Starting phenix.real_space_refine on Mon Jul 28 01:41:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jmr_9850/07_2025/6jmr_9850.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jmr_9850/07_2025/6jmr_9850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6jmr_9850/07_2025/6jmr_9850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jmr_9850/07_2025/6jmr_9850.map" model { file = "/net/cci-nas-00/data/ceres_data/6jmr_9850/07_2025/6jmr_9850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jmr_9850/07_2025/6jmr_9850.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.82, per 1000 atoms: 0.59 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: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.26 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: 3.19 Time building geometry restraints manager: 2.80 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.820 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.480 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.026 0.002 TRP E 47 HIS 0.010 0.003 HIS B 538 PHE 0.020 0.003 PHE B 551 TYR 0.023 0.003 TYR F 42 ARG 0.010 0.001 ARG B 211 Details of bonding type rmsd link_TRANS : bond 0.00344 ( 5) link_TRANS : angle 0.82220 ( 15) link_NAG-ASN : bond 0.00814 ( 4) link_NAG-ASN : angle 5.96459 ( 12) link_BETA1-4 : bond 0.02632 ( 1) link_BETA1-4 : angle 3.56857 ( 3) hydrogen bonds : bond 0.29337 ( 245) hydrogen bonds : angle 10.78227 ( 633) SS BOND : bond 0.00725 ( 8) SS BOND : angle 1.22626 ( 16) covalent geometry : bond 0.00659 (10028) covalent geometry : angle 1.05773 (13652) *********************** 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 : 1.056 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: symmetry clash REVERT: E 81 LYS cc_start: 0.7338 (mppt) cc_final: 0.7060 (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: 0.7914 (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: 0.8395 (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: 0.8355 (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: 0.7451 (t80) REVERT: B 579 GLN cc_start: 0.8417 (tm-30) cc_final: 0.7517 (tm-30) REVERT: C 2 VAL cc_start: 0.6445 (OUTLIER) cc_final: 0.6041 (m) 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: 0.6110 (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: 0.7636 (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: 0.8739 (tp) outliers start: 6 outliers final: 3 residues processed: 247 average time/residue: 0.2543 time to fit residues: 84.1273 Evaluate side-chains 148 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0970 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 529 GLN ** B 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.106575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.086845 restraints weight = 26115.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.089203 restraints weight = 16080.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.090875 restraints weight = 11493.632| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10046 Z= 0.152 Angle : 0.745 10.315 13698 Z= 0.374 Chirality : 0.047 0.243 1572 Planarity : 0.006 0.105 1741 Dihedral : 7.244 52.918 1464 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.21), residues: 1197 helix: -2.55 (0.34), residues: 146 sheet: -1.89 (0.23), residues: 394 loop : -2.24 (0.21), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 41 HIS 0.004 0.001 HIS C 204 PHE 0.024 0.002 PHE F 103 TYR 0.021 0.002 TYR E 94 ARG 0.006 0.001 ARG B 439 Details of bonding type rmsd link_TRANS : bond 0.00068 ( 5) link_TRANS : angle 0.50637 ( 15) link_NAG-ASN : bond 0.00855 ( 4) link_NAG-ASN : angle 4.52813 ( 12) link_BETA1-4 : bond 0.00682 ( 1) link_BETA1-4 : angle 1.72329 ( 3) hydrogen bonds : bond 0.04652 ( 245) hydrogen bonds : angle 7.40557 ( 633) SS BOND : bond 0.00567 ( 8) SS BOND : angle 1.39509 ( 16) covalent geometry : bond 0.00354 (10028) covalent geometry : angle 0.73180 (13652) *********************** 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 228 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 1.159 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: E 86 GLN cc_start: 0.7795 (mp10) cc_final: 0.7582 (mp10) REVERT: E 154 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8196 (tm-30) REVERT: F 175 ASP cc_start: 0.8381 (p0) cc_final: 0.7643 (p0) REVERT: B 283 ASN cc_start: 0.8030 (m-40) cc_final: 0.7808 (t0) REVERT: B 300 LYS cc_start: 0.8799 (mttm) cc_final: 0.8547 (mmmt) REVERT: B 471 GLU cc_start: 0.8016 (pm20) cc_final: 0.7786 (pm20) REVERT: B 472 ILE cc_start: 0.9419 (mt) cc_final: 0.9109 (mp) REVERT: C 48 LEU cc_start: 0.8038 (pp) cc_final: 0.7283 (mt) REVERT: C 72 ASP cc_start: 0.8236 (t0) cc_final: 0.8034 (t0) REVERT: C 77 GLN cc_start: 0.8439 (pm20) cc_final: 0.8127 (pm20) REVERT: C 201 ASN cc_start: 0.6135 (m-40) cc_final: 0.5400 (m110) REVERT: D 89 LEU cc_start: 0.6732 (pt) cc_final: 0.6225 (tt) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2686 time to fit residues: 85.6534 Evaluate side-chains 149 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 52 optimal weight: 0.0000 chunk 23 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.105971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.085949 restraints weight = 26683.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.088248 restraints weight = 16766.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.089895 restraints weight = 12140.294| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10046 Z= 0.148 Angle : 0.693 10.134 13698 Z= 0.348 Chirality : 0.046 0.214 1572 Planarity : 0.005 0.097 1741 Dihedral : 6.788 51.160 1464 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.22), residues: 1197 helix: -1.85 (0.36), residues: 141 sheet: -1.49 (0.24), residues: 396 loop : -2.22 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 433 HIS 0.004 0.001 HIS B 538 PHE 0.016 0.002 PHE E 80 TYR 0.015 0.002 TYR F 97 ARG 0.004 0.000 ARG B 603 Details of bonding type rmsd link_TRANS : bond 0.00076 ( 5) link_TRANS : angle 0.39608 ( 15) link_NAG-ASN : bond 0.00612 ( 4) link_NAG-ASN : angle 4.04703 ( 12) link_BETA1-4 : bond 0.00572 ( 1) link_BETA1-4 : angle 1.32579 ( 3) hydrogen bonds : bond 0.04015 ( 245) hydrogen bonds : angle 6.97074 ( 633) SS BOND : bond 0.00584 ( 8) SS BOND : angle 1.18626 ( 16) covalent geometry : bond 0.00343 (10028) covalent geometry : angle 0.68209 (13652) *********************** 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 207 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.026 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 89 ASP cc_start: 0.7215 (m-30) cc_final: 0.6871 (m-30) REVERT: E 154 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8215 (tm-30) REVERT: E 181 TYR cc_start: 0.7805 (m-10) cc_final: 0.7567 (m-10) REVERT: F 175 ASP cc_start: 0.8461 (p0) cc_final: 0.7852 (p0) REVERT: F 193 ARG cc_start: 0.7012 (mtm180) cc_final: 0.6763 (mtm180) REVERT: B 300 LYS cc_start: 0.8769 (mttm) cc_final: 0.8498 (mmmt) REVERT: C 48 LEU cc_start: 0.8011 (pp) cc_final: 0.7314 (mt) REVERT: C 77 GLN cc_start: 0.8488 (pm20) cc_final: 0.8187 (pm20) REVERT: C 164 LEU cc_start: 0.7784 (mp) cc_final: 0.7362 (tp) REVERT: C 213 LYS cc_start: 0.7957 (mmtt) cc_final: 0.7348 (mmmt) REVERT: D 48 GLN cc_start: 0.8850 (mp10) cc_final: 0.8536 (mp10) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2286 time to fit residues: 65.3482 Evaluate side-chains 142 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 35 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 26 optimal weight: 0.0070 chunk 110 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 65 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 overall best weight: 1.9204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.104148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.085014 restraints weight = 26921.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.087137 restraints weight = 17536.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.088605 restraints weight = 12934.946| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 10046 Z= 0.211 Angle : 0.745 9.772 13698 Z= 0.372 Chirality : 0.047 0.218 1572 Planarity : 0.006 0.093 1741 Dihedral : 6.789 49.440 1464 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.22), residues: 1197 helix: -1.49 (0.38), residues: 142 sheet: -1.42 (0.25), residues: 380 loop : -2.19 (0.21), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP E 194 HIS 0.006 0.001 HIS B 619 PHE 0.021 0.002 PHE B 544 TYR 0.016 0.002 TYR F 97 ARG 0.004 0.000 ARG C 38 Details of bonding type rmsd link_TRANS : bond 0.00138 ( 5) link_TRANS : angle 0.38171 ( 15) link_NAG-ASN : bond 0.00472 ( 4) link_NAG-ASN : angle 3.86877 ( 12) link_BETA1-4 : bond 0.00097 ( 1) link_BETA1-4 : angle 0.95995 ( 3) hydrogen bonds : bond 0.03797 ( 245) hydrogen bonds : angle 6.66593 ( 633) SS BOND : bond 0.00425 ( 8) SS BOND : angle 1.09018 ( 16) covalent geometry : bond 0.00485 (10028) covalent geometry : angle 0.73668 (13652) *********************** 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 186 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 89 ASP cc_start: 0.7624 (m-30) cc_final: 0.7118 (m-30) REVERT: E 154 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8345 (tm-30) REVERT: E 181 TYR cc_start: 0.7631 (m-10) cc_final: 0.7335 (m-10) REVERT: F 170 ASP cc_start: 0.8549 (p0) cc_final: 0.8332 (p0) REVERT: F 193 ARG cc_start: 0.7109 (mtm180) cc_final: 0.6895 (mtm180) REVERT: B 300 LYS cc_start: 0.8856 (mttm) cc_final: 0.8511 (mmmt) REVERT: C 48 LEU cc_start: 0.8083 (pp) cc_final: 0.7357 (mt) REVERT: C 77 GLN cc_start: 0.8792 (pm20) cc_final: 0.8392 (pm20) REVERT: C 164 LEU cc_start: 0.7737 (mp) cc_final: 0.7321 (tp) REVERT: D 48 GLN cc_start: 0.8926 (mp10) cc_final: 0.8644 (mp10) REVERT: D 87 GLU cc_start: 0.7244 (pm20) cc_final: 0.6883 (pm20) REVERT: D 181 MET cc_start: 0.7894 (tpp) cc_final: 0.7676 (tpp) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.3004 time to fit residues: 79.4000 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 : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 17 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 46 optimal weight: 0.0670 chunk 8 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 97 optimal weight: 0.1980 chunk 99 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 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 = 0.3707 r_free = 0.3707 target = 0.105783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.086238 restraints weight = 26600.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.088594 restraints weight = 16594.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.090189 restraints weight = 11903.202| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10046 Z= 0.141 Angle : 0.685 10.288 13698 Z= 0.339 Chirality : 0.047 0.304 1572 Planarity : 0.005 0.091 1741 Dihedral : 6.543 49.996 1464 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.23), residues: 1197 helix: -1.17 (0.41), residues: 142 sheet: -1.36 (0.26), residues: 379 loop : -1.98 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 194 HIS 0.003 0.001 HIS B 619 PHE 0.015 0.002 PHE B 345 TYR 0.016 0.002 TYR F 42 ARG 0.004 0.000 ARG B 534 Details of bonding type rmsd link_TRANS : bond 0.00091 ( 5) link_TRANS : angle 0.42814 ( 15) link_NAG-ASN : bond 0.00369 ( 4) link_NAG-ASN : angle 3.92306 ( 12) link_BETA1-4 : bond 0.00660 ( 1) link_BETA1-4 : angle 1.10532 ( 3) hydrogen bonds : bond 0.03406 ( 245) hydrogen bonds : angle 6.36725 ( 633) SS BOND : bond 0.00535 ( 8) SS BOND : angle 0.96018 ( 16) covalent geometry : bond 0.00331 (10028) covalent geometry : angle 0.67468 (13652) *********************** 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 197 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.064 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 154 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8293 (tm-30) REVERT: E 181 TYR cc_start: 0.7516 (m-10) cc_final: 0.7285 (m-10) REVERT: F 41 TRP cc_start: 0.8252 (m100) cc_final: 0.7788 (m100) REVERT: F 170 ASP cc_start: 0.8617 (p0) cc_final: 0.8405 (p0) REVERT: B 468 TYR cc_start: 0.8788 (p90) cc_final: 0.8572 (p90) REVERT: B 471 GLU cc_start: 0.8594 (pm20) cc_final: 0.8200 (pm20) REVERT: B 472 ILE cc_start: 0.9416 (mp) cc_final: 0.9059 (mp) REVERT: B 489 MET cc_start: 0.8215 (tpp) cc_final: 0.7996 (tpp) REVERT: C 48 LEU cc_start: 0.7947 (pp) cc_final: 0.7281 (mt) REVERT: C 77 GLN cc_start: 0.8825 (pm20) cc_final: 0.8352 (pm20) REVERT: C 164 LEU cc_start: 0.7692 (mp) cc_final: 0.7292 (tp) REVERT: D 48 GLN cc_start: 0.8862 (mp10) cc_final: 0.8603 (mp10) REVERT: D 181 MET cc_start: 0.7869 (tpp) cc_final: 0.7621 (tpp) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2216 time to fit residues: 60.5981 Evaluate side-chains 148 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 48 optimal weight: 0.2980 chunk 50 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 4 optimal weight: 0.0000 chunk 39 optimal weight: 1.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 HIS B 556 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.106869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.087878 restraints weight = 26578.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.090091 restraints weight = 17085.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.091614 restraints weight = 12483.853| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10046 Z= 0.133 Angle : 0.675 10.762 13698 Z= 0.336 Chirality : 0.046 0.248 1572 Planarity : 0.005 0.091 1741 Dihedral : 6.412 50.134 1464 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.23), residues: 1197 helix: -1.16 (0.41), residues: 147 sheet: -1.19 (0.27), residues: 346 loop : -1.92 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 219 HIS 0.006 0.001 HIS B 542 PHE 0.015 0.001 PHE E 152 TYR 0.014 0.002 TYR C 94 ARG 0.015 0.001 ARG C 92 Details of bonding type rmsd link_TRANS : bond 0.00069 ( 5) link_TRANS : angle 0.45352 ( 15) link_NAG-ASN : bond 0.00307 ( 4) link_NAG-ASN : angle 2.84466 ( 12) link_BETA1-4 : bond 0.00687 ( 1) link_BETA1-4 : angle 1.14909 ( 3) hydrogen bonds : bond 0.03356 ( 245) hydrogen bonds : angle 6.34278 ( 633) SS BOND : bond 0.00638 ( 8) SS BOND : angle 1.08594 ( 16) covalent geometry : bond 0.00312 (10028) covalent geometry : angle 0.66908 (13652) *********************** 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 197 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.101 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 154 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8151 (tm-30) REVERT: F 66 ASP cc_start: 0.8375 (t0) cc_final: 0.8102 (p0) REVERT: F 170 ASP cc_start: 0.8546 (p0) cc_final: 0.8323 (p0) REVERT: F 180 MET cc_start: 0.8678 (mmm) cc_final: 0.8467 (mmm) REVERT: B 300 LYS cc_start: 0.8952 (mmmt) cc_final: 0.8573 (mtmt) REVERT: B 471 GLU cc_start: 0.8383 (pm20) cc_final: 0.8007 (pm20) REVERT: B 472 ILE cc_start: 0.9446 (mp) cc_final: 0.9066 (mp) REVERT: B 489 MET cc_start: 0.8288 (tpp) cc_final: 0.7999 (tpp) REVERT: C 48 LEU cc_start: 0.7889 (pp) cc_final: 0.7195 (mt) REVERT: C 77 GLN cc_start: 0.8782 (pm20) cc_final: 0.8419 (pm20) REVERT: C 164 LEU cc_start: 0.7576 (mp) cc_final: 0.7204 (tp) REVERT: C 213 LYS cc_start: 0.8021 (mmtt) cc_final: 0.7618 (mmtt) REVERT: D 48 GLN cc_start: 0.8863 (mp10) cc_final: 0.8624 (mp10) REVERT: D 87 GLU cc_start: 0.7284 (pm20) cc_final: 0.6555 (mp0) REVERT: D 181 MET cc_start: 0.7884 (tpp) cc_final: 0.7654 (tpp) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2165 time to fit residues: 59.5481 Evaluate side-chains 146 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 102 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 98 optimal weight: 0.3980 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 13 GLN ** F 34 ASN ** 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 = 0.3661 r_free = 0.3661 target = 0.102676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.082671 restraints weight = 26635.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.084935 restraints weight = 16847.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.086503 restraints weight = 12168.787| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 10046 Z= 0.198 Angle : 0.732 10.712 13698 Z= 0.365 Chirality : 0.048 0.213 1572 Planarity : 0.005 0.092 1741 Dihedral : 6.503 48.958 1464 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.23), residues: 1197 helix: -1.07 (0.42), residues: 142 sheet: -1.37 (0.26), residues: 369 loop : -1.85 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 56 HIS 0.004 0.002 HIS E 35 PHE 0.023 0.002 PHE B 544 TYR 0.015 0.002 TYR B 468 ARG 0.007 0.001 ARG C 92 Details of bonding type rmsd link_TRANS : bond 0.00112 ( 5) link_TRANS : angle 0.41285 ( 15) link_NAG-ASN : bond 0.00113 ( 4) link_NAG-ASN : angle 2.65178 ( 12) link_BETA1-4 : bond 0.00627 ( 1) link_BETA1-4 : angle 0.73732 ( 3) hydrogen bonds : bond 0.03487 ( 245) hydrogen bonds : angle 6.28759 ( 633) SS BOND : bond 0.00511 ( 8) SS BOND : angle 1.08690 ( 16) covalent geometry : bond 0.00461 (10028) covalent geometry : angle 0.72777 (13652) *********************** 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 191 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 154 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8275 (tm-30) REVERT: F 170 ASP cc_start: 0.8736 (p0) cc_final: 0.8517 (p0) REVERT: F 193 ARG cc_start: 0.7173 (mtm180) cc_final: 0.6822 (mtm180) REVERT: B 300 LYS cc_start: 0.9081 (mmmt) cc_final: 0.8613 (mtmt) REVERT: B 489 MET cc_start: 0.8318 (tpp) cc_final: 0.8079 (tpp) REVERT: B 579 GLN cc_start: 0.7731 (tm-30) cc_final: 0.7192 (tm-30) REVERT: C 3 GLN cc_start: 0.7523 (mt0) cc_final: 0.7222 (mt0) REVERT: C 48 LEU cc_start: 0.8149 (pp) cc_final: 0.7460 (mt) REVERT: C 77 GLN cc_start: 0.8965 (pm20) cc_final: 0.8445 (pm20) REVERT: C 164 LEU cc_start: 0.7795 (mp) cc_final: 0.7418 (tp) REVERT: C 213 LYS cc_start: 0.8126 (mmtt) cc_final: 0.7671 (mmtt) REVERT: D 48 GLN cc_start: 0.8888 (mp10) cc_final: 0.8563 (mp10) REVERT: D 87 GLU cc_start: 0.7571 (pm20) cc_final: 0.6605 (mm-30) REVERT: D 181 MET cc_start: 0.7853 (tpp) cc_final: 0.7559 (tpp) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2436 time to fit residues: 64.6311 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 : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 66 optimal weight: 0.0970 chunk 0 optimal weight: 5.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 HIS ** 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 = 0.3668 r_free = 0.3668 target = 0.103262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.083314 restraints weight = 26743.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.085482 restraints weight = 16978.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.087050 restraints weight = 12380.556| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10046 Z= 0.181 Angle : 0.716 11.171 13698 Z= 0.358 Chirality : 0.048 0.227 1572 Planarity : 0.005 0.089 1741 Dihedral : 6.392 49.363 1464 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.23), residues: 1197 helix: -0.88 (0.43), residues: 141 sheet: -1.47 (0.27), residues: 363 loop : -1.83 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP F 168 HIS 0.011 0.002 HIS F 203 PHE 0.018 0.002 PHE B 544 TYR 0.016 0.002 TYR F 145 ARG 0.004 0.001 ARG C 38 Details of bonding type rmsd link_TRANS : bond 0.00087 ( 5) link_TRANS : angle 0.50806 ( 15) link_NAG-ASN : bond 0.00098 ( 4) link_NAG-ASN : angle 2.38899 ( 12) link_BETA1-4 : bond 0.00655 ( 1) link_BETA1-4 : angle 0.79912 ( 3) hydrogen bonds : bond 0.03422 ( 245) hydrogen bonds : angle 6.25703 ( 633) SS BOND : bond 0.00521 ( 8) SS BOND : angle 1.05795 ( 16) covalent geometry : bond 0.00424 (10028) covalent geometry : angle 0.71256 (13652) *********************** 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 189 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.076 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 89 ASP cc_start: 0.7426 (m-30) cc_final: 0.5621 (p0) REVERT: E 154 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8340 (tm-30) REVERT: E 181 TYR cc_start: 0.7665 (m-10) cc_final: 0.7455 (m-10) REVERT: F 170 ASP cc_start: 0.8718 (p0) cc_final: 0.8508 (p0) REVERT: F 180 MET cc_start: 0.8851 (tpt) cc_final: 0.8646 (tpt) REVERT: F 193 ARG cc_start: 0.7104 (mtm180) cc_final: 0.6779 (mtm180) REVERT: B 300 LYS cc_start: 0.9013 (mmmt) cc_final: 0.8539 (mtmt) REVERT: B 413 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6664 (mt-10) REVERT: B 471 GLU cc_start: 0.8258 (pm20) cc_final: 0.7980 (pm20) REVERT: B 489 MET cc_start: 0.8417 (tpp) cc_final: 0.7879 (tpp) REVERT: B 579 GLN cc_start: 0.7797 (tm-30) cc_final: 0.7332 (tm-30) REVERT: C 3 GLN cc_start: 0.7548 (mt0) cc_final: 0.7203 (mt0) REVERT: C 48 LEU cc_start: 0.8115 (pp) cc_final: 0.7445 (mt) REVERT: C 77 GLN cc_start: 0.8944 (pm20) cc_final: 0.8466 (pm20) REVERT: C 164 LEU cc_start: 0.7838 (mp) cc_final: 0.7454 (tp) REVERT: C 213 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7677 (mmtt) REVERT: D 48 GLN cc_start: 0.8870 (mp10) cc_final: 0.8580 (mp10) REVERT: D 87 GLU cc_start: 0.7365 (pm20) cc_final: 0.6818 (mm-30) REVERT: D 181 MET cc_start: 0.7881 (tpp) cc_final: 0.7562 (tpp) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2252 time to fit residues: 59.2592 Evaluate side-chains 140 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 42 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 74 optimal weight: 0.0570 chunk 54 optimal weight: 0.0570 chunk 85 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 98 optimal weight: 0.0470 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.107158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.087411 restraints weight = 26117.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.089758 restraints weight = 16396.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.091360 restraints weight = 11806.034| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10046 Z= 0.111 Angle : 0.664 11.094 13698 Z= 0.328 Chirality : 0.045 0.222 1572 Planarity : 0.005 0.090 1741 Dihedral : 5.891 50.886 1464 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % 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 : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.23), residues: 1197 helix: -0.76 (0.44), residues: 141 sheet: -1.12 (0.28), residues: 352 loop : -1.75 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP F 168 HIS 0.009 0.001 HIS F 203 PHE 0.017 0.001 PHE D 141 TYR 0.013 0.001 TYR F 31 ARG 0.003 0.000 ARG C 38 Details of bonding type rmsd link_TRANS : bond 0.00055 ( 5) link_TRANS : angle 0.52314 ( 15) link_NAG-ASN : bond 0.00477 ( 4) link_NAG-ASN : angle 2.09999 ( 12) link_BETA1-4 : bond 0.00740 ( 1) link_BETA1-4 : angle 1.47912 ( 3) hydrogen bonds : bond 0.03232 ( 245) hydrogen bonds : angle 6.05532 ( 633) SS BOND : bond 0.00442 ( 8) SS BOND : angle 0.81430 ( 16) covalent geometry : bond 0.00258 (10028) covalent geometry : angle 0.66086 (13652) *********************** 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 210 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.627 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 72 ASP cc_start: 0.7647 (m-30) cc_final: 0.7328 (t0) REVERT: E 89 ASP cc_start: 0.7502 (m-30) cc_final: 0.5708 (p0) REVERT: E 154 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8149 (tm-30) REVERT: E 181 TYR cc_start: 0.7638 (m-10) cc_final: 0.7371 (m-10) REVERT: F 189 ASP cc_start: 0.8243 (p0) cc_final: 0.7885 (p0) REVERT: B 300 LYS cc_start: 0.8817 (mmmt) cc_final: 0.8508 (mttt) REVERT: B 413 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6503 (mt-10) REVERT: B 452 LEU cc_start: 0.8894 (mt) cc_final: 0.8604 (mp) REVERT: B 579 GLN cc_start: 0.7783 (tm-30) cc_final: 0.7308 (tm-30) REVERT: C 3 GLN cc_start: 0.7490 (mt0) cc_final: 0.7101 (mt0) REVERT: C 48 LEU cc_start: 0.7939 (pp) cc_final: 0.7274 (mt) REVERT: C 77 GLN cc_start: 0.8737 (pm20) cc_final: 0.8351 (pm20) REVERT: C 164 LEU cc_start: 0.7813 (mp) cc_final: 0.7363 (tp) REVERT: C 213 LYS cc_start: 0.8087 (mmtt) cc_final: 0.7666 (mmtt) REVERT: D 87 GLU cc_start: 0.7526 (pm20) cc_final: 0.6514 (mm-30) REVERT: D 130 GLN cc_start: 0.8657 (tt0) cc_final: 0.8012 (tt0) REVERT: D 181 MET cc_start: 0.7822 (tpp) cc_final: 0.7546 (tpp) REVERT: D 192 TYR cc_start: 0.7882 (t80) cc_final: 0.7627 (t80) REVERT: D 199 THR cc_start: 0.7643 (p) cc_final: 0.7328 (t) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2059 time to fit residues: 61.2039 Evaluate side-chains 151 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 95 optimal weight: 0.1980 chunk 41 optimal weight: 0.3980 chunk 16 optimal weight: 0.0870 chunk 53 optimal weight: 0.0270 chunk 87 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 13 optimal weight: 0.0170 chunk 8 optimal weight: 5.9990 overall best weight: 0.1454 ------------------------------------------------------------------------------- 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 ** 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 = 0.3763 r_free = 0.3763 target = 0.108828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.089389 restraints weight = 25929.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.091761 restraints weight = 15953.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.093382 restraints weight = 11309.730| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10046 Z= 0.108 Angle : 0.662 10.769 13698 Z= 0.327 Chirality : 0.045 0.212 1572 Planarity : 0.005 0.087 1741 Dihedral : 5.672 51.003 1464 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.23), residues: 1197 helix: -0.76 (0.44), residues: 143 sheet: -1.13 (0.27), residues: 358 loop : -1.73 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 36 HIS 0.008 0.001 HIS F 203 PHE 0.028 0.001 PHE F 103 TYR 0.015 0.001 TYR B 422 ARG 0.007 0.000 ARG F 193 Details of bonding type rmsd link_TRANS : bond 0.00035 ( 5) link_TRANS : angle 0.51786 ( 15) link_NAG-ASN : bond 0.00340 ( 4) link_NAG-ASN : angle 1.87974 ( 12) link_BETA1-4 : bond 0.00712 ( 1) link_BETA1-4 : angle 1.38946 ( 3) hydrogen bonds : bond 0.03208 ( 245) hydrogen bonds : angle 6.01115 ( 633) SS BOND : bond 0.00299 ( 8) SS BOND : angle 0.93860 ( 16) covalent geometry : bond 0.00245 (10028) covalent geometry : angle 0.65923 (13652) ********************** 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 207 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 89 ASP cc_start: 0.7439 (m-30) cc_final: 0.5662 (p0) REVERT: E 154 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8110 (tm-30) REVERT: F 77 PHE cc_start: 0.7570 (p90) cc_final: 0.6851 (p90) REVERT: F 193 ARG cc_start: 0.7248 (mtm110) cc_final: 0.6915 (mtm180) REVERT: B 300 LYS cc_start: 0.8816 (mmmt) cc_final: 0.8331 (mtmt) REVERT: B 312 TYR cc_start: 0.8180 (p90) cc_final: 0.7961 (p90) REVERT: B 413 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6481 (mt-10) REVERT: B 579 GLN cc_start: 0.7680 (tm-30) cc_final: 0.7308 (tm-30) REVERT: C 3 GLN cc_start: 0.7533 (mt0) cc_final: 0.7303 (mt0) REVERT: C 48 LEU cc_start: 0.7933 (pp) cc_final: 0.7254 (mt) REVERT: C 72 ASP cc_start: 0.7726 (t0) cc_final: 0.7512 (t0) REVERT: C 77 GLN cc_start: 0.8592 (pm20) cc_final: 0.8045 (pm20) REVERT: C 164 LEU cc_start: 0.7781 (mp) cc_final: 0.7289 (tp) REVERT: C 210 LYS cc_start: 0.7597 (tptp) cc_final: 0.7396 (tptp) REVERT: C 213 LYS cc_start: 0.8101 (mmtt) cc_final: 0.7262 (mmmt) REVERT: D 87 GLU cc_start: 0.7618 (pm20) cc_final: 0.6372 (mm-30) REVERT: D 181 MET cc_start: 0.7816 (tpp) cc_final: 0.7553 (tpp) REVERT: D 192 TYR cc_start: 0.7830 (t80) cc_final: 0.7621 (t80) REVERT: D 199 THR cc_start: 0.7678 (p) cc_final: 0.7362 (t) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.3267 time to fit residues: 93.8031 Evaluate side-chains 148 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 33 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 0.0970 chunk 95 optimal weight: 5.9990 chunk 94 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.107309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.087629 restraints weight = 25971.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.089950 restraints weight = 16220.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.091545 restraints weight = 11602.058| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10046 Z= 0.130 Angle : 0.683 10.967 13698 Z= 0.340 Chirality : 0.045 0.198 1572 Planarity : 0.005 0.100 1741 Dihedral : 5.686 50.469 1464 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % 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 : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.24), residues: 1197 helix: -0.85 (0.43), residues: 150 sheet: -1.06 (0.28), residues: 357 loop : -1.65 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 168 HIS 0.007 0.001 HIS F 203 PHE 0.017 0.002 PHE F 103 TYR 0.017 0.002 TYR F 97 ARG 0.018 0.001 ARG B 534 Details of bonding type rmsd link_TRANS : bond 0.00047 ( 5) link_TRANS : angle 0.45057 ( 15) link_NAG-ASN : bond 0.00214 ( 4) link_NAG-ASN : angle 1.83939 ( 12) link_BETA1-4 : bond 0.00495 ( 1) link_BETA1-4 : angle 1.06173 ( 3) hydrogen bonds : bond 0.03245 ( 245) hydrogen bonds : angle 6.09790 ( 633) SS BOND : bond 0.00548 ( 8) SS BOND : angle 1.62706 ( 16) covalent geometry : bond 0.00306 (10028) covalent geometry : angle 0.67966 (13652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3740.85 seconds wall clock time: 68 minutes 46.28 seconds (4126.28 seconds total)