Starting phenix.real_space_refine on Sat Aug 23 22:43:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8shs_40493/08_2025/8shs_40493.cif Found real_map, /net/cci-nas-00/data/ceres_data/8shs_40493/08_2025/8shs_40493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8shs_40493/08_2025/8shs_40493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8shs_40493/08_2025/8shs_40493.map" model { file = "/net/cci-nas-00/data/ceres_data/8shs_40493/08_2025/8shs_40493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8shs_40493/08_2025/8shs_40493.cif" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 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 72 5.16 5 C 9642 2.51 5 N 2591 2.21 5 O 2851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15156 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3774 Classifications: {'peptide': 494} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 24, 'TRANS': 469} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3794 Classifications: {'peptide': 494} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 469} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3794 Classifications: {'peptide': 494} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 469} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3794 Classifications: {'peptide': 494} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 469} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 3.13, per 1000 atoms: 0.21 Number of scatterers: 15156 At special positions: 0 Unit cell: (98.2345, 103.187, 106.489, 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 72 16.00 O 2851 8.00 N 2591 7.00 C 9642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 519.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3584 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 20 sheets defined 45.3% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 72 through 87 Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 97 through 115 Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 130 through 137 Processing helix chain 'A' and resid 137 through 152 removed outlier: 3.537A pdb=" N GLY A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 187 through 202 Proline residue: A 198 - end of helix Processing helix chain 'A' and resid 215 through 229 removed outlier: 3.577A pdb=" N GLY A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 252 removed outlier: 4.425A pdb=" N GLY A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 Processing helix chain 'A' and resid 299 through 313 Processing helix chain 'A' and resid 314 through 317 Processing helix chain 'A' and resid 331 through 345 Processing helix chain 'A' and resid 363 through 380 Processing helix chain 'A' and resid 429 through 439 Processing helix chain 'A' and resid 452 through 463 Processing helix chain 'A' and resid 494 through 502 removed outlier: 4.057A pdb=" N LEU A 499 " --> pdb=" O GLY A 495 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN A 500 " --> pdb=" O GLU A 496 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA A 501 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 87 Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 97 through 115 Processing helix chain 'B' and resid 115 through 128 Processing helix chain 'B' and resid 130 through 137 Processing helix chain 'B' and resid 137 through 152 removed outlier: 3.537A pdb=" N GLY B 151 " --> pdb=" O ARG B 147 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP B 152 " --> pdb=" O TYR B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 187 through 202 Proline residue: B 198 - end of helix Processing helix chain 'B' and resid 215 through 229 removed outlier: 3.576A pdb=" N GLY B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 252 removed outlier: 4.424A pdb=" N GLY B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 278 Processing helix chain 'B' and resid 299 through 313 Processing helix chain 'B' and resid 314 through 317 Processing helix chain 'B' and resid 331 through 345 Processing helix chain 'B' and resid 363 through 380 Processing helix chain 'B' and resid 429 through 439 Processing helix chain 'B' and resid 452 through 463 Processing helix chain 'B' and resid 494 through 502 removed outlier: 4.057A pdb=" N LEU B 499 " --> pdb=" O GLY B 495 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN B 500 " --> pdb=" O GLU B 496 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA B 501 " --> pdb=" O TYR B 497 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR B 502 " --> pdb=" O GLY B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 87 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 97 through 115 Processing helix chain 'C' and resid 115 through 128 Processing helix chain 'C' and resid 130 through 137 Processing helix chain 'C' and resid 137 through 152 removed outlier: 3.536A pdb=" N GLY C 151 " --> pdb=" O ARG C 147 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP C 152 " --> pdb=" O TYR C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 187 through 202 Proline residue: C 198 - end of helix Processing helix chain 'C' and resid 215 through 229 removed outlier: 3.577A pdb=" N GLY C 229 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 252 removed outlier: 4.424A pdb=" N GLY C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 278 Processing helix chain 'C' and resid 299 through 313 Processing helix chain 'C' and resid 314 through 317 Processing helix chain 'C' and resid 331 through 345 Processing helix chain 'C' and resid 363 through 380 Processing helix chain 'C' and resid 429 through 439 Processing helix chain 'C' and resid 452 through 463 Processing helix chain 'C' and resid 494 through 502 removed outlier: 4.057A pdb=" N LEU C 499 " --> pdb=" O GLY C 495 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN C 500 " --> pdb=" O GLU C 496 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA C 501 " --> pdb=" O TYR C 497 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR C 502 " --> pdb=" O GLY C 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 87 Processing helix chain 'D' and resid 91 through 96 Processing helix chain 'D' and resid 97 through 115 Processing helix chain 'D' and resid 115 through 128 Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'D' and resid 137 through 152 removed outlier: 3.535A pdb=" N GLY D 151 " --> pdb=" O ARG D 147 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP D 152 " --> pdb=" O TYR D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 155 No H-bonds generated for 'chain 'D' and resid 153 through 155' Processing helix chain 'D' and resid 187 through 202 Proline residue: D 198 - end of helix Processing helix chain 'D' and resid 215 through 229 removed outlier: 3.577A pdb=" N GLY D 229 " --> pdb=" O ILE D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 252 removed outlier: 4.425A pdb=" N GLY D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 278 Processing helix chain 'D' and resid 299 through 313 Processing helix chain 'D' and resid 314 through 317 Processing helix chain 'D' and resid 331 through 345 Processing helix chain 'D' and resid 363 through 380 Processing helix chain 'D' and resid 429 through 439 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 494 through 502 removed outlier: 4.058A pdb=" N LEU D 499 " --> pdb=" O GLY D 495 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN D 500 " --> pdb=" O GLU D 496 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA D 501 " --> pdb=" O TYR D 497 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR D 502 " --> pdb=" O GLY D 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 57 removed outlier: 4.029A pdb=" N CYS A 66 " --> pdb=" O THR A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 175 removed outlier: 8.193A pdb=" N VAL B 468 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR A 507 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL B 470 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR A 509 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASN B 292 " --> pdb=" O PHE B 326 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLN B 328 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE B 294 " --> pdb=" O GLN B 328 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR B 325 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N PHE B 427 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL B 327 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B 402 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 235 through 239 removed outlier: 3.919A pdb=" N VAL A 210 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS A 179 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LYS A 209 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLN A 181 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 261 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 284 " --> pdb=" O SER A 490 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 383 through 386 removed outlier: 6.586A pdb=" N VAL A 402 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR A 325 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N PHE A 427 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL A 327 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASN A 292 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLN A 328 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ILE A 294 " --> pdb=" O GLN A 328 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 442 through 443 removed outlier: 3.712A pdb=" N GLY A 443 " --> pdb=" O TYR A 485 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 57 removed outlier: 4.029A pdb=" N CYS B 66 " --> pdb=" O THR B 56 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 235 through 239 removed outlier: 3.919A pdb=" N VAL B 210 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS B 179 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LYS B 209 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLN B 181 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 261 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 284 " --> pdb=" O SER B 490 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 442 through 443 removed outlier: 3.713A pdb=" N GLY B 443 " --> pdb=" O TYR B 485 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 57 removed outlier: 4.029A pdb=" N CYS C 66 " --> pdb=" O THR C 56 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 167 through 175 removed outlier: 8.205A pdb=" N VAL D 468 " --> pdb=" O VAL C 505 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 507 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL D 470 " --> pdb=" O THR C 507 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR C 509 " --> pdb=" O VAL D 470 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASN D 292 " --> pdb=" O PHE D 326 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N GLN D 328 " --> pdb=" O ASN D 292 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ILE D 294 " --> pdb=" O GLN D 328 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR D 325 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N PHE D 427 " --> pdb=" O THR D 325 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL D 327 " --> pdb=" O PHE D 427 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL D 402 " --> pdb=" O LEU D 385 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 235 through 239 removed outlier: 3.919A pdb=" N VAL C 210 " --> pdb=" O VAL C 238 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS C 179 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LYS C 209 " --> pdb=" O CYS C 179 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLN C 181 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR C 261 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 284 " --> pdb=" O SER C 490 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 383 through 386 removed outlier: 6.586A pdb=" N VAL C 402 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR C 325 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N PHE C 427 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL C 327 " --> pdb=" O PHE C 427 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASN C 292 " --> pdb=" O PHE C 326 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLN C 328 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE C 294 " --> pdb=" O GLN C 328 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 442 through 443 removed outlier: 3.713A pdb=" N GLY C 443 " --> pdb=" O TYR C 485 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 39 through 41 Processing sheet with id=AB9, first strand: chain 'D' and resid 53 through 57 removed outlier: 4.029A pdb=" N CYS D 66 " --> pdb=" O THR D 56 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 235 through 239 removed outlier: 3.920A pdb=" N VAL D 210 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS D 179 " --> pdb=" O VAL D 207 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LYS D 209 " --> pdb=" O CYS D 179 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLN D 181 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 261 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 284 " --> pdb=" O SER D 490 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 442 through 443 removed outlier: 3.713A pdb=" N GLY D 443 " --> pdb=" O TYR D 485 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 2160 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: 2.47 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5030 1.34 - 1.46: 3216 1.46 - 1.58: 7138 1.58 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 15492 Sorted by residual: bond pdb=" N GLY B 240 " pdb=" CA GLY B 240 " ideal model delta sigma weight residual 1.456 1.447 0.009 1.32e-02 5.74e+03 4.57e-01 bond pdb=" N GLY D 240 " pdb=" CA GLY D 240 " ideal model delta sigma weight residual 1.456 1.447 0.009 1.32e-02 5.74e+03 4.56e-01 bond pdb=" N GLY A 240 " pdb=" CA GLY A 240 " ideal model delta sigma weight residual 1.456 1.448 0.008 1.32e-02 5.74e+03 3.94e-01 bond pdb=" N GLY C 240 " pdb=" CA GLY C 240 " ideal model delta sigma weight residual 1.456 1.448 0.008 1.32e-02 5.74e+03 3.93e-01 bond pdb=" C CYS C 179 " pdb=" N GLY C 180 " ideal model delta sigma weight residual 1.332 1.329 0.003 5.00e-03 4.00e+04 3.26e-01 ... (remaining 15487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.74: 19804 0.74 - 1.49: 946 1.49 - 2.23: 177 2.23 - 2.98: 65 2.98 - 3.72: 39 Bond angle restraints: 21031 Sorted by residual: angle pdb=" N PHE D 241 " pdb=" CA PHE D 241 " pdb=" C PHE D 241 " ideal model delta sigma weight residual 107.57 111.22 -3.65 1.94e+00 2.66e-01 3.54e+00 angle pdb=" N PHE B 241 " pdb=" CA PHE B 241 " pdb=" C PHE B 241 " ideal model delta sigma weight residual 107.57 111.18 -3.61 1.94e+00 2.66e-01 3.47e+00 angle pdb=" N PHE C 241 " pdb=" CA PHE C 241 " pdb=" C PHE C 241 " ideal model delta sigma weight residual 107.57 111.18 -3.61 1.94e+00 2.66e-01 3.47e+00 angle pdb=" N PHE A 241 " pdb=" CA PHE A 241 " pdb=" C PHE A 241 " ideal model delta sigma weight residual 107.57 111.18 -3.61 1.94e+00 2.66e-01 3.47e+00 angle pdb=" N PRO C 215 " pdb=" CA PRO C 215 " pdb=" C PRO C 215 " ideal model delta sigma weight residual 112.47 116.19 -3.72 2.06e+00 2.36e-01 3.27e+00 ... (remaining 21026 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.88: 8460 10.88 - 21.76: 513 21.76 - 32.63: 140 32.63 - 43.51: 40 43.51 - 54.39: 36 Dihedral angle restraints: 9189 sinusoidal: 3565 harmonic: 5624 Sorted by residual: dihedral pdb=" CA ARG A 103 " pdb=" CB ARG A 103 " pdb=" CG ARG A 103 " pdb=" CD ARG A 103 " ideal model delta sinusoidal sigma weight residual -180.00 -125.61 -54.39 3 1.50e+01 4.44e-03 9.28e+00 dihedral pdb=" CA ARG C 103 " pdb=" CB ARG C 103 " pdb=" CG ARG C 103 " pdb=" CD ARG C 103 " ideal model delta sinusoidal sigma weight residual -180.00 -125.65 -54.35 3 1.50e+01 4.44e-03 9.28e+00 dihedral pdb=" CA ARG B 103 " pdb=" CB ARG B 103 " pdb=" CG ARG B 103 " pdb=" CD ARG B 103 " ideal model delta sinusoidal sigma weight residual -180.00 -125.68 -54.32 3 1.50e+01 4.44e-03 9.27e+00 ... (remaining 9186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1454 0.026 - 0.052: 479 0.052 - 0.078: 187 0.078 - 0.104: 136 0.104 - 0.130: 60 Chirality restraints: 2316 Sorted by residual: chirality pdb=" CA VAL D 207 " pdb=" N VAL D 207 " pdb=" C VAL D 207 " pdb=" CB VAL D 207 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA VAL A 207 " pdb=" N VAL A 207 " pdb=" C VAL A 207 " pdb=" CB VAL A 207 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE B 182 " pdb=" N ILE B 182 " pdb=" C ILE B 182 " pdb=" CB ILE B 182 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 2313 not shown) Planarity restraints: 2763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 214 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO D 215 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO D 215 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 215 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 214 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO B 215 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 215 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 215 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 214 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO A 215 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " -0.019 5.00e-02 4.00e+02 ... (remaining 2760 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4724 2.83 - 3.35: 14118 3.35 - 3.86: 25862 3.86 - 4.38: 31214 4.38 - 4.90: 53452 Nonbonded interactions: 129370 Sorted by model distance: nonbonded pdb=" OG1 THR C 202 " pdb=" ND2 ASN C 204 " model vdw 2.309 3.120 nonbonded pdb=" OG1 THR B 202 " pdb=" ND2 ASN B 204 " model vdw 2.309 3.120 nonbonded pdb=" OG1 THR A 202 " pdb=" ND2 ASN A 204 " model vdw 2.310 3.120 nonbonded pdb=" OG1 THR D 202 " pdb=" ND2 ASN D 204 " model vdw 2.310 3.120 nonbonded pdb=" NH1 ARG B 101 " pdb=" O ALA B 201 " model vdw 2.320 3.120 ... (remaining 129365 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 24 through 29 or (resid 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 through 379 or (resid 380 and (name N or n \ ame CA or name C or name O or name CB )) or resid 381 through 414 or (resid 415 \ through 416 and (name N or name CA or name C or name O or name CB )) or resid 41 \ 7 through 430 or (resid 431 and (name N or name CA or name C or name O or name C \ B )) or resid 432 through 517)) selection = (chain 'C' and (resid 24 through 29 or (resid 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 through 379 or (resid 380 and (name N or n \ ame CA or name C or name O or name CB )) or resid 381 through 414 or (resid 415 \ through 416 and (name N or name CA or name C or name O or name CB )) or resid 41 \ 7 through 430 or (resid 431 and (name N or name CA or name C or name O or name C \ B )) or resid 432 through 517)) selection = (chain 'D' and (resid 24 through 29 or (resid 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 through 379 or (resid 380 and (name N or n \ ame CA or name C or name O or name CB )) or resid 381 through 414 or (resid 415 \ through 416 and (name N or name CA or name C or name O or name CB )) or resid 41 \ 7 through 430 or (resid 431 and (name N or name CA or name C or name O or name C \ B )) or resid 432 through 517)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.750 Find NCS groups from input model: 0.210 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:7.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 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 : 0.002 0.018 15492 Z= 0.088 Angle : 0.417 3.723 21031 Z= 0.236 Chirality : 0.040 0.130 2316 Planarity : 0.004 0.034 2763 Dihedral : 8.936 54.391 5605 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.50 % Allowed : 2.33 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.20), residues: 1968 helix: 1.87 (0.18), residues: 824 sheet: 0.66 (0.28), residues: 388 loop : 0.44 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 147 TYR 0.005 0.001 TYR C 149 PHE 0.012 0.001 PHE C 367 TRP 0.006 0.001 TRP C 469 HIS 0.003 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00169 (15492) covalent geometry : angle 0.41662 (21031) hydrogen bonds : bond 0.13956 ( 744) hydrogen bonds : angle 6.14695 ( 2160) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 220 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 228 average time/residue: 0.6787 time to fit residues: 166.7920 Evaluate side-chains 113 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.0470 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 46 HIS A 173 HIS A 192 GLN A 315 GLN A 317 GLN A 407 GLN B 30 GLN B 43 ASN B 46 HIS B 173 HIS B 192 GLN B 315 GLN B 317 GLN B 407 GLN B 423 GLN C 43 ASN C 46 HIS C 173 HIS C 192 GLN C 315 GLN C 317 GLN C 407 GLN D 30 GLN D 43 ASN D 46 HIS D 173 HIS D 192 GLN D 315 GLN D 317 GLN D 407 GLN D 423 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.105325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.081410 restraints weight = 26018.919| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.85 r_work: 0.2956 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15492 Z= 0.114 Angle : 0.443 4.449 21031 Z= 0.234 Chirality : 0.042 0.165 2316 Planarity : 0.004 0.032 2763 Dihedral : 3.724 34.809 2124 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.39 % Allowed : 8.32 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.20), residues: 1968 helix: 1.83 (0.18), residues: 836 sheet: 0.51 (0.27), residues: 412 loop : 0.47 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 492 TYR 0.009 0.001 TYR D 485 PHE 0.015 0.001 PHE B 367 TRP 0.005 0.000 TRP A 45 HIS 0.002 0.000 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00258 (15492) covalent geometry : angle 0.44274 (21031) hydrogen bonds : bond 0.03514 ( 744) hydrogen bonds : angle 4.67085 ( 2160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: B 30 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7875 (mm110) REVERT: C 241 PHE cc_start: 0.8094 (t80) cc_final: 0.7869 (t80) REVERT: D 30 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7966 (mm-40) REVERT: D 241 PHE cc_start: 0.8119 (t80) cc_final: 0.7896 (t80) REVERT: D 256 ASP cc_start: 0.8560 (m-30) cc_final: 0.8285 (m-30) outliers start: 22 outliers final: 2 residues processed: 138 average time/residue: 0.6011 time to fit residues: 90.4259 Evaluate side-chains 112 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain D residue 30 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 26 optimal weight: 7.9990 chunk 184 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 317 GLN A 361 GLN B 30 GLN B 100 HIS B 317 GLN B 361 GLN C 100 HIS C 317 GLN C 361 GLN D 30 GLN D 100 HIS D 317 GLN D 361 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.098483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.074582 restraints weight = 27134.508| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.81 r_work: 0.2857 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.047 15492 Z= 0.402 Angle : 0.604 8.071 21031 Z= 0.319 Chirality : 0.048 0.144 2316 Planarity : 0.005 0.041 2763 Dihedral : 4.573 44.428 2124 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.13 % Allowed : 9.96 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.20), residues: 1968 helix: 1.43 (0.18), residues: 836 sheet: 0.31 (0.26), residues: 400 loop : 0.36 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 147 TYR 0.014 0.002 TYR D 149 PHE 0.023 0.002 PHE B 241 TRP 0.006 0.001 TRP C 45 HIS 0.005 0.001 HIS D 308 Details of bonding type rmsd covalent geometry : bond 0.00956 (15492) covalent geometry : angle 0.60433 (21031) hydrogen bonds : bond 0.05101 ( 744) hydrogen bonds : angle 4.88741 ( 2160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.587 Fit side-chains REVERT: A 241 PHE cc_start: 0.8185 (t80) cc_final: 0.7971 (t80) REVERT: B 241 PHE cc_start: 0.8226 (t80) cc_final: 0.8012 (t80) REVERT: D 241 PHE cc_start: 0.8202 (t80) cc_final: 0.7974 (t80) outliers start: 18 outliers final: 8 residues processed: 124 average time/residue: 0.5245 time to fit residues: 71.7521 Evaluate side-chains 107 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 504 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 17 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN B 317 GLN B 423 GLN C 317 GLN D 317 GLN D 423 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.102367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.078581 restraints weight = 26519.461| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.82 r_work: 0.2919 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15492 Z= 0.129 Angle : 0.436 4.385 21031 Z= 0.233 Chirality : 0.041 0.163 2316 Planarity : 0.003 0.034 2763 Dihedral : 4.158 36.822 2124 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.57 % Allowed : 10.40 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.20), residues: 1968 helix: 1.62 (0.18), residues: 836 sheet: 0.24 (0.25), residues: 400 loop : 0.44 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 51 TYR 0.008 0.001 TYR C 149 PHE 0.012 0.001 PHE D 367 TRP 0.005 0.001 TRP B 45 HIS 0.001 0.001 HIS C 308 Details of bonding type rmsd covalent geometry : bond 0.00296 (15492) covalent geometry : angle 0.43619 (21031) hydrogen bonds : bond 0.03367 ( 744) hydrogen bonds : angle 4.43962 ( 2160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.363 Fit side-chains REVERT: A 241 PHE cc_start: 0.8164 (t80) cc_final: 0.7900 (t80) REVERT: B 241 PHE cc_start: 0.8199 (t80) cc_final: 0.7940 (t80) REVERT: D 241 PHE cc_start: 0.8140 (t80) cc_final: 0.7851 (t80) REVERT: D 493 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7353 (pm20) outliers start: 9 outliers final: 0 residues processed: 111 average time/residue: 0.4794 time to fit residues: 58.8857 Evaluate side-chains 100 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 493 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN B 317 GLN C 317 GLN D 317 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.099173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.074982 restraints weight = 26946.548| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.89 r_work: 0.2873 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 15492 Z= 0.289 Angle : 0.523 7.026 21031 Z= 0.275 Chirality : 0.045 0.145 2316 Planarity : 0.004 0.040 2763 Dihedral : 4.436 39.406 2124 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.63 % Allowed : 11.34 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.20), residues: 1968 helix: 1.50 (0.19), residues: 836 sheet: 0.08 (0.25), residues: 400 loop : 0.36 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 107 TYR 0.011 0.001 TYR B 149 PHE 0.017 0.002 PHE D 367 TRP 0.004 0.001 TRP D 45 HIS 0.005 0.001 HIS D 308 Details of bonding type rmsd covalent geometry : bond 0.00689 (15492) covalent geometry : angle 0.52268 (21031) hydrogen bonds : bond 0.04370 ( 744) hydrogen bonds : angle 4.61116 ( 2160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.588 Fit side-chains REVERT: A 241 PHE cc_start: 0.8227 (t80) cc_final: 0.7957 (t80) REVERT: B 241 PHE cc_start: 0.8248 (t80) cc_final: 0.7950 (t80) REVERT: D 241 PHE cc_start: 0.8230 (t80) cc_final: 0.7931 (t80) outliers start: 10 outliers final: 4 residues processed: 118 average time/residue: 0.5444 time to fit residues: 71.0475 Evaluate side-chains 103 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 504 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 34 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN B 317 GLN C 317 GLN D 317 GLN D 423 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.102427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.078484 restraints weight = 26532.975| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.88 r_work: 0.2921 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15492 Z= 0.113 Angle : 0.425 4.010 21031 Z= 0.227 Chirality : 0.041 0.157 2316 Planarity : 0.003 0.033 2763 Dihedral : 4.083 33.483 2124 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.69 % Allowed : 11.41 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.20), residues: 1968 helix: 1.84 (0.19), residues: 812 sheet: 0.06 (0.25), residues: 400 loop : 0.47 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 492 TYR 0.007 0.001 TYR C 442 PHE 0.010 0.001 PHE D 367 TRP 0.004 0.001 TRP B 45 HIS 0.001 0.000 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00261 (15492) covalent geometry : angle 0.42467 (21031) hydrogen bonds : bond 0.03122 ( 744) hydrogen bonds : angle 4.29182 ( 2160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.594 Fit side-chains REVERT: A 241 PHE cc_start: 0.8201 (t80) cc_final: 0.7892 (t80) REVERT: B 241 PHE cc_start: 0.8227 (t80) cc_final: 0.7927 (t80) REVERT: C 504 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8335 (tp30) REVERT: D 241 PHE cc_start: 0.8173 (t80) cc_final: 0.7891 (t80) REVERT: D 504 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8329 (tp30) outliers start: 11 outliers final: 5 residues processed: 115 average time/residue: 0.6134 time to fit residues: 77.4427 Evaluate side-chains 103 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 504 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 110 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 160 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN B 317 GLN C 317 GLN D 317 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.100325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.076486 restraints weight = 26543.635| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.80 r_work: 0.2890 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 15492 Z= 0.234 Angle : 0.482 6.126 21031 Z= 0.255 Chirality : 0.043 0.148 2316 Planarity : 0.004 0.036 2763 Dihedral : 4.239 34.996 2124 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.07 % Allowed : 11.15 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.20), residues: 1968 helix: 1.78 (0.19), residues: 812 sheet: 0.04 (0.25), residues: 400 loop : 0.42 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 492 TYR 0.010 0.001 TYR B 149 PHE 0.014 0.001 PHE D 367 TRP 0.004 0.001 TRP B 45 HIS 0.004 0.001 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00556 (15492) covalent geometry : angle 0.48207 (21031) hydrogen bonds : bond 0.03870 ( 744) hydrogen bonds : angle 4.40935 ( 2160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.604 Fit side-chains REVERT: A 241 PHE cc_start: 0.8239 (t80) cc_final: 0.7922 (t80) REVERT: A 504 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8360 (tp30) REVERT: B 241 PHE cc_start: 0.8252 (t80) cc_final: 0.7895 (t80) REVERT: B 504 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8354 (tp30) REVERT: C 493 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7347 (pm20) REVERT: C 504 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8372 (tp30) REVERT: D 241 PHE cc_start: 0.8235 (t80) cc_final: 0.7935 (t80) REVERT: D 504 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8364 (tp30) outliers start: 17 outliers final: 4 residues processed: 114 average time/residue: 0.6443 time to fit residues: 81.4555 Evaluate side-chains 105 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain C residue 493 GLU Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 504 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 170 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 153 optimal weight: 0.1980 chunk 50 optimal weight: 0.7980 chunk 82 optimal weight: 0.4980 chunk 174 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 163 optimal weight: 0.3980 chunk 97 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN B 317 GLN C 317 GLN D 317 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.103182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.079500 restraints weight = 26495.942| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.83 r_work: 0.2921 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15492 Z= 0.092 Angle : 0.408 4.462 21031 Z= 0.219 Chirality : 0.041 0.134 2316 Planarity : 0.003 0.032 2763 Dihedral : 3.932 30.242 2124 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.32 % Allowed : 11.66 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.20), residues: 1968 helix: 1.96 (0.19), residues: 812 sheet: 0.13 (0.25), residues: 400 loop : 0.56 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 51 TYR 0.006 0.001 TYR A 170 PHE 0.008 0.001 PHE C 241 TRP 0.005 0.001 TRP A 45 HIS 0.001 0.000 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00205 (15492) covalent geometry : angle 0.40846 (21031) hydrogen bonds : bond 0.02855 ( 744) hydrogen bonds : angle 4.15095 ( 2160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.669 Fit side-chains REVERT: A 241 PHE cc_start: 0.8201 (t80) cc_final: 0.7867 (t80) REVERT: A 493 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7237 (pm20) REVERT: A 504 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8323 (tp30) REVERT: B 241 PHE cc_start: 0.8206 (t80) cc_final: 0.7836 (t80) REVERT: B 504 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8349 (tp30) REVERT: C 504 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8290 (tp30) REVERT: D 241 PHE cc_start: 0.8149 (t80) cc_final: 0.7825 (t80) REVERT: D 504 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8315 (tp30) outliers start: 5 outliers final: 0 residues processed: 112 average time/residue: 0.6896 time to fit residues: 85.0170 Evaluate side-chains 106 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 504 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 169 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 92 optimal weight: 0.0770 chunk 194 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 20 optimal weight: 0.0370 chunk 26 optimal weight: 5.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN B 317 GLN C 317 GLN D 317 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.102274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.078411 restraints weight = 26564.263| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.89 r_work: 0.2928 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15492 Z= 0.124 Angle : 0.422 5.553 21031 Z= 0.224 Chirality : 0.041 0.164 2316 Planarity : 0.003 0.033 2763 Dihedral : 3.898 29.169 2124 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.57 % Allowed : 11.91 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.20), residues: 1968 helix: 2.02 (0.19), residues: 812 sheet: 0.15 (0.25), residues: 400 loop : 0.57 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 394 TYR 0.008 0.001 TYR A 149 PHE 0.010 0.001 PHE D 367 TRP 0.004 0.000 TRP A 45 HIS 0.002 0.001 HIS D 308 Details of bonding type rmsd covalent geometry : bond 0.00292 (15492) covalent geometry : angle 0.42192 (21031) hydrogen bonds : bond 0.03115 ( 744) hydrogen bonds : angle 4.15412 ( 2160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.552 Fit side-chains REVERT: A 241 PHE cc_start: 0.8212 (t80) cc_final: 0.7873 (t80) REVERT: A 493 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7253 (pm20) REVERT: A 504 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8318 (tp30) REVERT: B 241 PHE cc_start: 0.8211 (t80) cc_final: 0.7836 (t80) REVERT: B 504 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8374 (tp30) REVERT: C 504 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8343 (tp30) REVERT: D 241 PHE cc_start: 0.8151 (t80) cc_final: 0.7819 (t80) REVERT: D 504 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8374 (tp30) outliers start: 9 outliers final: 4 residues processed: 110 average time/residue: 0.7004 time to fit residues: 84.8163 Evaluate side-chains 107 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 504 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 150 optimal weight: 1.9990 chunk 172 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.100090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.076067 restraints weight = 27106.769| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.86 r_work: 0.2880 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 15492 Z= 0.271 Angle : 0.503 5.682 21031 Z= 0.266 Chirality : 0.044 0.160 2316 Planarity : 0.004 0.036 2763 Dihedral : 4.298 34.244 2124 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.82 % Allowed : 11.66 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.20), residues: 1968 helix: 1.84 (0.19), residues: 812 sheet: 0.09 (0.25), residues: 400 loop : 0.44 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 114 TYR 0.013 0.001 TYR A 149 PHE 0.016 0.002 PHE D 367 TRP 0.003 0.001 TRP B 194 HIS 0.004 0.001 HIS C 308 Details of bonding type rmsd covalent geometry : bond 0.00645 (15492) covalent geometry : angle 0.50323 (21031) hydrogen bonds : bond 0.04158 ( 744) hydrogen bonds : angle 4.46978 ( 2160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.653 Fit side-chains REVERT: A 241 PHE cc_start: 0.8223 (t80) cc_final: 0.7876 (t80) REVERT: A 493 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7356 (pm20) REVERT: A 504 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8416 (tp30) REVERT: B 241 PHE cc_start: 0.8245 (t80) cc_final: 0.7864 (t80) REVERT: B 504 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8419 (tp30) REVERT: C 504 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8369 (tp30) REVERT: D 241 PHE cc_start: 0.8219 (t80) cc_final: 0.7870 (t80) REVERT: D 504 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8386 (tp30) outliers start: 13 outliers final: 4 residues processed: 108 average time/residue: 0.5721 time to fit residues: 68.9049 Evaluate side-chains 101 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 504 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 122 optimal weight: 4.9990 chunk 186 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 158 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.101872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.077976 restraints weight = 26486.595| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.88 r_work: 0.2935 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15492 Z= 0.115 Angle : 0.419 5.443 21031 Z= 0.224 Chirality : 0.041 0.155 2316 Planarity : 0.003 0.032 2763 Dihedral : 4.038 31.149 2124 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.63 % Allowed : 11.78 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.20), residues: 1968 helix: 2.00 (0.19), residues: 812 sheet: 0.10 (0.25), residues: 400 loop : 0.54 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 492 TYR 0.007 0.001 TYR A 170 PHE 0.009 0.001 PHE A 427 TRP 0.004 0.001 TRP D 45 HIS 0.002 0.001 HIS D 308 Details of bonding type rmsd covalent geometry : bond 0.00268 (15492) covalent geometry : angle 0.41897 (21031) hydrogen bonds : bond 0.03109 ( 744) hydrogen bonds : angle 4.23166 ( 2160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3426.46 seconds wall clock time: 59 minutes 38.80 seconds (3578.80 seconds total)