Starting phenix.real_space_refine on Fri Sep 27 06:10:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shs_40493/09_2024/8shs_40493.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shs_40493/09_2024/8shs_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shs_40493/09_2024/8shs_40493.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shs_40493/09_2024/8shs_40493.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shs_40493/09_2024/8shs_40493.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shs_40493/09_2024/8shs_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.84, per 1000 atoms: 0.58 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: 3.10 Conformation dependent library (CDL) restraints added in 1.8 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: 1.63 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: 4.95 Time building geometry restraints manager: 3.72 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: 2.080 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: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 33.520 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 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:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.650 ------------------------------------------------------------------------------- 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= 0.110 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 *********************** 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 fitting. rotamer outliers: 8 poor density : 220 time to evaluate : 1.714 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: 1.6424 time to fit residues: 405.7428 Evaluate side-chains 113 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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= 0.269 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 *********************** 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 fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 1.592 Fit side-chains outliers start: 21 outliers final: 0 residues processed: 132 average time/residue: 1.4537 time to fit residues: 209.9777 Evaluate side-chains 105 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 4.9990 chunk 55 optimal weight: 0.0770 chunk 148 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 178 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1564 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= 0.213 Angle : 0.430 4.270 21031 Z= 0.228 Chirality : 0.042 0.133 2316 Planarity : 0.004 0.036 2763 Dihedral : 3.898 35.348 2124 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.82 % Allowed : 9.77 % Favored : 89.41 % 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: 1.43 (0.20), residues: 1968 helix: 1.75 (0.18), residues: 836 sheet: 0.40 (0.26), residues: 412 loop : 0.48 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 45 HIS 0.002 0.001 HIS D 308 PHE 0.021 0.001 PHE B 241 TYR 0.008 0.001 TYR B 149 ARG 0.003 0.000 ARG B 51 *********************** 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 127 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.548 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 119 average time/residue: 1.3620 time to fit residues: 178.8755 Evaluate side-chains 111 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 415 GLU 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 176 optimal weight: 0.0770 chunk 134 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 51 optimal weight: 0.0970 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN B 361 GLN D 361 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1692 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= 0.221 Angle : 0.432 4.422 21031 Z= 0.229 Chirality : 0.042 0.149 2316 Planarity : 0.003 0.034 2763 Dihedral : 3.913 34.375 2124 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.88 % Allowed : 10.40 % Favored : 88.72 % 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: 1.40 (0.20), residues: 1968 helix: 1.76 (0.18), residues: 836 sheet: 0.30 (0.26), residues: 412 loop : 0.50 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 45 HIS 0.002 0.001 HIS B 308 PHE 0.012 0.001 PHE C 367 TYR 0.009 0.001 TYR A 149 ARG 0.001 0.000 ARG C 394 *********************** 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 120 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 1.679 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 115 average time/residue: 1.3455 time to fit residues: 171.4452 Evaluate side-chains 114 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain B residue 89 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 96 optimal weight: 0.9980 chunk 170 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 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 C 361 GLN D 317 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 15492 Z= 0.453 Angle : 0.523 6.863 21031 Z= 0.276 Chirality : 0.045 0.144 2316 Planarity : 0.004 0.038 2763 Dihedral : 4.337 38.880 2124 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.07 % Allowed : 10.59 % Favored : 88.34 % 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: 1.19 (0.20), residues: 1968 helix: 1.57 (0.18), residues: 836 sheet: 0.16 (0.25), residues: 400 loop : 0.43 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 45 HIS 0.005 0.001 HIS D 308 PHE 0.018 0.002 PHE D 367 TYR 0.012 0.001 TYR D 149 ARG 0.003 0.000 ARG D 147 *********************** 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 135 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 1.724 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 127 average time/residue: 1.2508 time to fit residues: 176.3861 Evaluate side-chains 106 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 1.753 ------------------------------------------------------------------------------- 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 63 optimal weight: 0.5980 chunk 170 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15492 Z= 0.193 Angle : 0.431 4.539 21031 Z= 0.229 Chirality : 0.041 0.157 2316 Planarity : 0.003 0.034 2763 Dihedral : 4.081 34.401 2124 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.82 % Allowed : 11.41 % 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 (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: 1.42 (0.20), residues: 1968 helix: 1.88 (0.19), residues: 812 sheet: 0.17 (0.25), residues: 400 loop : 0.50 (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 C 308 PHE 0.011 0.001 PHE D 367 TYR 0.008 0.001 TYR B 149 ARG 0.002 0.000 ARG B 492 *********************** 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 fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 1.694 Fit side-chains outliers start: 13 outliers final: 2 residues processed: 113 average time/residue: 1.2951 time to fit residues: 162.3601 Evaluate side-chains 95 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 504 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 108 optimal weight: 0.0470 chunk 138 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 188 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15492 Z= 0.148 Angle : 0.417 5.318 21031 Z= 0.220 Chirality : 0.041 0.140 2316 Planarity : 0.003 0.032 2763 Dihedral : 3.883 30.415 2124 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.76 % Allowed : 11.78 % 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: 1.58 (0.20), residues: 1968 helix: 1.99 (0.19), residues: 812 sheet: 0.22 (0.25), residues: 400 loop : 0.62 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP D 45 HIS 0.001 0.001 HIS D 308 PHE 0.009 0.001 PHE D 367 TYR 0.007 0.001 TYR A 149 ARG 0.002 0.000 ARG A 492 *********************** 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 116 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 1.628 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 114 average time/residue: 1.4304 time to fit residues: 180.7596 Evaluate side-chains 97 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain D residue 503 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN B 271 GLN B 317 GLN C 271 GLN C 317 GLN D 317 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1987 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= 0.352 Angle : 0.486 5.863 21031 Z= 0.253 Chirality : 0.043 0.156 2316 Planarity : 0.004 0.034 2763 Dihedral : 4.098 32.762 2124 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.32 % Allowed : 12.54 % Favored : 87.15 % 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: 1.43 (0.20), residues: 1968 helix: 1.90 (0.19), residues: 812 sheet: 0.15 (0.25), residues: 400 loop : 0.50 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 45 HIS 0.004 0.001 HIS B 308 PHE 0.014 0.001 PHE D 367 TYR 0.011 0.001 TYR A 149 ARG 0.002 0.000 ARG A 114 *********************** 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 101 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 1.667 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 101 average time/residue: 1.2306 time to fit residues: 138.7494 Evaluate side-chains 99 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 1.726 ------------------------------------------------------------------------------- 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 D residue 503 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 8.9990 chunk 180 optimal weight: 0.7980 chunk 165 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 175 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15492 Z= 0.172 Angle : 0.437 6.752 21031 Z= 0.229 Chirality : 0.041 0.147 2316 Planarity : 0.003 0.033 2763 Dihedral : 3.957 30.615 2124 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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: 1.56 (0.20), residues: 1968 helix: 2.01 (0.19), residues: 812 sheet: 0.17 (0.25), residues: 400 loop : 0.60 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP D 45 HIS 0.002 0.001 HIS C 308 PHE 0.009 0.001 PHE D 367 TYR 0.007 0.001 TYR B 149 ARG 0.002 0.000 ARG C 394 *********************** 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 107 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 1.805 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 107 average time/residue: 1.3783 time to fit residues: 163.0856 Evaluate side-chains 101 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain D residue 503 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 113 optimal weight: 0.0010 chunk 88 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.9590 ------------------------------------------------------------------------------- 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 D 317 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15492 Z= 0.183 Angle : 0.437 7.629 21031 Z= 0.228 Chirality : 0.041 0.146 2316 Planarity : 0.003 0.032 2763 Dihedral : 3.898 28.933 2124 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.25 % Allowed : 12.85 % Favored : 86.89 % 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: 1.62 (0.20), residues: 1968 helix: 2.06 (0.19), residues: 812 sheet: 0.22 (0.25), residues: 400 loop : 0.61 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP D 45 HIS 0.002 0.001 HIS C 308 PHE 0.010 0.001 PHE D 367 TYR 0.007 0.001 TYR A 149 ARG 0.002 0.000 ARG C 394 ********************** 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 104 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 1.637 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 104 average time/residue: 1.2443 time to fit residues: 146.1263 Evaluate side-chains 100 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain D residue 503 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.102099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.078409 restraints weight = 26489.220| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.83 r_work: 0.2934 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 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 : 0.003 0.041 15492 Z= 0.217 Angle : 0.451 7.370 21031 Z= 0.235 Chirality : 0.042 0.155 2316 Planarity : 0.003 0.032 2763 Dihedral : 3.926 28.913 2124 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.25 % Allowed : 12.85 % Favored : 86.89 % 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: 1.61 (0.20), residues: 1968 helix: 2.08 (0.19), residues: 812 sheet: 0.21 (0.25), residues: 400 loop : 0.59 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 45 HIS 0.002 0.001 HIS B 308 PHE 0.011 0.001 PHE B 367 TYR 0.008 0.001 TYR B 149 ARG 0.002 0.000 ARG D 394 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4070.65 seconds wall clock time: 72 minutes 38.19 seconds (4358.19 seconds total)