Starting phenix.real_space_refine on Fri Jun 13 15:54:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8shs_40493/06_2025/8shs_40493.cif Found real_map, /net/cci-nas-00/data/ceres_data/8shs_40493/06_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_40493/06_2025/8shs_40493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8shs_40493/06_2025/8shs_40493.map" model { file = "/net/cci-nas-00/data/ceres_data/8shs_40493/06_2025/8shs_40493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8shs_40493/06_2025/8shs_40493.cif" } resolution = 2.66 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= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.44, per 1000 atoms: 0.62 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: 3.34 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.94 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: 5.75 Time building geometry restraints manager: 4.01 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: 4.240 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: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.960 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.470 ------------------------------------------------------------------------------- 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 (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: 1.56 (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 TRP 0.006 0.001 TRP C 469 HIS 0.003 0.001 HIS B 173 PHE 0.012 0.001 PHE C 367 TYR 0.005 0.001 TYR C 149 ARG 0.002 0.000 ARG B 147 Details of bonding type rmsd hydrogen bonds : bond 0.13956 ( 744) hydrogen bonds : angle 6.14695 ( 2160) covalent geometry : bond 0.00169 (15492) covalent geometry : angle 0.41662 (21031) *********************** 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 : 2.604 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: 1.6020 time to fit residues: 395.5170 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 : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 46 HIS A 100 HIS A 173 HIS A 192 GLN A 315 GLN A 317 GLN A 407 GLN A 516 ASN B 30 GLN B 43 ASN B 46 HIS B 100 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 100 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 100 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: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.103458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.079455 restraints weight = 26221.188| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.85 r_work: 0.2931 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 15492 Z= 0.176 Angle : 0.465 4.827 21031 Z= 0.247 Chirality : 0.043 0.157 2316 Planarity : 0.004 0.034 2763 Dihedral : 3.836 36.740 2124 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.32 % Allowed : 8.82 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.46 (0.20), residues: 1968 helix: 1.76 (0.18), residues: 836 sheet: 0.51 (0.27), residues: 412 loop : 0.46 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 45 HIS 0.003 0.001 HIS B 308 PHE 0.015 0.001 PHE B 367 TYR 0.009 0.001 TYR B 149 ARG 0.002 0.000 ARG B 492 Details of bonding type rmsd hydrogen bonds : bond 0.04068 ( 744) hydrogen bonds : angle 4.80697 ( 2160) covalent geometry : bond 0.00414 (15492) covalent geometry : angle 0.46539 (21031) *********************** 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 140 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 1.774 Fit side-chains REVERT: B 30 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7821 (mm-40) REVERT: D 30 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7779 (mm-40) REVERT: D 241 PHE cc_start: 0.8136 (t80) cc_final: 0.7927 (t80) REVERT: D 256 ASP cc_start: 0.8525 (m-30) cc_final: 0.8298 (m-30) outliers start: 21 outliers final: 0 residues processed: 132 average time/residue: 1.5340 time to fit residues: 221.0152 Evaluate side-chains 107 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 GLN 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 39 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 184 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN A 361 GLN B 30 GLN B 317 GLN B 361 GLN C 317 GLN C 361 GLN D 30 GLN D 317 GLN D 361 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.101191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.077269 restraints weight = 26575.947| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.84 r_work: 0.2898 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1712 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= 0.250 Angle : 0.503 6.203 21031 Z= 0.267 Chirality : 0.044 0.142 2316 Planarity : 0.004 0.039 2763 Dihedral : 4.245 40.197 2124 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.07 % Allowed : 10.02 % 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 (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: 1.30 (0.20), residues: 1968 helix: 1.59 (0.18), residues: 836 sheet: 0.39 (0.26), residues: 400 loop : 0.45 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 45 HIS 0.004 0.001 HIS B 308 PHE 0.021 0.002 PHE B 241 TYR 0.011 0.001 TYR B 149 ARG 0.003 0.000 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.04270 ( 744) hydrogen bonds : angle 4.66759 ( 2160) covalent geometry : bond 0.00596 (15492) covalent geometry : angle 0.50298 (21031) *********************** 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 131 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.841 Fit side-chains REVERT: A 241 PHE cc_start: 0.8180 (t80) cc_final: 0.7963 (t80) REVERT: A 355 LYS cc_start: 0.8897 (mtpp) cc_final: 0.8690 (mtmm) REVERT: B 241 PHE cc_start: 0.8216 (t80) cc_final: 0.7986 (t80) REVERT: C 241 PHE cc_start: 0.8224 (t80) cc_final: 0.7967 (t80) REVERT: D 241 PHE cc_start: 0.8165 (t80) cc_final: 0.7934 (t80) outliers start: 17 outliers final: 9 residues processed: 123 average time/residue: 1.2913 time to fit residues: 176.1083 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 : 1.534 ------------------------------------------------------------------------------- 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 415 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 92 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.101002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.077228 restraints weight = 26495.825| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.80 r_work: 0.2908 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15492 Z= 0.189 Angle : 0.466 5.357 21031 Z= 0.247 Chirality : 0.043 0.157 2316 Planarity : 0.004 0.036 2763 Dihedral : 4.204 38.057 2124 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.44 % Allowed : 10.65 % 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 (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: 1.27 (0.20), residues: 1968 helix: 1.63 (0.19), residues: 836 sheet: 0.28 (0.26), residues: 400 loop : 0.43 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 45 HIS 0.003 0.001 HIS B 308 PHE 0.014 0.001 PHE D 367 TYR 0.010 0.001 TYR D 149 ARG 0.002 0.000 ARG B 147 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 744) hydrogen bonds : angle 4.50635 ( 2160) covalent geometry : bond 0.00448 (15492) covalent geometry : angle 0.46583 (21031) *********************** 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 117 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 1.793 Fit side-chains REVERT: A 241 PHE cc_start: 0.8178 (t80) cc_final: 0.7913 (t80) REVERT: A 355 LYS cc_start: 0.8880 (mtpp) cc_final: 0.8670 (mtmm) REVERT: B 241 PHE cc_start: 0.8213 (t80) cc_final: 0.7951 (t80) REVERT: B 254 ASP cc_start: 0.7621 (m-30) cc_final: 0.7412 (t0) REVERT: C 241 PHE cc_start: 0.8213 (t80) cc_final: 0.7918 (t80) REVERT: D 241 PHE cc_start: 0.8157 (t80) cc_final: 0.7874 (t80) REVERT: D 254 ASP cc_start: 0.7718 (m-30) cc_final: 0.7476 (t0) outliers start: 7 outliers final: 4 residues processed: 115 average time/residue: 1.3887 time to fit residues: 176.1198 Evaluate side-chains 108 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 1.601 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 21 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 153 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 161 optimal weight: 0.0770 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 GLN D 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.102128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.078261 restraints weight = 26821.981| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.82 r_work: 0.2913 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15492 Z= 0.154 Angle : 0.437 4.751 21031 Z= 0.232 Chirality : 0.042 0.135 2316 Planarity : 0.003 0.034 2763 Dihedral : 4.088 34.875 2124 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.76 % Allowed : 10.78 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.41 (0.20), residues: 1968 helix: 1.87 (0.19), residues: 812 sheet: 0.23 (0.25), residues: 400 loop : 0.45 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 45 HIS 0.002 0.001 HIS B 308 PHE 0.012 0.001 PHE D 367 TYR 0.008 0.001 TYR A 149 ARG 0.002 0.000 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 744) hydrogen bonds : angle 4.36060 ( 2160) covalent geometry : bond 0.00363 (15492) covalent geometry : angle 0.43682 (21031) *********************** 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 127 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 1.607 Fit side-chains REVERT: A 241 PHE cc_start: 0.8176 (t80) cc_final: 0.7896 (t80) REVERT: B 241 PHE cc_start: 0.8216 (t80) cc_final: 0.7905 (t80) REVERT: B 355 LYS cc_start: 0.8893 (mtpp) cc_final: 0.8691 (mtmm) REVERT: C 241 PHE cc_start: 0.8210 (t80) cc_final: 0.7901 (t80) REVERT: D 241 PHE cc_start: 0.8168 (t80) cc_final: 0.7848 (t80) REVERT: D 254 ASP cc_start: 0.7704 (m-30) cc_final: 0.7500 (t0) outliers start: 12 outliers final: 8 residues processed: 124 average time/residue: 1.3650 time to fit residues: 187.9105 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 : 1.717 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 70 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 188 optimal weight: 0.8980 chunk 94 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.100855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.076777 restraints weight = 26645.431| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.88 r_work: 0.2897 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 15492 Z= 0.198 Angle : 0.462 5.507 21031 Z= 0.245 Chirality : 0.043 0.161 2316 Planarity : 0.004 0.035 2763 Dihedral : 4.167 34.948 2124 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.01 % Allowed : 11.47 % 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 (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: 1.38 (0.20), residues: 1968 helix: 1.85 (0.19), residues: 812 sheet: 0.18 (0.25), residues: 400 loop : 0.44 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 45 HIS 0.003 0.001 HIS B 308 PHE 0.013 0.001 PHE D 367 TYR 0.010 0.001 TYR B 149 ARG 0.002 0.000 ARG D 147 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 744) hydrogen bonds : angle 4.39429 ( 2160) covalent geometry : bond 0.00471 (15492) covalent geometry : angle 0.46182 (21031) *********************** 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 118 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 1.793 Fit side-chains REVERT: A 241 PHE cc_start: 0.8210 (t80) cc_final: 0.7908 (t80) REVERT: B 241 PHE cc_start: 0.8242 (t80) cc_final: 0.7904 (t80) REVERT: B 355 LYS cc_start: 0.8875 (mtpp) cc_final: 0.8673 (mtmm) REVERT: B 504 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8226 (tp30) REVERT: C 241 PHE cc_start: 0.8238 (t80) cc_final: 0.7911 (t80) REVERT: C 504 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8185 (tp30) REVERT: D 241 PHE cc_start: 0.8216 (t80) cc_final: 0.7933 (t80) REVERT: D 254 ASP cc_start: 0.7737 (m-30) cc_final: 0.7489 (t0) REVERT: D 504 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8174 (tp30) outliers start: 16 outliers final: 5 residues processed: 118 average time/residue: 1.4248 time to fit residues: 186.0619 Evaluate side-chains 106 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 2.883 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 157 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 193 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 182 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.100276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.076368 restraints weight = 26828.930| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.81 r_work: 0.2883 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15492 Z= 0.224 Angle : 0.479 6.096 21031 Z= 0.254 Chirality : 0.043 0.151 2316 Planarity : 0.004 0.036 2763 Dihedral : 4.284 35.953 2124 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.82 % Allowed : 11.72 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.33 (0.20), residues: 1968 helix: 1.82 (0.19), residues: 812 sheet: 0.15 (0.25), residues: 400 loop : 0.41 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 45 HIS 0.003 0.001 HIS C 308 PHE 0.015 0.001 PHE D 367 TYR 0.011 0.001 TYR C 149 ARG 0.003 0.000 ARG D 492 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 744) hydrogen bonds : angle 4.45714 ( 2160) covalent geometry : bond 0.00532 (15492) covalent geometry : angle 0.47943 (21031) *********************** 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 110 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.619 Fit side-chains REVERT: A 241 PHE cc_start: 0.8226 (t80) cc_final: 0.7941 (t80) REVERT: A 504 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8291 (tp30) REVERT: B 241 PHE cc_start: 0.8244 (t80) cc_final: 0.7954 (t80) REVERT: B 504 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8277 (tp30) REVERT: C 241 PHE cc_start: 0.8241 (t80) cc_final: 0.7893 (t80) REVERT: C 504 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8341 (tp30) REVERT: D 241 PHE cc_start: 0.8238 (t80) cc_final: 0.7940 (t80) REVERT: D 254 ASP cc_start: 0.7821 (m-30) cc_final: 0.7512 (t0) REVERT: D 504 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8331 (tp30) outliers start: 13 outliers final: 4 residues processed: 110 average time/residue: 1.1971 time to fit residues: 147.7700 Evaluate side-chains 104 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 1.516 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 79 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN C 317 GLN D 317 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.102654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.078751 restraints weight = 26493.458| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.88 r_work: 0.2944 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15492 Z= 0.107 Angle : 0.416 4.549 21031 Z= 0.222 Chirality : 0.041 0.159 2316 Planarity : 0.003 0.033 2763 Dihedral : 3.978 30.809 2124 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.50 % Allowed : 12.04 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.52 (0.20), residues: 1968 helix: 1.98 (0.19), residues: 812 sheet: 0.22 (0.25), residues: 400 loop : 0.54 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 45 HIS 0.001 0.001 HIS B 252 PHE 0.008 0.001 PHE A 367 TYR 0.007 0.001 TYR D 442 ARG 0.002 0.000 ARG D 394 Details of bonding type rmsd hydrogen bonds : bond 0.02979 ( 744) hydrogen bonds : angle 4.20656 ( 2160) covalent geometry : bond 0.00246 (15492) covalent geometry : angle 0.41612 (21031) *********************** 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 110 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 1.584 Fit side-chains REVERT: A 241 PHE cc_start: 0.8214 (t80) cc_final: 0.7882 (t80) REVERT: A 504 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8229 (tp30) REVERT: B 241 PHE cc_start: 0.8231 (t80) cc_final: 0.7886 (t80) REVERT: B 504 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8193 (tp30) REVERT: C 241 PHE cc_start: 0.8247 (t80) cc_final: 0.7840 (t80) REVERT: C 504 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8297 (tp30) REVERT: D 241 PHE cc_start: 0.8190 (t80) cc_final: 0.7820 (t80) REVERT: D 254 ASP cc_start: 0.7731 (m-30) cc_final: 0.7510 (t0) REVERT: D 504 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8278 (tp30) outliers start: 8 outliers final: 0 residues processed: 106 average time/residue: 1.2261 time to fit residues: 145.4637 Evaluate side-chains 101 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 1.613 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 94 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 chunk 167 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 49 optimal weight: 0.0570 chunk 182 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 overall best weight: 1.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN C 317 GLN D 317 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.101003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.077204 restraints weight = 26665.684| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.81 r_work: 0.2905 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 : 0.004 0.034 15492 Z= 0.189 Angle : 0.453 5.297 21031 Z= 0.240 Chirality : 0.043 0.160 2316 Planarity : 0.003 0.035 2763 Dihedral : 4.097 31.947 2124 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.82 % Allowed : 12.10 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.45 (0.20), residues: 1968 helix: 1.93 (0.19), residues: 812 sheet: 0.18 (0.25), residues: 400 loop : 0.48 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 45 HIS 0.003 0.001 HIS B 308 PHE 0.013 0.001 PHE D 367 TYR 0.010 0.001 TYR B 149 ARG 0.002 0.000 ARG C 114 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 744) hydrogen bonds : angle 4.29690 ( 2160) covalent geometry : bond 0.00449 (15492) covalent geometry : angle 0.45256 (21031) *********************** 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 108 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 1.765 Fit side-chains REVERT: A 241 PHE cc_start: 0.8222 (t80) cc_final: 0.7927 (t80) REVERT: A 504 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8327 (tp30) REVERT: B 241 PHE cc_start: 0.8227 (t80) cc_final: 0.7921 (t80) REVERT: B 504 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8278 (tp30) REVERT: C 241 PHE cc_start: 0.8262 (t80) cc_final: 0.7928 (t80) REVERT: C 504 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8297 (tp30) REVERT: D 241 PHE cc_start: 0.8220 (t80) cc_final: 0.7914 (t80) REVERT: D 254 ASP cc_start: 0.7815 (m-30) cc_final: 0.7564 (t0) REVERT: D 504 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8285 (tp30) outliers start: 13 outliers final: 2 residues processed: 106 average time/residue: 1.1817 time to fit residues: 142.5109 Evaluate side-chains 99 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 124 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 85 optimal weight: 0.0570 chunk 78 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.5502 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.100931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.077020 restraints weight = 26768.686| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.88 r_work: 0.2918 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15492 Z= 0.169 Angle : 0.438 4.359 21031 Z= 0.234 Chirality : 0.042 0.151 2316 Planarity : 0.003 0.034 2763 Dihedral : 4.097 32.098 2124 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.50 % Allowed : 12.29 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.45 (0.20), residues: 1968 helix: 1.94 (0.19), residues: 812 sheet: 0.19 (0.25), residues: 400 loop : 0.47 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 45 HIS 0.002 0.001 HIS C 308 PHE 0.012 0.001 PHE D 367 TYR 0.009 0.001 TYR A 149 ARG 0.002 0.000 ARG D 394 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 744) hydrogen bonds : angle 4.29347 ( 2160) covalent geometry : bond 0.00400 (15492) covalent geometry : angle 0.43813 (21031) ********************** 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 101 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 1.626 Fit side-chains REVERT: A 241 PHE cc_start: 0.8204 (t80) cc_final: 0.7906 (t80) REVERT: A 504 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8319 (tp30) REVERT: B 241 PHE cc_start: 0.8232 (t80) cc_final: 0.7926 (t80) REVERT: B 504 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8301 (tp30) REVERT: C 241 PHE cc_start: 0.8250 (t80) cc_final: 0.7914 (t80) REVERT: C 415 GLU cc_start: 0.8235 (mm-30) cc_final: 0.8014 (mp0) REVERT: C 504 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8322 (tp30) REVERT: D 241 PHE cc_start: 0.8195 (t80) cc_final: 0.7889 (t80) REVERT: D 254 ASP cc_start: 0.7850 (m-30) cc_final: 0.7515 (t0) REVERT: D 504 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8313 (tp30) outliers start: 8 outliers final: 4 residues processed: 101 average time/residue: 1.1518 time to fit residues: 130.8959 Evaluate side-chains 99 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 1.704 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 146 optimal weight: 3.9990 chunk 167 optimal weight: 0.0370 chunk 134 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 0.0980 chunk 61 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 overall best weight: 0.9862 ------------------------------------------------------------------------------- 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 = 0.3409 r_free = 0.3409 target = 0.102183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.078382 restraints weight = 26549.129| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.84 r_work: 0.2933 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15492 Z= 0.120 Angle : 0.413 4.271 21031 Z= 0.221 Chirality : 0.041 0.151 2316 Planarity : 0.003 0.033 2763 Dihedral : 3.969 29.982 2124 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.38 % Allowed : 12.35 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.55 (0.20), residues: 1968 helix: 2.02 (0.19), residues: 812 sheet: 0.23 (0.25), residues: 400 loop : 0.53 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 45 HIS 0.002 0.001 HIS C 308 PHE 0.009 0.001 PHE B 367 TYR 0.007 0.001 TYR D 149 ARG 0.002 0.000 ARG D 394 Details of bonding type rmsd hydrogen bonds : bond 0.03129 ( 744) hydrogen bonds : angle 4.18494 ( 2160) covalent geometry : bond 0.00279 (15492) covalent geometry : angle 0.41327 (21031) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7970.54 seconds wall clock time: 137 minutes 51.69 seconds (8271.69 seconds total)