pm20) cc_final: 0.8529 (pm20) REVERT: C 213 LYS cc_start: 0.7973 (mmtt) cc_final: 0.7316 (mmmt) REVERT: D 87 GLU cc_start: 0.7049 (pm20) cc_final: 0.6172 (mp0) REVERT: D 181 MET cc_start: 0.7891 (tpp) cc_final: 0.7613 (tpp) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.0839 time to fit residues: 19.7821 Evaluate side-chains 110 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 42 optimal weight: 0.1980 chunk 28 optimal weight: 0.9980 chunk 65 optimal weight: 0.0980 chunk 58 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 129 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 = 0.3693 r_free = 0.3693 target = 0.104433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.084657 restraints weight = 26649.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.086927 restraints weight = 16788.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.088486 restraints weight = 12137.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.089565 restraints weight = 9599.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.090270 restraints weight = 8095.300| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10046 Z= 0.134 Angle : 0.704 10.845 13698 Z= 0.349 Chirality : 0.047 0.258 1572 Planarity : 0.005 0.086 1741 Dihedral : 5.981 39.276 1359 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: -2.50 (0.23), residues: 1197 helix: -1.32 (0.41), residues: 147 sheet: -1.49 (0.26), residues: 375 loop : -1.84 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 92 TYR 0.017 0.002 TYR F 97 PHE 0.027 0.002 PHE F 123 TRP 0.010 0.001 TRP B 219 HIS 0.003 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (10028) covalent geometry : angle 0.69620 / 0.35 (13652) SS BOND : bond 0.00509 / 0.30 ( 8) SS BOND : angle 1.20733 / 0.75 ( 16) hydrogen bonds : bond 0.03414 / 2.33 ( 245) hydrogen bonds : angle 6.36517 / 4.50 ( 633) link_BETA1-4 : bond 0.00609 / 0.32 ( 1) link_BETA1-4 : angle 0.96862 / 0.51 ( 3) link_NAG-ASN : bond 0.00683 / 0.34 ( 4) link_NAG-ASN : angle 3.38154 / 2.03 ( 12) link_TRANS : bond 0.00073 / 0.04 ( 5) link_TRANS : angle 0.65577 / 0.45 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 154 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8253 (tm-30) REVERT: F 41 TRP cc_start: 0.8146 (m100) cc_final: 0.7688 (m100) REVERT: F 170 ASP cc_start: 0.8627 (p0) cc_final: 0.8404 (p0) REVERT: F 193 ARG cc_start: 0.7184 (mtm180) cc_final: 0.6917 (mtm180) REVERT: B 452 LEU cc_start: 0.8920 (mt) cc_final: 0.8685 (mp) REVERT: B 468 TYR cc_start: 0.8955 (p90) cc_final: 0.8541 (p90) REVERT: B 471 GLU cc_start: 0.8336 (pm20) cc_final: 0.7814 (pm20) REVERT: C 48 LEU cc_start: 0.8090 (pp) cc_final: 0.7322 (mt) REVERT: C 77 GLN cc_start: 0.8924 (pm20) cc_final: 0.8449 (pm20) REVERT: C 213 LYS cc_start: 0.8065 (mmtt) cc_final: 0.7648 (mmtt) REVERT: D 181 MET cc_start: 0.7814 (tpp) cc_final: 0.7548 (tpp) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.0932 time to fit residues: 24.0015 Evaluate side-chains 127 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 HIS B 556 HIS ** C 16 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 = 0.3676 r_free = 0.3676 target = 0.103373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.083536 restraints weight = 26757.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.085736 restraints weight = 17070.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.087234 restraints weight = 12463.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.088265 restraints weight = 9983.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.088922 restraints weight = 8494.399| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10046 Z= 0.167 Angle : 0.706 11.151 13698 Z= 0.353 Chirality : 0.047 0.234 1572 Planarity : 0.005 0.092 1741 Dihedral : 5.837 37.448 1359 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: -2.35 (0.23), residues: 1197 helix: -1.06 (0.42), residues: 141 sheet: -1.37 (0.27), residues: 371 loop : -1.78 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 534 TYR 0.012 0.002 TYR F 42 PHE 0.019 0.002 PHE B 544 TRP 0.012 0.001 TRP E 47 HIS 0.006 0.001 HIS B 542 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (10028) covalent geometry : angle 0.70174 / 0.35 (13652) SS BOND : bond 0.00498 / 0.25 ( 8) SS BOND : angle 1.17393 / 0.80 ( 16) hydrogen bonds : bond 0.03336 / 2.30 ( 245) hydrogen bonds : angle 6.20866 / 4.35 ( 633) link_BETA1-4 : bond 0.00359 / 0.19 ( 1) link_BETA1-4 : angle 0.79737 / 0.42 ( 3) link_NAG-ASN : bond 0.00133 / 0.07 ( 4) link_NAG-ASN : angle 2.53236 / 1.49 ( 12) link_TRANS : bond 0.00086 / 0.05 ( 5) link_TRANS : angle 0.50384 / 0.37 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.223 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: E 154 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8314 (tm-30) REVERT: F 170 ASP cc_start: 0.8757 (p0) cc_final: 0.8538 (p0) REVERT: F 193 ARG cc_start: 0.7208 (mtm180) cc_final: 0.6889 (mtm180) REVERT: B 300 LYS cc_start: 0.9006 (mmmt) cc_final: 0.8489 (mtmt) REVERT: B 413 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6530 (mt-10) REVERT: C 3 GLN cc_start: 0.7427 (mt0) cc_final: 0.7154 (mt0) REVERT: C 48 LEU cc_start: 0.8139 (pp) cc_final: 0.7346 (mt) REVERT: C 77 GLN cc_start: 0.8978 (pm20) cc_final: 0.8459 (pm20) REVERT: C 164 LEU cc_start: 0.7744 (mp) cc_final: 0.7506 (tp) REVERT: D 48 GLN cc_start: 0.8864 (mp10) cc_final: 0.8571 (mp10) REVERT: D 181 MET cc_start: 0.7820 (tpp) cc_final: 0.7531 (tpp) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.0904 time to fit residues: 22.2383 Evaluate side-chains 126 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 100 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 0.3980 chunk 78 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN B 454 GLN B 538 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.103619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.083735 restraints weight = 26735.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.085945 restraints weight = 17011.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.087475 restraints weight = 12380.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.088541 restraints weight = 9857.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.089274 restraints weight = 8352.070| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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 : 0.004 0.049 10046 Z= 0.161 Angle : 0.714 11.312 13698 Z= 0.358 Chirality : 0.047 0.225 1572 Planarity : 0.005 0.088 1741 Dihedral : 5.814 37.784 1359 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.09 % 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: -2.37 (0.23), residues: 1197 helix: -1.12 (0.41), residues: 141 sheet: -1.43 (0.27), residues: 356 loop : -1.77 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 216 TYR 0.014 0.002 TYR F 42 PHE 0.018 0.002 PHE B 544 TRP 0.011 0.001 TRP B 219 HIS 0.004 0.001 HIS B 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (10028) covalent geometry : angle 0.71108 / 0.36 (13652) SS BOND : bond 0.00549 / 0.25 ( 8) SS BOND : angle 1.12119 / 0.72 ( 16) hydrogen bonds : bond 0.03512 / 2.42 ( 245) hydrogen bonds : angle 6.20381 / 4.36 ( 633) link_BETA1-4 : bond 0.00524 / 0.28 ( 1) link_BETA1-4 : angle 0.72675 / 0.38 ( 3) link_NAG-ASN : bond 0.00168 / 0.08 ( 4) link_NAG-ASN : angle 2.17342 / 1.28 ( 12) link_TRANS : bond 0.00094 / 0.05 ( 5) link_TRANS : angle 0.51650 / 0.38 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.393 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: E 89 ASP cc_start: 0.7443 (m-30) cc_final: 0.5549 (p0) REVERT: F 193 ARG cc_start: 0.7059 (mtm180) cc_final: 0.6574 (mtm180) REVERT: B 300 LYS cc_start: 0.8961 (mmmt) cc_final: 0.8480 (mtmt) REVERT: B 413 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6510 (mt-10) REVERT: B 449 LEU cc_start: 0.8914 (mp) cc_final: 0.8674 (mp) REVERT: B 472 ILE cc_start: 0.9088 (mt) cc_final: 0.8775 (mp) REVERT: B 579 GLN cc_start: 0.7688 (tm-30) cc_final: 0.7253 (tm-30) REVERT: C 3 GLN cc_start: 0.7549 (mt0) cc_final: 0.7221 (mt0) REVERT: C 48 LEU cc_start: 0.8105 (pp) cc_final: 0.7311 (mt) REVERT: C 77 GLN cc_start: 0.8958 (pm20) cc_final: 0.8483 (pm20) REVERT: C 164 LEU cc_start: 0.7830 (mp) cc_final: 0.7530 (tp) REVERT: D 48 GLN cc_start: 0.8856 (mp10) cc_final: 0.8578 (mp10) REVERT: D 181 MET cc_start: 0.7794 (tpp) cc_final: 0.7486 (tpp) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.0979 time to fit residues: 23.8066 Evaluate side-chains 135 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 40 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 67 optimal weight: 0.1980 chunk 83 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 129 GLN B 619 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.104788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.084804 restraints weight = 26584.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.087037 restraints weight = 16905.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.088580 restraints weight = 12301.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.089643 restraints weight = 9803.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.090387 restraints weight = 8295.358| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10046 Z= 0.142 Angle : 0.707 11.735 13698 Z= 0.354 Chirality : 0.046 0.215 1572 Planarity : 0.005 0.089 1741 Dihedral : 5.721 37.268 1359 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.18 % 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: -2.25 (0.24), residues: 1197 helix: -0.98 (0.42), residues: 141 sheet: -1.40 (0.27), residues: 359 loop : -1.66 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 534 TYR 0.016 0.002 TYR B 422 PHE 0.035 0.002 PHE F 103 TRP 0.013 0.001 TRP F 41 HIS 0.004 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (10028) covalent geometry : angle 0.70504 / 0.35 (13652) SS BOND : bond 0.00630 / 0.27 ( 8) SS BOND : angle 1.06640 / 0.70 ( 16) hydrogen bonds : bond 0.03411 / 2.36 ( 245) hydrogen bonds : angle 6.16689 / 4.37 ( 633) link_BETA1-4 : bond 0.00872 / 0.46 ( 1) link_BETA1-4 : angle 0.84061 / 0.44 ( 3) link_NAG-ASN : bond 0.00191 / 0.10 ( 4) link_NAG-ASN : angle 1.94810 / 1.15 ( 12) link_TRANS : bond 0.00085 / 0.04 ( 5) link_TRANS : angle 0.52510 / 0.38 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 89 ASP cc_start: 0.7447 (m-30) cc_final: 0.5615 (p0) REVERT: E 154 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8270 (tm-30) REVERT: E 181 TYR cc_start: 0.7703 (m-10) cc_final: 0.7452 (m-10) REVERT: F 193 ARG cc_start: 0.7045 (mtm180) cc_final: 0.6758 (mtm180) REVERT: B 300 LYS cc_start: 0.8911 (mmmt) cc_final: 0.8684 (mmmm) REVERT: B 413 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6516 (mt-10) REVERT: B 472 ILE cc_start: 0.9463 (mt) cc_final: 0.9241 (mp) REVERT: B 579 GLN cc_start: 0.7722 (tm-30) cc_final: 0.7276 (tm-30) REVERT: C 3 GLN cc_start: 0.7538 (mt0) cc_final: 0.7266 (mt0) REVERT: C 48 LEU cc_start: 0.8070 (pp) cc_final: 0.7306 (mt) REVERT: C 77 GLN cc_start: 0.8909 (pm20) cc_final: 0.8315 (pm20) REVERT: C 164 LEU cc_start: 0.7741 (mp) cc_final: 0.7439 (tp) REVERT: D 48 GLN cc_start: 0.8828 (mp10) cc_final: 0.8561 (mp10) REVERT: D 181 MET cc_start: 0.7765 (tpp) cc_final: 0.7475 (tpp) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.0930 time to fit residues: 22.4802 Evaluate side-chains 137 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 35 HIS ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.105242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.085383 restraints weight = 26283.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.087681 restraints weight = 16537.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.089227 restraints weight = 11938.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.090314 restraints weight = 9444.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.091028 restraints weight = 7938.965| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10046 Z= 0.136 Angle : 0.700 11.569 13698 Z= 0.350 Chirality : 0.046 0.210 1572 Planarity : 0.005 0.094 1741 Dihedral : 5.602 37.641 1359 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.09 % 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: -2.25 (0.23), residues: 1197 helix: -1.12 (0.41), residues: 147 sheet: -1.29 (0.27), residues: 353 loop : -1.69 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 216 TYR 0.014 0.001 TYR E 100 PHE 0.020 0.002 PHE F 103 TRP 0.014 0.001 TRP B 557 HIS 0.005 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10028) covalent geometry : angle 0.69752 / 0.35 (13652) SS BOND : bond 0.00605 / 0.27 ( 8) SS BOND : angle 1.02895 / 0.66 ( 16) hydrogen bonds : bond 0.03446 / 2.41 ( 245) hydrogen bonds : angle 6.10644 / 4.34 ( 633) link_BETA1-4 : bond 0.00485 / 0.26 ( 1) link_BETA1-4 : angle 0.94201 / 0.49 ( 3) link_NAG-ASN : bond 0.00202 / 0.10 ( 4) link_NAG-ASN : angle 1.83121 / 1.09 ( 12) link_TRANS : bond 0.00071 / 0.04 ( 5) link_TRANS : angle 0.52591 / 0.38 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 89 ASP cc_start: 0.7409 (m-30) cc_final: 0.5672 (p0) REVERT: E 154 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8249 (tm-30) REVERT: E 181 TYR cc_start: 0.7718 (m-10) cc_final: 0.7479 (m-10) REVERT: B 300 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8663 (mmmm) REVERT: B 413 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6578 (mt-10) REVERT: B 454 GLN cc_start: 0.8143 (mt0) cc_final: 0.7849 (pp30) REVERT: B 472 ILE cc_start: 0.9475 (mt) cc_final: 0.9243 (mp) REVERT: B 557 TRP cc_start: 0.8000 (t-100) cc_final: 0.7747 (t-100) REVERT: B 579 GLN cc_start: 0.7599 (tm-30) cc_final: 0.7156 (tm-30) REVERT: C 3 GLN cc_start: 0.7410 (mt0) cc_final: 0.7087 (mt0) REVERT: C 48 LEU cc_start: 0.8043 (pp) cc_final: 0.7274 (mt) REVERT: C 77 GLN cc_start: 0.8849 (pm20) cc_final: 0.8269 (pm20) REVERT: C 164 LEU cc_start: 0.7733 (mp) cc_final: 0.7424 (tp) REVERT: D 48 GLN cc_start: 0.8808 (mp10) cc_final: 0.8554 (mp10) REVERT: D 181 MET cc_start: 0.7749 (tpp) cc_final: 0.7461 (tpp) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.0934 time to fit residues: 22.7717 Evaluate side-chains 137 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 103 optimal weight: 0.0040 chunk 106 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 overall best weight: 1.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** 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 = 0.3667 r_free = 0.3667 target = 0.102884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.083025 restraints weight = 27018.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.085241 restraints weight = 17155.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.086760 restraints weight = 12428.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.087816 restraints weight = 9861.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.088557 restraints weight = 8326.193| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10046 Z= 0.173 Angle : 0.731 11.753 13698 Z= 0.366 Chirality : 0.047 0.207 1572 Planarity : 0.005 0.095 1741 Dihedral : 5.730 38.044 1359 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.09 % 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: -2.23 (0.24), residues: 1197 helix: -1.00 (0.42), residues: 142 sheet: -1.32 (0.27), residues: 355 loop : -1.68 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 97 TYR 0.014 0.002 TYR D 55 PHE 0.020 0.002 PHE B 544 TRP 0.011 0.001 TRP C 108 HIS 0.004 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (10028) covalent geometry : angle 0.72916 / 0.37 (13652) SS BOND : bond 0.00658 / 0.33 ( 8) SS BOND : angle 1.08111 / 0.72 ( 16) hydrogen bonds : bond 0.03557 / 2.49 ( 245) hydrogen bonds : angle 6.15740 / 4.36 ( 633) link_BETA1-4 : bond 0.00559 / 0.29 ( 1) link_BETA1-4 : angle 0.59578 / 0.33 ( 3) link_NAG-ASN : bond 0.00132 / 0.07 ( 4) link_NAG-ASN : angle 1.92963 / 1.15 ( 12) link_TRANS : bond 0.00107 / 0.06 ( 5) link_TRANS : angle 0.50875 / 0.37 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1482.46 seconds wall clock time: 26 minutes 26.92 seconds (1586.92 seconds total)