Starting phenix.real_space_refine on Wed Mar 4 01:37:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jmr_9850/03_2026/6jmr_9850.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jmr_9850/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6jmr_9850/03_2026/6jmr_9850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jmr_9850/03_2026/6jmr_9850.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6jmr_9850/03_2026/6jmr_9850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jmr_9850/03_2026/6jmr_9850.map" } 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-dev-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.23, per 1000 atoms: 0.23 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: 0.75 Conformation dependent library (CDL) restraints added in 387.1 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: 0.30 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: 1.48 Time building geometry restraints manager: 1.03 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: 5281 15.59 - 31.18: 650 31.18 - 46.77: 119 46.77 - 62.36: 23 62.36 - 77.95: 9 Dihedral angle restraints: 6082 sinusoidal: 2363 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 6079 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: 0.600 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.460 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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 : 14.096 77.952 3645 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 covalent geometry : bond 0.00659 (10028) covalent geometry : angle 1.05773 (13652) SS BOND : bond 0.00725 ( 8) SS BOND : angle 1.22626 ( 16) hydrogen bonds : bond 0.29337 ( 245) hydrogen bonds : angle 10.78227 ( 633) link_BETA1-4 : bond 0.02632 ( 1) link_BETA1-4 : angle 3.56857 ( 3) link_NAG-ASN : bond 0.00814 ( 4) link_NAG-ASN : angle 5.96459 ( 12) link_TRANS : bond 0.00344 ( 5) link_TRANS : angle 0.82220 ( 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 : 0.319 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: 0.1024 time to fit residues: 34.0707 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 : 0.342 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: E 13 GLN F 44 GLN F 95 GLN F 129 GLN F 150 ASN B 216 GLN B 267 ASN B 322 GLN B 395 ASN ** B 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.105256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.085450 restraints weight = 26421.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.087748 restraints weight = 16525.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.089374 restraints weight = 11931.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.090461 restraints weight = 9387.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.091218 restraints weight = 7898.104| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 10046 Z= 0.175 Angle : 0.766 10.288 13698 Z= 0.385 Chirality : 0.047 0.245 1572 Planarity : 0.006 0.106 1741 Dihedral : 7.386 53.173 1464 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % 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: -3.33 (0.21), residues: 1197 helix: -2.55 (0.34), residues: 146 sheet: -1.91 (0.23), residues: 403 loop : -2.32 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 439 TYR 0.023 0.002 TYR E 94 PHE 0.023 0.002 PHE F 103 TRP 0.013 0.001 TRP F 41 HIS 0.005 0.001 HIS B 538 Details of bonding type rmsd covalent geometry : bond 0.00406 (10028) covalent geometry : angle 0.75215 (13652) SS BOND : bond 0.00644 ( 8) SS BOND : angle 1.57455 ( 16) hydrogen bonds : bond 0.05035 ( 245) hydrogen bonds : angle 7.50570 ( 633) link_BETA1-4 : bond 0.00361 ( 1) link_BETA1-4 : angle 1.61606 ( 3) link_NAG-ASN : bond 0.00817 ( 4) link_NAG-ASN : angle 4.64494 ( 12) link_TRANS : bond 0.00072 ( 5) link_TRANS : angle 0.45530 ( 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 213 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.376 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 86 GLN cc_start: 0.7811 (mp10) cc_final: 0.7434 (mp10) REVERT: E 89 ASP cc_start: 0.7329 (m-30) cc_final: 0.6104 (p0) REVERT: E 154 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8255 (tm-30) REVERT: F 175 ASP cc_start: 0.8387 (p0) cc_final: 0.7636 (p0) REVERT: B 283 ASN cc_start: 0.8136 (m-40) cc_final: 0.7849 (t0) REVERT: B 300 LYS cc_start: 0.8804 (mttm) cc_final: 0.8553 (mmmt) REVERT: B 472 ILE cc_start: 0.9440 (mt) cc_final: 0.9209 (mp) REVERT: C 72 ASP cc_start: 0.8240 (t0) cc_final: 0.8032 (t0) REVERT: C 77 GLN cc_start: 0.8492 (pm20) cc_final: 0.8184 (pm20) REVERT: C 201 ASN cc_start: 0.6164 (m-40) cc_final: 0.5453 (m110) REVERT: D 89 LEU cc_start: 0.6772 (pt) cc_final: 0.6264 (tt) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.0937 time to fit residues: 27.9932 Evaluate side-chains 143 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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: 0.9980 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 93 optimal weight: 0.0370 chunk 45 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 202 ASN F 129 GLN 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 = 0.3741 r_free = 0.3741 target = 0.107984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.088180 restraints weight = 26779.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.090592 restraints weight = 16574.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.092270 restraints weight = 11863.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.093417 restraints weight = 9301.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.094231 restraints weight = 7781.464| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10046 Z= 0.137 Angle : 0.692 9.798 13698 Z= 0.346 Chirality : 0.046 0.220 1572 Planarity : 0.005 0.097 1741 Dihedral : 6.744 51.298 1464 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % 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: -2.89 (0.22), residues: 1197 helix: -2.02 (0.35), residues: 148 sheet: -1.47 (0.25), residues: 395 loop : -2.19 (0.21), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 603 TYR 0.019 0.002 TYR F 97 PHE 0.022 0.002 PHE F 103 TRP 0.045 0.002 TRP E 194 HIS 0.005 0.001 HIS B 619 Details of bonding type rmsd covalent geometry : bond 0.00318 (10028) covalent geometry : angle 0.68153 (13652) SS BOND : bond 0.00595 ( 8) SS BOND : angle 1.06250 ( 16) hydrogen bonds : bond 0.03927 ( 245) hydrogen bonds : angle 6.82479 ( 633) link_BETA1-4 : bond 0.00658 ( 1) link_BETA1-4 : angle 1.32747 ( 3) link_NAG-ASN : bond 0.00610 ( 4) link_NAG-ASN : angle 3.97559 ( 12) link_TRANS : bond 0.00070 ( 5) link_TRANS : angle 0.42821 ( 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 200 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 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: E 89 ASP cc_start: 0.7270 (m-30) cc_final: 0.6721 (m-30) REVERT: E 154 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8193 (tm-30) REVERT: E 181 TYR cc_start: 0.7915 (m-10) cc_final: 0.7668 (m-10) REVERT: F 175 ASP cc_start: 0.8530 (p0) cc_final: 0.7933 (p0) REVERT: F 193 ARG cc_start: 0.7001 (mtm180) cc_final: 0.6746 (mtm180) REVERT: B 300 LYS cc_start: 0.8771 (mttm) cc_final: 0.8497 (mmmt) REVERT: B 439 ARG cc_start: 0.7778 (mtp85) cc_final: 0.7578 (mtp85) REVERT: B 471 GLU cc_start: 0.8568 (pm20) cc_final: 0.8342 (pm20) REVERT: B 561 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7298 (mm-30) REVERT: C 48 LEU cc_start: 0.7947 (pp) cc_final: 0.7229 (mt) REVERT: C 77 GLN cc_start: 0.8479 (pm20) cc_final: 0.8106 (pm20) REVERT: C 213 LYS cc_start: 0.7946 (mmtt) cc_final: 0.7327 (mmmt) REVERT: D 48 GLN cc_start: 0.8842 (mp10) cc_final: 0.8478 (mp10) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.0953 time to fit residues: 26.6359 Evaluate side-chains 144 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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: 3.9990 chunk 70 optimal weight: 0.6980 chunk 13 optimal weight: 0.0470 chunk 52 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 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: 0.5980 overall best weight: 1.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.106733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.087171 restraints weight = 26898.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.089605 restraints weight = 16526.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.091287 restraints weight = 11716.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.092373 restraints weight = 9154.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.093169 restraints weight = 7691.386| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 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 0.046 10046 Z= 0.145 Angle : 0.680 9.911 13698 Z= 0.339 Chirality : 0.045 0.202 1572 Planarity : 0.005 0.093 1741 Dihedral : 6.443 50.326 1464 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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: -2.64 (0.22), residues: 1197 helix: -1.42 (0.39), residues: 141 sheet: -1.36 (0.26), residues: 380 loop : -2.09 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 92 TYR 0.019 0.002 TYR E 94 PHE 0.013 0.002 PHE E 152 TRP 0.010 0.001 TRP E 194 HIS 0.004 0.001 HIS B 619 Details of bonding type rmsd covalent geometry : bond 0.00340 (10028) covalent geometry : angle 0.67031 (13652) SS BOND : bond 0.00473 ( 8) SS BOND : angle 1.25448 ( 16) hydrogen bonds : bond 0.03581 ( 245) hydrogen bonds : angle 6.54699 ( 633) link_BETA1-4 : bond 0.00674 ( 1) link_BETA1-4 : angle 1.18309 ( 3) link_NAG-ASN : bond 0.00647 ( 4) link_NAG-ASN : angle 3.71906 ( 12) link_TRANS : bond 0.00095 ( 5) link_TRANS : angle 0.40680 ( 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 189 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.361 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: 0.8557 (tm-30) cc_final: 0.8274 (tm-30) REVERT: E 181 TYR cc_start: 0.7830 (m-10) cc_final: 0.7585 (m-10) REVERT: F 175 ASP cc_start: 0.8538 (p0) cc_final: 0.8033 (p0) REVERT: B 471 GLU cc_start: 0.8585 (pm20) cc_final: 0.8198 (pm20) REVERT: C 48 LEU cc_start: 0.7858 (pp) cc_final: 0.7095 (mt) REVERT: C 77 GLN cc_start: 0.8491 (pm20) cc_final: 0.8118 (pm20) REVERT: D 48 GLN cc_start: 0.8826 (mp10) cc_final: 0.8498 (mp10) REVERT: D 87 GLU cc_start: 0.7098 (pm20) cc_final: 0.6764 (pm20) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.0900 time to fit residues: 24.1281 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 : 0.249 ------------------------------------------------------------------------------- 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: 4.9990 chunk 62 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 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 = 0.3628 r_free = 0.3628 target = 0.100653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.080911 restraints weight = 27305.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.082992 restraints weight = 17810.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.084401 restraints weight = 13183.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.085372 restraints weight = 10651.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.085997 restraints weight = 9138.817| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 10046 Z= 0.282 Angle : 0.829 10.040 13698 Z= 0.413 Chirality : 0.051 0.236 1572 Planarity : 0.006 0.095 1741 Dihedral : 7.072 48.262 1464 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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: -2.74 (0.22), residues: 1197 helix: -1.59 (0.39), residues: 148 sheet: -1.58 (0.26), residues: 365 loop : -2.02 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 92 TYR 0.019 0.003 TYR D 55 PHE 0.029 0.003 PHE B 544 TRP 0.012 0.002 TRP B 219 HIS 0.007 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00644 (10028) covalent geometry : angle 0.82231 (13652) SS BOND : bond 0.00790 ( 8) SS BOND : angle 1.19585 ( 16) hydrogen bonds : bond 0.03968 ( 245) hydrogen bonds : angle 6.70892 ( 633) link_BETA1-4 : bond 0.00717 ( 1) link_BETA1-4 : angle 0.65305 ( 3) link_NAG-ASN : bond 0.00257 ( 4) link_NAG-ASN : angle 3.66419 ( 12) link_TRANS : bond 0.00168 ( 5) link_TRANS : angle 0.38250 ( 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 171 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 181 TYR cc_start: 0.7727 (m-10) cc_final: 0.7454 (m-10) REVERT: F 170 ASP cc_start: 0.8771 (p0) cc_final: 0.8542 (p0) REVERT: B 300 LYS cc_start: 0.9022 (mmmt) cc_final: 0.8579 (mtmt) REVERT: B 489 MET cc_start: 0.8435 (tpp) cc_final: 0.8083 (tpp) REVERT: C 77 GLN cc_start: 0.9013 (pm20) cc_final: 0.8459 (pm20) REVERT: C 213 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7549 (mmmt) REVERT: D 48 GLN cc_start: 0.8945 (mp10) cc_final: 0.8664 (mp10) REVERT: D 87 GLU cc_start: 0.7396 (pm20) cc_final: 0.6209 (mp0) REVERT: D 181 MET cc_start: 0.7840 (tpp) cc_final: 0.7391 (tpp) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.0931 time to fit residues: 22.3679 Evaluate side-chains 122 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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: 0.0670 chunk 28 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.105277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.085568 restraints weight = 26561.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.087872 restraints weight = 16687.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.089435 restraints weight = 12016.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.090486 restraints weight = 9498.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.091264 restraints weight = 8033.034| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10046 Z= 0.125 Angle : 0.683 10.458 13698 Z= 0.337 Chirality : 0.046 0.274 1572 Planarity : 0.005 0.088 1741 Dihedral : 6.434 50.637 1464 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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: -2.42 (0.23), residues: 1197 helix: -1.19 (0.42), residues: 147 sheet: -1.43 (0.27), residues: 349 loop : -1.81 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 92 TYR 0.015 0.002 TYR F 97 PHE 0.013 0.002 PHE B 345 TRP 0.010 0.001 TRP B 219 HIS 0.002 0.001 HIS B 619 Details of bonding type rmsd covalent geometry : bond 0.00293 (10028) covalent geometry : angle 0.67802 (13652) SS BOND : bond 0.00600 ( 8) SS BOND : angle 0.82867 ( 16) hydrogen bonds : bond 0.03313 ( 245) hydrogen bonds : angle 6.21409 ( 633) link_BETA1-4 : bond 0.00623 ( 1) link_BETA1-4 : angle 1.45723 ( 3) link_NAG-ASN : bond 0.00465 ( 4) link_NAG-ASN : angle 2.72609 ( 12) link_TRANS : bond 0.00081 ( 5) link_TRANS : angle 0.51889 ( 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 : 0.326 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 154 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8217 (tm-30) REVERT: F 170 ASP cc_start: 0.8595 (p0) cc_final: 0.8381 (p0) REVERT: F 193 ARG cc_start: 0.7280 (mtm180) cc_final: 0.6892 (mtm180) REVERT: B 248 LEU cc_start: 0.9143 (mm) cc_final: 0.8935 (mt) REVERT: B 300 LYS cc_start: 0.8754 (mmmt) cc_final: 0.8346 (mtmt) REVERT: B 452 LEU cc_start: 0.8936 (mt) cc_final: 0.8714 (mp) REVERT: B 489 MET cc_start: 0.8212 (tpp) cc_final: 0.7831 (tpp) REVERT: B 579 GLN cc_start: 0.7814 (tm-30) cc_final: 0.7245 (tm-30) REVERT: C 48 LEU cc_start: 0.7993 (pp) cc_final: 0.7207 (mt) REVERT: C 77 GLN cc_start: 0.8870 (pm20) cc_final: 0.8410 (pm20) REVERT: C 210 LYS cc_start: 0.7709 (tptp) cc_final: 0.7457 (tptp) REVERT: C 213 LYS cc_start: 0.8066 (mmtt) cc_final: 0.7837 (tptm) REVERT: D 48 GLN cc_start: 0.8839 (mp10) cc_final: 0.8586 (mp10) REVERT: D 87 GLU cc_start: 0.7128 (pm20) cc_final: 0.6386 (mm-30) REVERT: D 181 MET cc_start: 0.7774 (tpp) cc_final: 0.7483 (tpp) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.0912 time to fit residues: 23.6143 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 : 0.297 ------------------------------------------------------------------------------- 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: 0.8980 chunk 58 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 78 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3685 r_free = 0.3685 target = 0.104010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.084419 restraints weight = 26513.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.086685 restraints weight = 16714.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.088244 restraints weight = 12053.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.089277 restraints weight = 9530.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.090057 restraints weight = 8052.445| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10046 Z= 0.168 Angle : 0.703 10.864 13698 Z= 0.350 Chirality : 0.047 0.228 1572 Planarity : 0.005 0.093 1741 Dihedral : 6.396 49.541 1464 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: -2.36 (0.23), residues: 1197 helix: -0.93 (0.43), residues: 141 sheet: -1.40 (0.27), residues: 361 loop : -1.81 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 92 TYR 0.012 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 D 195 Details of bonding type rmsd covalent geometry : bond 0.00396 (10028) covalent geometry : angle 0.69869 (13652) SS BOND : bond 0.00654 ( 8) SS BOND : angle 1.33448 ( 16) hydrogen bonds : bond 0.03377 ( 245) hydrogen bonds : angle 6.14472 ( 633) link_BETA1-4 : bond 0.00611 ( 1) link_BETA1-4 : angle 0.90192 ( 3) link_NAG-ASN : bond 0.00215 ( 4) link_NAG-ASN : angle 2.53102 ( 12) link_TRANS : bond 0.00080 ( 5) link_TRANS : angle 0.50065 ( 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 176 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.373 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: 0.8553 (tm-30) cc_final: 0.8301 (tm-30) REVERT: F 170 ASP cc_start: 0.8731 (p0) cc_final: 0.8510 (p0) REVERT: F 193 ARG cc_start: 0.7141 (mtm180) cc_final: 0.6825 (mtm180) REVERT: B 300 LYS cc_start: 0.8809 (mmmt) cc_final: 0.8368 (mtmt) REVERT: B 413 GLU cc_start: 0.7389 (mm-30) cc_final: 0.6789 (mt-10) REVERT: B 439 ARG cc_start: 0.7746 (mtp85) cc_final: 0.7414 (mtp85) REVERT: B 579 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7334 (tm-30) REVERT: C 3 GLN cc_start: 0.7601 (mt0) cc_final: 0.7311 (mt0) REVERT: C 48 LEU cc_start: 0.8126 (pp) cc_final: 0.7371 (mt) REVERT: C 77 GLN cc_start: 0.8953 (pm20) cc_final: 0.8461 (pm20) REVERT: C 213 LYS cc_start: 0.8101 (mmtt) cc_final: 0.7535 (mmmt) REVERT: D 48 GLN cc_start: 0.8872 (mp10) cc_final: 0.8590 (mp10) REVERT: D 87 GLU cc_start: 0.7095 (pm20) cc_final: 0.6643 (mm-30) REVERT: D 181 MET cc_start: 0.7794 (tpp) cc_final: 0.7465 (tpp) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.0866 time to fit residues: 21.6294 Evaluate side-chains 130 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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: 0.6980 chunk 61 optimal weight: 0.0980 chunk 100 optimal weight: 7.9990 chunk 48 optimal weight: 0.0870 chunk 74 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 95 GLN B 542 HIS B 556 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.106250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.086541 restraints weight = 26166.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.088869 restraints weight = 16389.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.090463 restraints weight = 11710.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.091560 restraints weight = 9235.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.092262 restraints weight = 7748.668| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10046 Z= 0.128 Angle : 0.686 11.214 13698 Z= 0.338 Chirality : 0.046 0.224 1572 Planarity : 0.005 0.088 1741 Dihedral : 6.209 50.257 1464 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: -2.27 (0.23), residues: 1197 helix: -0.79 (0.43), residues: 141 sheet: -1.26 (0.28), residues: 343 loop : -1.81 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 216 TYR 0.014 0.002 TYR F 42 PHE 0.012 0.002 PHE E 80 TRP 0.010 0.001 TRP B 219 HIS 0.005 0.001 HIS B 538 Details of bonding type rmsd covalent geometry : bond 0.00305 (10028) covalent geometry : angle 0.68193 (13652) SS BOND : bond 0.00683 ( 8) SS BOND : angle 1.30643 ( 16) hydrogen bonds : bond 0.03311 ( 245) hydrogen bonds : angle 6.09540 ( 633) link_BETA1-4 : bond 0.00608 ( 1) link_BETA1-4 : angle 1.18569 ( 3) link_NAG-ASN : bond 0.00282 ( 4) link_NAG-ASN : angle 2.23760 ( 12) link_TRANS : bond 0.00050 ( 5) link_TRANS : angle 0.49664 ( 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 176 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.241 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 86 GLN cc_start: 0.7973 (mp10) cc_final: 0.7625 (mp10) REVERT: E 89 ASP cc_start: 0.7819 (m-30) cc_final: 0.5846 (p0) REVERT: E 154 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8252 (tm-30) REVERT: F 193 ARG cc_start: 0.7034 (mtm180) cc_final: 0.6693 (mtm110) REVERT: B 300 LYS cc_start: 0.8731 (mmmt) cc_final: 0.8329 (mtmt) REVERT: B 413 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6647 (mt-10) REVERT: B 439 ARG cc_start: 0.7631 (mtp85) cc_final: 0.7381 (mtp85) REVERT: B 449 LEU cc_start: 0.9012 (mp) cc_final: 0.8778 (mp) REVERT: B 489 MET cc_start: 0.8294 (tpp) cc_final: 0.7798 (tpp) REVERT: B 579 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7257 (tm-30) REVERT: C 3 GLN cc_start: 0.7367 (mt0) cc_final: 0.7006 (mt0) REVERT: C 48 LEU cc_start: 0.7985 (pp) cc_final: 0.7196 (mt) REVERT: C 77 GLN cc_start: 0.8848 (pm20) cc_final: 0.8399 (pm20) REVERT: C 164 LEU cc_start: 0.7776 (mp) cc_final: 0.7485 (tp) REVERT: C 210 LYS cc_start: 0.7725 (tptp) cc_final: 0.7435 (tptp) REVERT: C 213 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7531 (mmmt) REVERT: D 48 GLN cc_start: 0.8822 (mp10) cc_final: 0.8562 (mp10) REVERT: D 87 GLU cc_start: 0.7196 (pm20) cc_final: 0.6757 (mm-30) REVERT: D 181 MET cc_start: 0.7749 (tpp) cc_final: 0.7440 (tpp) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.0831 time to fit residues: 20.8885 Evaluate side-chains 136 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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: 10.0000 chunk 70 optimal weight: 0.0010 chunk 22 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 67 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 65 optimal weight: 0.0020 chunk 24 optimal weight: 0.0570 overall best weight: 0.3312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 35 HIS F 34 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.108142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.088631 restraints weight = 25744.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.091006 restraints weight = 15954.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.092636 restraints weight = 11309.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.093733 restraints weight = 8824.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.094482 restraints weight = 7391.874| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10046 Z= 0.112 Angle : 0.668 11.411 13698 Z= 0.332 Chirality : 0.045 0.217 1572 Planarity : 0.005 0.092 1741 Dihedral : 5.893 50.792 1464 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.09 % Allowed : 0.19 % Favored : 99.72 % 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: -2.11 (0.23), residues: 1197 helix: -0.57 (0.44), residues: 141 sheet: -1.17 (0.27), residues: 353 loop : -1.72 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 534 TYR 0.014 0.001 TYR E 100 PHE 0.019 0.001 PHE B 458 TRP 0.013 0.001 TRP C 108 HIS 0.013 0.001 HIS B 538 Details of bonding type rmsd covalent geometry : bond 0.00262 (10028) covalent geometry : angle 0.66483 (13652) SS BOND : bond 0.00495 ( 8) SS BOND : angle 1.10777 ( 16) hydrogen bonds : bond 0.03181 ( 245) hydrogen bonds : angle 5.86692 ( 633) link_BETA1-4 : bond 0.00791 ( 1) link_BETA1-4 : angle 1.34887 ( 3) link_NAG-ASN : bond 0.00336 ( 4) link_NAG-ASN : angle 2.08737 ( 12) link_TRANS : bond 0.00042 ( 5) link_TRANS : angle 0.50751 ( 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 187 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 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: symmetry clash REVERT: E 46 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6313 (mm-30) REVERT: E 89 ASP cc_start: 0.7783 (m-30) cc_final: 0.6000 (p0) REVERT: E 154 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8204 (tm-30) REVERT: F 193 ARG cc_start: 0.6932 (mtm180) cc_final: 0.6385 (mtm180) REVERT: B 413 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6579 (mt-10) REVERT: B 439 ARG cc_start: 0.7556 (mtp85) cc_final: 0.7345 (mtp85) REVERT: B 579 GLN cc_start: 0.7627 (tm-30) cc_final: 0.7095 (tm-30) REVERT: C 3 GLN cc_start: 0.7447 (mt0) cc_final: 0.7191 (mt0) REVERT: C 48 LEU cc_start: 0.7927 (pp) cc_final: 0.7144 (mt) REVERT: C 77 GLN cc_start: 0.8681 (pm20) cc_final: 0.8074 (pm20) REVERT: C 164 LEU cc_start: 0.7736 (mp) cc_final: 0.7408 (tp) REVERT: C 210 LYS cc_start: 0.7690 (tptp) cc_final: 0.7418 (tptp) REVERT: C 213 LYS cc_start: 0.8081 (mmtt) cc_final: 0.7563 (mmmt) REVERT: D 87 GLU cc_start: 0.7218 (pm20) cc_final: 0.6423 (mm-30) REVERT: D 130 GLN cc_start: 0.8635 (tt0) cc_final: 0.7974 (tt0) REVERT: D 181 MET cc_start: 0.7732 (tpp) cc_final: 0.7431 (tpp) outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.0913 time to fit residues: 24.1079 Evaluate side-chains 136 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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: 3.9990 chunk 57 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 GLN ** F 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.104674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.085010 restraints weight = 26296.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.087278 restraints weight = 16664.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.088812 restraints weight = 12030.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.089875 restraints weight = 9518.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.090625 restraints weight = 8018.720| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10046 Z= 0.177 Angle : 0.721 11.291 13698 Z= 0.359 Chirality : 0.047 0.204 1572 Planarity : 0.005 0.090 1741 Dihedral : 6.182 49.619 1464 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % 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: -2.10 (0.24), residues: 1197 helix: -0.57 (0.44), residues: 141 sheet: -1.29 (0.28), residues: 346 loop : -1.64 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 374 TYR 0.014 0.002 TYR B 468 PHE 0.019 0.002 PHE E 80 TRP 0.026 0.002 TRP E 36 HIS 0.010 0.002 HIS F 203 Details of bonding type rmsd covalent geometry : bond 0.00415 (10028) covalent geometry : angle 0.71808 (13652) SS BOND : bond 0.00571 ( 8) SS BOND : angle 1.21734 ( 16) hydrogen bonds : bond 0.03517 ( 245) hydrogen bonds : angle 5.96167 ( 633) link_BETA1-4 : bond 0.00592 ( 1) link_BETA1-4 : angle 0.75072 ( 3) link_NAG-ASN : bond 0.00110 ( 4) link_NAG-ASN : angle 2.13309 ( 12) link_TRANS : bond 0.00091 ( 5) link_TRANS : angle 0.44364 ( 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 163 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.349 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 46 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6817 (mm-30) REVERT: E 89 ASP cc_start: 0.7680 (m-30) cc_final: 0.5753 (p0) REVERT: B 413 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6516 (mt-10) REVERT: B 579 GLN cc_start: 0.7731 (tm-30) cc_final: 0.7225 (tm-30) REVERT: C 3 GLN cc_start: 0.7511 (mt0) cc_final: 0.7161 (mt0) REVERT: C 48 LEU cc_start: 0.8102 (pp) cc_final: 0.7315 (mt) REVERT: C 77 GLN cc_start: 0.8807 (pm20) cc_final: 0.8205 (pm20) REVERT: C 164 LEU cc_start: 0.7784 (mp) cc_final: 0.7442 (tp) REVERT: C 210 LYS cc_start: 0.7685 (tptp) cc_final: 0.7356 (tptp) REVERT: C 213 LYS cc_start: 0.8083 (mmtt) cc_final: 0.7533 (mmmt) REVERT: D 87 GLU cc_start: 0.7298 (pm20) cc_final: 0.6803 (mm-30) REVERT: D 181 MET cc_start: 0.7769 (tpp) cc_final: 0.7430 (tpp) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.0845 time to fit residues: 19.5652 Evaluate side-chains 124 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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: 9.9990 chunk 66 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 0.0870 chunk 7 optimal weight: 3.9990 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 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 = 0.3660 r_free = 0.3660 target = 0.102802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.083109 restraints weight = 26905.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.085300 restraints weight = 17095.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.086833 restraints weight = 12425.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.087794 restraints weight = 9862.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.088584 restraints weight = 8420.936| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 10046 Z= 0.209 Angle : 0.760 11.636 13698 Z= 0.379 Chirality : 0.048 0.195 1572 Planarity : 0.006 0.091 1741 Dihedral : 6.442 49.111 1464 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: -2.28 (0.24), residues: 1197 helix: -0.88 (0.43), residues: 143 sheet: -1.45 (0.27), residues: 351 loop : -1.69 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 374 TYR 0.017 0.002 TYR B 468 PHE 0.023 0.002 PHE B 544 TRP 0.026 0.002 TRP E 36 HIS 0.020 0.003 HIS B 538 Details of bonding type rmsd covalent geometry : bond 0.00489 (10028) covalent geometry : angle 0.75746 (13652) SS BOND : bond 0.00661 ( 8) SS BOND : angle 1.25378 ( 16) hydrogen bonds : bond 0.03679 ( 245) hydrogen bonds : angle 6.10571 ( 633) link_BETA1-4 : bond 0.00416 ( 1) link_BETA1-4 : angle 0.64689 ( 3) link_NAG-ASN : bond 0.00087 ( 4) link_NAG-ASN : angle 2.08279 ( 12) link_TRANS : bond 0.00122 ( 5) link_TRANS : angle 0.43659 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1440.33 seconds wall clock time: 25 minutes 46.21 seconds (1546.21 seconds total)