Starting phenix.real_space_refine on Fri Feb 14 06:50:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jmr_9850/02_2025/6jmr_9850.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jmr_9850/02_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_9850/02_2025/6jmr_9850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jmr_9850/02_2025/6jmr_9850.map" model { file = "/net/cci-nas-00/data/ceres_data/6jmr_9850/02_2025/6jmr_9850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jmr_9850/02_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-5592/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: 5.36, per 1000 atoms: 0.55 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: 2.35 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: 1.41 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: 3.28 Time building geometry restraints manager: 2.72 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: 0.310 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.810 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.530 ------------------------------------------------------------------------------- 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 10028 Z= 0.422 Angle : 1.058 11.251 13652 Z= 0.593 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 *********************** 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 : 1.060 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: 0.2672 time to fit residues: 88.1632 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 : 1.506 ------------------------------------------------------------------------------- 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: 2.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 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: 0.7580 ------------------------------------------------------------------------------- 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 322 GLN B 395 ASN B 529 GLN C 16 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.106603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.086645 restraints weight = 26175.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.089064 restraints weight = 16248.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.090733 restraints weight = 11576.719| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10028 Z= 0.225 Angle : 0.732 10.386 13652 Z= 0.372 Chirality : 0.046 0.245 1572 Planarity : 0.006 0.104 1741 Dihedral : 7.295 53.015 1464 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.18 % Rama-Z (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: -3.28 (0.21), residues: 1197 helix: -2.56 (0.34), residues: 146 sheet: -1.92 (0.23), residues: 396 loop : -2.24 (0.21), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 41 HIS 0.004 0.001 HIS B 619 PHE 0.029 0.002 PHE F 103 TYR 0.022 0.002 TYR E 94 ARG 0.007 0.001 ARG B 439 *********************** 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 : 1.004 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 154 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8195 (tm-30) REVERT: F 102 THR cc_start: 0.6504 (p) cc_final: 0.6223 (p) REVERT: F 175 ASP cc_start: 0.8392 (p0) cc_final: 0.7651 (p0) REVERT: B 283 ASN cc_start: 0.8038 (m-40) cc_final: 0.7814 (t0) REVERT: B 300 LYS cc_start: 0.8802 (mttm) cc_final: 0.8544 (mmmt) REVERT: B 472 ILE cc_start: 0.9421 (mt) cc_final: 0.9135 (mp) REVERT: C 48 LEU cc_start: 0.8027 (pp) cc_final: 0.7241 (mt) REVERT: C 72 ASP cc_start: 0.8250 (t0) cc_final: 0.8038 (t0) REVERT: C 77 GLN cc_start: 0.8437 (pm20) cc_final: 0.8134 (pm20) REVERT: C 201 ASN cc_start: 0.6162 (m-40) cc_final: 0.5438 (m110) REVERT: D 89 LEU cc_start: 0.6763 (pt) cc_final: 0.6262 (tt) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2270 time to fit residues: 70.8857 Evaluate side-chains 145 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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: 3.9990 chunk 70 optimal weight: 0.9990 chunk 56 optimal weight: 0.0670 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.3322 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.105948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.086169 restraints weight = 27030.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.088536 restraints weight = 16778.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.090155 restraints weight = 12025.131| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10028 Z= 0.251 Angle : 0.704 9.657 13652 Z= 0.357 Chirality : 0.047 0.209 1572 Planarity : 0.005 0.096 1741 Dihedral : 6.815 50.403 1464 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.18 % Rama-Z (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: -1.51 (0.25), residues: 394 loop : -2.21 (0.21), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP E 194 HIS 0.006 0.001 HIS B 619 PHE 0.016 0.002 PHE E 80 TYR 0.020 0.002 TYR E 94 ARG 0.004 0.000 ARG B 625 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 89 ASP cc_start: 0.7720 (m-30) cc_final: 0.6128 (p0) REVERT: E 154 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8269 (tm-30) REVERT: E 181 TYR cc_start: 0.7787 (m-10) cc_final: 0.7511 (m-10) REVERT: F 97 TYR cc_start: 0.7075 (m-80) cc_final: 0.6835 (m-80) REVERT: F 175 ASP cc_start: 0.8547 (p0) cc_final: 0.7980 (p0) REVERT: F 189 ASP cc_start: 0.8301 (p0) cc_final: 0.7478 (p0) REVERT: B 300 LYS cc_start: 0.8817 (mttm) cc_final: 0.8503 (mmmt) REVERT: B 471 GLU cc_start: 0.8691 (pm20) cc_final: 0.8389 (pm20) REVERT: B 625 ARG cc_start: 0.8507 (ttp80) cc_final: 0.8103 (ttp80) REVERT: C 48 LEU cc_start: 0.8007 (pp) cc_final: 0.7290 (mt) REVERT: C 77 GLN cc_start: 0.8560 (pm20) cc_final: 0.8155 (pm20) REVERT: C 164 LEU cc_start: 0.7927 (mp) cc_final: 0.7521 (tp) REVERT: C 213 LYS cc_start: 0.7985 (mmtt) cc_final: 0.7363 (mmmt) REVERT: D 48 GLN cc_start: 0.8868 (mp10) cc_final: 0.8515 (mp10) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2341 time to fit residues: 64.3365 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 : 1.119 ------------------------------------------------------------------------------- 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: 3.9990 chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 85 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.106595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.087033 restraints weight = 26502.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.089447 restraints weight = 16416.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.091077 restraints weight = 11690.313| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10028 Z= 0.216 Angle : 0.681 10.417 13652 Z= 0.343 Chirality : 0.046 0.228 1572 Planarity : 0.005 0.091 1741 Dihedral : 6.507 50.795 1464 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % 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: -2.66 (0.22), residues: 1197 helix: -1.44 (0.39), residues: 141 sheet: -1.31 (0.26), residues: 376 loop : -2.14 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 219 HIS 0.004 0.001 HIS B 619 PHE 0.014 0.002 PHE E 80 TYR 0.020 0.002 TYR E 94 ARG 0.003 0.000 ARG F 193 *********************** 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 197 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 154 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8250 (tm-30) REVERT: F 170 ASP cc_start: 0.8562 (p0) cc_final: 0.8361 (p0) REVERT: F 175 ASP cc_start: 0.8415 (p0) cc_final: 0.7847 (p0) REVERT: B 300 LYS cc_start: 0.8789 (mttm) cc_final: 0.8458 (mmmt) REVERT: B 439 ARG cc_start: 0.7701 (mtp85) cc_final: 0.7491 (mtp85) REVERT: B 471 GLU cc_start: 0.8520 (pm20) cc_final: 0.7871 (pm20) REVERT: C 48 LEU cc_start: 0.7985 (pp) cc_final: 0.7306 (mt) REVERT: C 77 GLN cc_start: 0.8526 (pm20) cc_final: 0.8253 (pm20) REVERT: C 164 LEU cc_start: 0.7678 (mp) cc_final: 0.7265 (tp) REVERT: D 48 GLN cc_start: 0.8879 (mp10) cc_final: 0.8641 (mp10) REVERT: D 192 TYR cc_start: 0.7639 (t80) cc_final: 0.7417 (t80) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2305 time to fit residues: 62.7614 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 : 1.141 ------------------------------------------------------------------------------- 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: 7.9990 chunk 41 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 16 optimal weight: 0.0270 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.2840 ------------------------------------------------------------------------------- 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 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.105568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.086480 restraints weight = 26637.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.088620 restraints weight = 17235.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.090103 restraints weight = 12698.995| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10028 Z= 0.242 Angle : 0.687 9.974 13652 Z= 0.344 Chirality : 0.047 0.263 1572 Planarity : 0.005 0.092 1741 Dihedral : 6.535 49.751 1464 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % 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: -1.07 (0.43), residues: 140 sheet: -1.38 (0.26), residues: 372 loop : -1.99 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 219 HIS 0.004 0.001 HIS B 619 PHE 0.016 0.002 PHE B 544 TYR 0.017 0.002 TYR F 42 ARG 0.005 0.000 ARG B 534 *********************** 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 193 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 154 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8249 (tm-30) REVERT: F 170 ASP cc_start: 0.8484 (p0) cc_final: 0.8261 (p0) REVERT: F 175 ASP cc_start: 0.8432 (p0) cc_final: 0.7863 (p0) REVERT: C 48 LEU cc_start: 0.7911 (pp) cc_final: 0.7178 (mt) REVERT: C 77 GLN cc_start: 0.8795 (pm20) cc_final: 0.8338 (pm20) REVERT: C 164 LEU cc_start: 0.7800 (mp) cc_final: 0.7368 (tp) REVERT: C 213 LYS cc_start: 0.8086 (mmtt) cc_final: 0.7497 (mmmt) REVERT: D 48 GLN cc_start: 0.8871 (mp10) cc_final: 0.8620 (mp10) REVERT: D 181 MET cc_start: 0.7837 (tpp) cc_final: 0.7614 (tpp) REVERT: D 198 TYR cc_start: 0.6211 (m-80) cc_final: 0.5927 (m-80) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2252 time to fit residues: 61.1370 Evaluate side-chains 135 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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: 0.9980 chunk 75 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.107099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.087691 restraints weight = 26875.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.090073 restraints weight = 16747.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.091684 restraints weight = 11979.416| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10028 Z= 0.198 Angle : 0.660 10.458 13652 Z= 0.329 Chirality : 0.045 0.220 1572 Planarity : 0.005 0.089 1741 Dihedral : 6.247 50.205 1464 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z (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: -2.30 (0.23), residues: 1197 helix: -0.97 (0.43), residues: 141 sheet: -1.17 (0.27), residues: 352 loop : -1.87 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 108 HIS 0.004 0.001 HIS B 619 PHE 0.014 0.001 PHE E 152 TYR 0.013 0.002 TYR F 42 ARG 0.012 0.001 ARG C 92 *********************** 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 198 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.098 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 47 TRP cc_start: 0.7168 (t-100) cc_final: 0.6676 (t-100) REVERT: E 48 LEU cc_start: 0.7854 (mt) cc_final: 0.7635 (mt) REVERT: E 154 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8125 (tm-30) REVERT: F 66 ASP cc_start: 0.8384 (t0) cc_final: 0.8125 (p0) REVERT: F 170 ASP cc_start: 0.8582 (p0) cc_final: 0.8370 (p0) REVERT: F 193 ARG cc_start: 0.7211 (mtm180) cc_final: 0.6798 (mtm180) REVERT: B 452 LEU cc_start: 0.8928 (mt) cc_final: 0.8699 (mp) REVERT: C 48 LEU cc_start: 0.7821 (pp) cc_final: 0.7171 (mt) REVERT: C 77 GLN cc_start: 0.8803 (pm20) cc_final: 0.8345 (pm20) REVERT: C 164 LEU cc_start: 0.7691 (mp) cc_final: 0.7276 (tp) REVERT: C 213 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7474 (mmmt) REVERT: D 48 GLN cc_start: 0.8832 (mp10) cc_final: 0.8548 (mp10) REVERT: D 87 GLU cc_start: 0.7513 (pm20) cc_final: 0.6342 (mp0) REVERT: D 181 MET cc_start: 0.7817 (tpp) cc_final: 0.7580 (tpp) REVERT: D 192 TYR cc_start: 0.7749 (t80) cc_final: 0.7535 (t80) REVERT: D 198 TYR cc_start: 0.5759 (m-80) cc_final: 0.5455 (m-80) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2231 time to fit residues: 62.4158 Evaluate side-chains 147 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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: 0.5980 chunk 95 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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** ** F 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 HIS B 542 HIS B 556 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.103331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.084177 restraints weight = 27382.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.086203 restraints weight = 18007.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.087618 restraints weight = 13421.173| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 10028 Z= 0.364 Angle : 0.766 10.882 13652 Z= 0.382 Chirality : 0.048 0.204 1572 Planarity : 0.006 0.095 1741 Dihedral : 6.598 48.616 1464 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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: -2.43 (0.23), residues: 1197 helix: -1.13 (0.42), residues: 142 sheet: -1.34 (0.27), residues: 363 loop : -1.90 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP F 168 HIS 0.010 0.002 HIS F 203 PHE 0.028 0.003 PHE B 544 TYR 0.019 0.002 TYR F 145 ARG 0.004 0.001 ARG B 534 *********************** 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 177 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.149 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: 0.8527 (tm-30) cc_final: 0.8279 (tm-30) REVERT: F 66 ASP cc_start: 0.8408 (t0) cc_final: 0.8121 (p0) REVERT: F 193 ARG cc_start: 0.7231 (mtm180) cc_final: 0.6916 (mtm180) REVERT: B 413 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6732 (mt-10) REVERT: C 3 GLN cc_start: 0.7471 (mt0) cc_final: 0.7217 (mt0) REVERT: C 48 LEU cc_start: 0.8189 (pp) cc_final: 0.7485 (mt) REVERT: C 77 GLN cc_start: 0.9022 (pm20) cc_final: 0.8534 (pm20) REVERT: C 164 LEU cc_start: 0.7691 (mp) cc_final: 0.7294 (tt) REVERT: C 213 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7540 (mmmt) REVERT: D 48 GLN cc_start: 0.8912 (mp10) cc_final: 0.8661 (mp10) REVERT: D 87 GLU cc_start: 0.7522 (pm20) cc_final: 0.7193 (mm-30) REVERT: D 181 MET cc_start: 0.7866 (tpp) cc_final: 0.7465 (tpp) REVERT: D 198 TYR cc_start: 0.5757 (m-80) cc_final: 0.5466 (m-80) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2067 time to fit residues: 52.0031 Evaluate side-chains 133 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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: 2.9990 chunk 12 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 71 optimal weight: 0.0770 chunk 89 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN B 538 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.105814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.085987 restraints weight = 26574.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.088376 restraints weight = 16611.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.089985 restraints weight = 11896.545| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10028 Z= 0.190 Angle : 0.682 11.804 13652 Z= 0.339 Chirality : 0.046 0.224 1572 Planarity : 0.005 0.085 1741 Dihedral : 6.190 50.220 1464 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % 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: -2.27 (0.23), residues: 1197 helix: -0.79 (0.43), residues: 141 sheet: -1.27 (0.28), residues: 349 loop : -1.82 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP F 168 HIS 0.006 0.001 HIS F 203 PHE 0.014 0.001 PHE B 458 TYR 0.012 0.001 TYR F 31 ARG 0.005 0.000 ARG B 534 *********************** 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 195 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.149 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: 0.7833 (m-30) cc_final: 0.5942 (p0) REVERT: E 154 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8204 (tm-30) REVERT: F 66 ASP cc_start: 0.8391 (t0) cc_final: 0.8064 (p0) REVERT: F 193 ARG cc_start: 0.6897 (mtm180) cc_final: 0.6579 (mtm110) REVERT: B 413 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6653 (mt-10) REVERT: B 452 LEU cc_start: 0.8906 (mt) cc_final: 0.8658 (mp) REVERT: B 471 GLU cc_start: 0.8155 (pm20) cc_final: 0.7816 (pm20) REVERT: B 579 GLN cc_start: 0.7711 (tm-30) cc_final: 0.7218 (tm-30) REVERT: C 3 GLN cc_start: 0.7480 (mt0) cc_final: 0.7228 (mt0) REVERT: C 48 LEU cc_start: 0.7995 (pp) cc_final: 0.7358 (mt) REVERT: C 77 GLN cc_start: 0.8853 (pm20) cc_final: 0.8402 (pm20) REVERT: C 164 LEU cc_start: 0.7818 (mp) cc_final: 0.7407 (tp) REVERT: C 213 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7539 (mmmt) REVERT: D 48 GLN cc_start: 0.8808 (mp10) cc_final: 0.8566 (mp10) REVERT: D 87 GLU cc_start: 0.7610 (pm20) cc_final: 0.6497 (mm-30) REVERT: D 181 MET cc_start: 0.7779 (tpp) cc_final: 0.7500 (tpp) REVERT: D 199 THR cc_start: 0.7810 (p) cc_final: 0.7510 (t) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2206 time to fit residues: 60.5283 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 : 1.203 ------------------------------------------------------------------------------- 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: 6.9990 chunk 31 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 0.0070 chunk 85 optimal weight: 0.0570 chunk 8 optimal weight: 5.9990 chunk 98 optimal weight: 0.0970 chunk 35 optimal weight: 0.0070 chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.2132 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.108062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.088414 restraints weight = 25990.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.090742 restraints weight = 16115.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.092436 restraints weight = 11539.684| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10028 Z= 0.163 Angle : 0.659 11.975 13652 Z= 0.325 Chirality : 0.045 0.208 1572 Planarity : 0.005 0.085 1741 Dihedral : 5.771 50.959 1464 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: -2.14 (0.23), residues: 1197 helix: -0.68 (0.42), residues: 141 sheet: -1.13 (0.28), residues: 354 loop : -1.76 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 219 HIS 0.005 0.001 HIS C 204 PHE 0.013 0.001 PHE D 141 TYR 0.015 0.001 TYR E 100 ARG 0.004 0.000 ARG B 625 *********************** 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 199 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 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: E 47 TRP cc_start: 0.7144 (t-100) cc_final: 0.6847 (t-100) REVERT: E 72 ASP cc_start: 0.7723 (m-30) cc_final: 0.7367 (t0) REVERT: E 89 ASP cc_start: 0.7640 (m-30) cc_final: 0.5913 (p0) REVERT: E 154 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8153 (tm-30) REVERT: F 66 ASP cc_start: 0.8354 (t0) cc_final: 0.7994 (p0) REVERT: F 193 ARG cc_start: 0.6875 (mtm180) cc_final: 0.6567 (mtm110) REVERT: B 300 LYS cc_start: 0.8733 (mmmt) cc_final: 0.8359 (mtmt) REVERT: B 413 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6570 (mt-10) REVERT: B 471 GLU cc_start: 0.8108 (pm20) cc_final: 0.7787 (pm20) REVERT: B 579 GLN cc_start: 0.7707 (tm-30) cc_final: 0.7286 (tm-30) REVERT: C 3 GLN cc_start: 0.7337 (mt0) cc_final: 0.7088 (mt0) REVERT: C 48 LEU cc_start: 0.7944 (pp) cc_final: 0.7326 (mt) REVERT: C 77 GLN cc_start: 0.8679 (pm20) cc_final: 0.8283 (pm20) REVERT: C 164 LEU cc_start: 0.7818 (mp) cc_final: 0.7353 (tp) REVERT: C 210 LYS cc_start: 0.7646 (tptp) cc_final: 0.7415 (tptp) REVERT: C 213 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7769 (mmtt) REVERT: D 87 GLU cc_start: 0.7397 (pm20) cc_final: 0.6535 (mm-30) REVERT: D 181 MET cc_start: 0.7772 (tpp) cc_final: 0.7516 (tpp) REVERT: D 199 THR cc_start: 0.7778 (p) cc_final: 0.7490 (t) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.2128 time to fit residues: 60.0292 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 : 1.053 ------------------------------------------------------------------------------- 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: 0.9990 chunk 69 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 0.0020 chunk 53 optimal weight: 0.4980 chunk 87 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 13 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.106297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.086507 restraints weight = 26094.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.088830 restraints weight = 16314.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.090404 restraints weight = 11721.868| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10028 Z= 0.205 Angle : 0.681 12.000 13652 Z= 0.338 Chirality : 0.045 0.197 1572 Planarity : 0.006 0.101 1741 Dihedral : 5.769 50.348 1464 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: -2.04 (0.23), residues: 1197 helix: -0.56 (0.43), residues: 142 sheet: -1.10 (0.28), residues: 347 loop : -1.68 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 168 HIS 0.006 0.001 HIS F 203 PHE 0.019 0.002 PHE D 68 TYR 0.015 0.001 TYR E 100 ARG 0.010 0.000 ARG D 67 ********************** 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 186 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 89 ASP cc_start: 0.7488 (m-30) cc_final: 0.5776 (p0) REVERT: E 154 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8146 (tm-30) REVERT: F 66 ASP cc_start: 0.8422 (t0) cc_final: 0.7993 (p0) REVERT: F 170 ASP cc_start: 0.8563 (p0) cc_final: 0.8351 (p0) REVERT: F 193 ARG cc_start: 0.6963 (mtm180) cc_final: 0.6448 (mtm180) REVERT: B 413 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6603 (mt-10) REVERT: B 579 GLN cc_start: 0.7713 (tm-30) cc_final: 0.7339 (tm-30) REVERT: C 3 GLN cc_start: 0.7383 (mt0) cc_final: 0.7121 (mt0) REVERT: C 48 LEU cc_start: 0.8004 (pp) cc_final: 0.7320 (mt) REVERT: C 77 GLN cc_start: 0.8682 (pm20) cc_final: 0.8157 (pm20) REVERT: C 164 LEU cc_start: 0.7858 (mp) cc_final: 0.7389 (tp) REVERT: C 210 LYS cc_start: 0.7674 (tptp) cc_final: 0.7433 (tptp) REVERT: C 213 LYS cc_start: 0.7916 (mmtt) cc_final: 0.7376 (mmmt) REVERT: D 87 GLU cc_start: 0.7134 (pm20) cc_final: 0.5965 (mm-30) REVERT: D 181 MET cc_start: 0.7809 (tpp) cc_final: 0.7508 (tpp) REVERT: D 199 THR cc_start: 0.7778 (p) cc_final: 0.7499 (t) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2173 time to fit residues: 57.2637 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 : 1.092 ------------------------------------------------------------------------------- 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: 0.3980 chunk 58 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 93 optimal weight: 0.0170 chunk 95 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.6022 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.106794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.087113 restraints weight = 25978.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.089446 restraints weight = 16309.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.091045 restraints weight = 11702.217| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10028 Z= 0.181 Angle : 0.666 11.792 13652 Z= 0.327 Chirality : 0.045 0.194 1572 Planarity : 0.005 0.087 1741 Dihedral : 5.662 50.543 1464 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % 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: -1.95 (0.23), residues: 1197 helix: -0.53 (0.43), residues: 141 sheet: -1.01 (0.28), residues: 347 loop : -1.63 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 168 HIS 0.004 0.001 HIS F 203 PHE 0.011 0.001 PHE E 152 TYR 0.014 0.001 TYR E 100 ARG 0.014 0.001 ARG D 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2904.56 seconds wall clock time: 53 minutes 4.67 seconds (3184.67 seconds total)