Starting phenix.real_space_refine on Sun Aug 24 05:52:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tpw_41495/08_2025/8tpw_41495.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tpw_41495/08_2025/8tpw_41495.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tpw_41495/08_2025/8tpw_41495.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tpw_41495/08_2025/8tpw_41495.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tpw_41495/08_2025/8tpw_41495.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tpw_41495/08_2025/8tpw_41495.map" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.043 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 49 5.16 5 C 10720 2.51 5 N 3131 2.21 5 O 3353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17254 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6788 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 903, 6727 Classifications: {'peptide': 903} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 46, 'TRANS': 856} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 903, 6727 Classifications: {'peptide': 903} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 46, 'TRANS': 856} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 6787 Chain: "B" Number of atoms: 6765 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 900, 6704 Classifications: {'peptide': 900} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 46, 'TRANS': 853} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 900, 6704 Classifications: {'peptide': 900} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 46, 'TRANS': 853} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 6765 Chain: "H" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1539 Classifications: {'peptide': 205} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 193} Chain breaks: 2 Chain: "L" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1596 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 194} Chain breaks: 2 Chain: "C" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 566 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4HH:plan-3': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AARG A 58 " occ=0.20 ... (20 atoms not shown) pdb=" NH2BARG A 58 " occ=0.80 residue: pdb=" N AGLU A 161 " occ=0.12 ... (16 atoms not shown) pdb=" OE2BGLU A 161 " occ=0.88 residue: pdb=" N AGLU B 161 " occ=0.81 ... (16 atoms not shown) pdb=" OE2BGLU B 161 " occ=0.19 residue: pdb=" N AARG B 486 " occ=0.58 ... (20 atoms not shown) pdb=" NH2BARG B 486 " occ=0.42 Time building chain proxies: 7.13, per 1000 atoms: 0.41 Number of scatterers: 17254 At special positions: 0 Unit cell: (95.532, 118.158, 193.578, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 1 15.00 O 3353 8.00 N 3131 7.00 C 10720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 24 " - pdb=" SG CYS H 100 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 39 " - pdb=" SG CYS L 109 " distance=2.04 Simple disulfide: pdb=" SG CYS L 156 " - pdb=" SG CYS L 216 " distance=2.03 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: 1.21 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.2 microseconds 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4164 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 23 sheets defined 40.2% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 3 through 31 Processing helix chain 'A' and resid 49 through 60 Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.502A pdb=" N HIS A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 removed outlier: 4.022A pdb=" N PHE A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 118 Processing helix chain 'A' and resid 119 through 136 removed outlier: 3.815A pdb=" N ARG A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 144 removed outlier: 3.548A pdb=" N ARG A 144 " --> pdb=" O HIS A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 removed outlier: 3.683A pdb=" N THR A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 191 removed outlier: 3.958A pdb=" N SER A 183 " --> pdb=" O PRO A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 220 removed outlier: 3.565A pdb=" N VAL A 208 " --> pdb=" O SER A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 245 removed outlier: 3.780A pdb=" N GLN A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 310 through 326 Processing helix chain 'A' and resid 328 through 332 removed outlier: 3.988A pdb=" N VAL A 332 " --> pdb=" O PRO A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 357 removed outlier: 3.857A pdb=" N ILE A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 3.733A pdb=" N ILE A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 381 No H-bonds generated for 'chain 'A' and resid 379 through 381' Processing helix chain 'A' and resid 382 through 398 Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.972A pdb=" N SER A 417 " --> pdb=" O ASP A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 496 Processing helix chain 'A' and resid 502 through 514 removed outlier: 4.376A pdb=" N ARG A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 541 removed outlier: 3.828A pdb=" N GLY A 541 " --> pdb=" O GLU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 582 Processing helix chain 'A' and resid 582 through 597 removed outlier: 3.572A pdb=" N ALA A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 619 through 640 Proline residue: A 625 - end of helix Processing helix chain 'A' and resid 653 through 662 removed outlier: 3.912A pdb=" N ALA A 657 " --> pdb=" O GLN A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 684 removed outlier: 4.175A pdb=" N SER A 683 " --> pdb=" O ARG A 679 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 704 Processing helix chain 'A' and resid 727 through 742 Processing helix chain 'A' and resid 756 through 763 removed outlier: 4.118A pdb=" N ARG A 763 " --> pdb=" O GLU A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 770 removed outlier: 3.909A pdb=" N GLU A 768 " --> pdb=" O GLU A 764 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR A 769 " --> pdb=" O GLU A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 805 Processing helix chain 'A' and resid 810 through 822 Processing helix chain 'A' and resid 835 through 846 Processing helix chain 'A' and resid 864 through 877 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.664A pdb=" N VAL A 886 " --> pdb=" O ARG A 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 32 removed outlier: 3.908A pdb=" N ASP B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.715A pdb=" N HIS B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 109 removed outlier: 3.838A pdb=" N PHE B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 118 Processing helix chain 'B' and resid 119 through 136 removed outlier: 3.605A pdb=" N ARG B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 127 " --> pdb=" O ARG B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 144 removed outlier: 3.628A pdb=" N ARG B 144 " --> pdb=" O HIS B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 180 through 191 Processing helix chain 'B' and resid 204 through 219 removed outlier: 3.884A pdb=" N VAL B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 245 removed outlier: 3.683A pdb=" N GLN B 245 " --> pdb=" O ASP B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 285 Processing helix chain 'B' and resid 310 through 326 Processing helix chain 'B' and resid 344 through 355 removed outlier: 3.752A pdb=" N ILE B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 381 No H-bonds generated for 'chain 'B' and resid 379 through 381' Processing helix chain 'B' and resid 382 through 398 removed outlier: 3.731A pdb=" N GLY B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 390 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.580A pdb=" N SER B 417 " --> pdb=" O ASP B 414 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY B 418 " --> pdb=" O TRP B 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 414 through 418' Processing helix chain 'B' and resid 481 through 497 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 527 through 540 Processing helix chain 'B' and resid 576 through 581 removed outlier: 3.650A pdb=" N SER B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 597 Processing helix chain 'B' and resid 604 through 610 Processing helix chain 'B' and resid 619 through 641 removed outlier: 3.565A pdb=" N VAL B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Proline residue: B 625 - end of helix removed outlier: 3.672A pdb=" N TYR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 663 removed outlier: 4.173A pdb=" N ILE B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 682 Processing helix chain 'B' and resid 701 through 705 Processing helix chain 'B' and resid 727 through 742 removed outlier: 4.411A pdb=" N ALA B 740 " --> pdb=" O GLU B 736 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 761 removed outlier: 4.025A pdb=" N GLU B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG B 761 " --> pdb=" O PRO B 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 756 through 761' Processing helix chain 'B' and resid 762 through 771 removed outlier: 3.587A pdb=" N LEU B 767 " --> pdb=" O ARG B 763 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 768 " --> pdb=" O GLU B 764 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 807 Processing helix chain 'B' and resid 810 through 822 Processing helix chain 'B' and resid 835 through 846 Processing helix chain 'B' and resid 865 through 877 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.766A pdb=" N VAL B 886 " --> pdb=" O ARG B 883 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 34 removed outlier: 3.893A pdb=" N ASP H 33 " --> pdb=" O THR H 30 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TYR H 34 " --> pdb=" O PHE H 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 30 through 34' Processing helix chain 'H' and resid 55 through 59 Processing helix chain 'H' and resid 91 through 95 Processing helix chain 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'L' and resid 100 through 104 removed outlier: 3.784A pdb=" N VAL L 104 " --> pdb=" O ALA L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 150 Processing helix chain 'L' and resid 205 through 211 removed outlier: 3.936A pdb=" N HIS L 211 " --> pdb=" O ASP L 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 1415 through 1426 removed outlier: 3.524A pdb=" N GLU C1426 " --> pdb=" O ASN C1422 " (cutoff:3.500A) Processing helix chain 'C' and resid 1441 through 1446 Processing helix chain 'C' and resid 1448 through 1463 removed outlier: 3.551A pdb=" N THR C1463 " --> pdb=" O LEU C1459 " (cutoff:3.500A) Processing helix chain 'C' and resid 1470 through 1475 Processing helix chain 'C' and resid 1477 through 1486 removed outlier: 3.975A pdb=" N ALA C1482 " --> pdb=" O VAL C1478 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN C1483 " --> pdb=" O THR C1479 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N HIS C1484 " --> pdb=" O ALA C1480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 199 removed outlier: 8.607A pdb=" N ILE A 197 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL A 150 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL A 199 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU A 152 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER A 38 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU A 276 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE A 36 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA A 290 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE A 453 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER A 295 " --> pdb=" O HIS A 451 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N HIS A 451 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU A 297 " --> pdb=" O ASN A 449 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN A 449 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA A 334 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 370 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LEU A 367 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AA3, first strand: chain 'A' and resid 399 through 400 removed outlier: 3.559A pdb=" N GLN A 427 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 479 Processing sheet with id=AA5, first strand: chain 'A' and resid 647 through 649 removed outlier: 6.347A pdb=" N VAL A 561 " --> pdb=" O ILE A 827 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 715 through 716 Processing sheet with id=AA7, first strand: chain 'B' and resid 196 through 199 removed outlier: 6.515A pdb=" N VAL B 150 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL B 199 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 152 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY B 228 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA B 230 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL B 270 " --> pdb=" O CYS B 41 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N CYS B 41 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU B 272 " --> pdb=" O MET B 39 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N MET B 39 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU B 274 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA B 290 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE B 453 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER B 295 " --> pdb=" O HIS B 451 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS B 451 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU B 297 " --> pdb=" O ASN B 449 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASN B 449 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA B 334 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N SER B 441 " --> pdb=" O ALA B 334 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU B 367 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 66 Processing sheet with id=AA9, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AB1, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AB2, first strand: chain 'B' and resid 473 through 478 Processing sheet with id=AB3, first strand: chain 'B' and resid 781 through 783 removed outlier: 4.819A pdb=" N GLY B 650 " --> pdb=" O HIS B 783 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 560 " --> pdb=" O ALA B 647 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N VAL B 649 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE B 562 " --> pdb=" O VAL B 649 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N PHE B 826 " --> pdb=" O VAL B 855 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 715 through 716 removed outlier: 4.175A pdb=" N ALA B 715 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 5 through 9 Processing sheet with id=AB6, first strand: chain 'H' and resid 12 through 14 removed outlier: 6.798A pdb=" N MET H 36 " --> pdb=" O PHE H 52 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N PHE H 52 " --> pdb=" O MET H 36 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP H 38 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 12 through 14 removed outlier: 4.300A pdb=" N TYR H 109 " --> pdb=" O ARG H 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 127 through 131 removed outlier: 6.123A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 127 through 131 removed outlier: 6.123A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER H 184 " --> pdb=" O VAL H 176 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL H 176 " --> pdb=" O SER H 184 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 158 through 161 Processing sheet with id=AC2, first strand: chain 'L' and resid 21 through 22 Processing sheet with id=AC3, first strand: chain 'L' and resid 74 through 75 removed outlier: 6.520A pdb=" N TRP L 56 " --> pdb=" O LEU L 68 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N TYR L 70 " --> pdb=" O LEU L 54 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU L 54 " --> pdb=" O TYR L 70 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 136 through 140 removed outlier: 5.943A pdb=" N TYR L 195 " --> pdb=" O ASN L 160 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 167 through 170 798 hydrogen bonds defined for protein. 2219 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.94 Time building geometry restraints manager: 1.57 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: 6040 1.34 - 1.46: 3824 1.46 - 1.58: 7652 1.58 - 1.70: 2 1.70 - 1.82: 79 Bond restraints: 17597 Sorted by residual: bond pdb=" N THR A 513 " pdb=" CA THR A 513 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.27e-02 6.20e+03 4.97e+00 bond pdb=" C THR A 513 " pdb=" O THR A 513 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.11e-02 8.12e+03 1.69e+00 bond pdb=" C ALA A 597 " pdb=" N PRO A 598 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.16e+00 bond pdb=" C GLY B 573 " pdb=" O GLY B 573 " ideal model delta sigma weight residual 1.245 1.235 0.010 1.19e-02 7.06e+03 7.48e-01 bond pdb=" CB MET A 596 " pdb=" CG MET A 596 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.34e-01 ... (remaining 17592 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 23822 2.77 - 5.54: 111 5.54 - 8.30: 5 8.30 - 11.07: 3 11.07 - 13.84: 1 Bond angle restraints: 23942 Sorted by residual: angle pdb=" CB MET A 596 " pdb=" CG MET A 596 " pdb=" SD MET A 596 " ideal model delta sigma weight residual 112.70 126.54 -13.84 3.00e+00 1.11e-01 2.13e+01 angle pdb=" N VAL A 372 " pdb=" CA VAL A 372 " pdb=" C VAL A 372 " ideal model delta sigma weight residual 113.42 109.29 4.13 1.17e+00 7.31e-01 1.25e+01 angle pdb=" CA MET B 596 " pdb=" CB MET B 596 " pdb=" CG MET B 596 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.87e+00 angle pdb=" CB MET B 681 " pdb=" CG MET B 681 " pdb=" SD MET B 681 " ideal model delta sigma weight residual 112.70 121.65 -8.95 3.00e+00 1.11e-01 8.91e+00 angle pdb=" CA THR A 513 " pdb=" CB THR A 513 " pdb=" OG1 THR A 513 " ideal model delta sigma weight residual 109.60 105.17 4.43 1.50e+00 4.44e-01 8.74e+00 ... (remaining 23937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 9586 17.82 - 35.65: 739 35.65 - 53.47: 168 53.47 - 71.29: 31 71.29 - 89.12: 19 Dihedral angle restraints: 10543 sinusoidal: 4032 harmonic: 6511 Sorted by residual: dihedral pdb=" CA ASP B 864 " pdb=" CB ASP B 864 " pdb=" CG ASP B 864 " pdb=" OD1 ASP B 864 " ideal model delta sinusoidal sigma weight residual -30.00 -88.50 58.50 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CG ARG B 810 " pdb=" CD ARG B 810 " pdb=" NE ARG B 810 " pdb=" CZ ARG B 810 " ideal model delta sinusoidal sigma weight residual 180.00 135.22 44.78 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB GLU B 787 " pdb=" CG GLU B 787 " pdb=" CD GLU B 787 " pdb=" OE1 GLU B 787 " ideal model delta sinusoidal sigma weight residual 0.00 -88.52 88.52 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 10540 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1679 0.027 - 0.055: 621 0.055 - 0.082: 182 0.082 - 0.109: 166 0.109 - 0.136: 46 Chirality restraints: 2694 Sorted by residual: chirality pdb=" CA PRO A 598 " pdb=" N PRO A 598 " pdb=" C PRO A 598 " pdb=" CB PRO A 598 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA VAL H 39 " pdb=" N VAL H 39 " pdb=" C VAL H 39 " pdb=" CB VAL H 39 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA VAL A 270 " pdb=" N VAL A 270 " pdb=" C VAL A 270 " pdb=" CB VAL A 270 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 2691 not shown) Planarity restraints: 3193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 727 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO B 728 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 728 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 728 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 756 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO A 757 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 757 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 757 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 597 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO A 598 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 598 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 598 " 0.022 5.00e-02 4.00e+02 ... (remaining 3190 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1030 2.73 - 3.27: 17591 3.27 - 3.82: 28275 3.82 - 4.36: 31190 4.36 - 4.90: 55299 Nonbonded interactions: 133385 Sorted by model distance: nonbonded pdb=" OD1 ASP A 98 " pdb=" N ASP A 99 " model vdw 2.188 3.120 nonbonded pdb=" NH2 ARG A 558 " pdb=" O ASP A 851 " model vdw 2.220 3.120 nonbonded pdb=" O TRP L 170 " pdb=" NZ LYS L 171 " model vdw 2.231 3.120 nonbonded pdb=" O ALA A 753 " pdb=" OG SER A 756 " model vdw 2.238 3.040 nonbonded pdb=" O LYS C1457 " pdb=" OG SER C1460 " model vdw 2.244 3.040 ... (remaining 133380 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' and (resid 3 through 12 or resid 14 through 26 or resid 28 through 47 \ or resid 49 through 57 or resid 59 through 160 or resid 162 through 169 or (res \ id 170 and (name N or name CA or name C or name O or name CB )) or resid 171 thr \ ough 485 or resid 487 through 573 or (resid 574 and (name N or name CA or name C \ or name O or name CB )) or resid 575 through 691 or resid 700 through 859 or (r \ esid 860 and (name N or name CA or name C or name O or name CB )) or resid 861 t \ hrough 910)) selection = (chain 'B' and (resid 3 through 12 or resid 14 through 26 or resid 28 through 47 \ or resid 49 through 57 or resid 59 through 160 or resid 162 through 485 or resi \ d 487 through 709 or resid 713 through 809 or (resid 810 and (name N or name CA \ or name C or name O or name CB )) or resid 811 through 910)) } 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=0.00 max=1.00 mean=0.99 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: 7.610 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.360 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 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 : 0.003 0.033 17601 Z= 0.118 Angle : 0.495 13.838 23950 Z= 0.254 Chirality : 0.040 0.136 2694 Planarity : 0.003 0.041 3193 Dihedral : 14.064 89.116 6367 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.33 % Favored : 95.63 % Rotamer: Outliers : 1.46 % Allowed : 9.30 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.18), residues: 2299 helix: 2.55 (0.19), residues: 773 sheet: 0.72 (0.26), residues: 416 loop : -0.45 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 520 TYR 0.008 0.001 TYR B 357 PHE 0.013 0.001 PHE H 52 TRP 0.013 0.001 TRP A 571 HIS 0.004 0.001 HIS C1475 Details of bonding type rmsd covalent geometry : bond 0.00257 (17597) covalent geometry : angle 0.49542 (23942) SS BOND : bond 0.00269 ( 4) SS BOND : angle 0.49819 ( 8) hydrogen bonds : bond 0.15113 ( 778) hydrogen bonds : angle 5.52736 ( 2219) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.8389 (mmt) cc_final: 0.7803 (mmt) REVERT: A 690 MET cc_start: 0.8604 (mmt) cc_final: 0.7875 (mmp) REVERT: A 780 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8720 (m) REVERT: B 599 MET cc_start: 0.9315 (mmp) cc_final: 0.8818 (mtt) REVERT: B 791 MET cc_start: 0.8725 (ppp) cc_final: 0.7892 (ppp) REVERT: H 36 MET cc_start: 0.9374 (mmp) cc_final: 0.9001 (mmp) REVERT: L 100 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8614 (mm-30) REVERT: L 211 HIS cc_start: 0.8082 (OUTLIER) cc_final: 0.7756 (p90) REVERT: C 1422 ASN cc_start: 0.9241 (m110) cc_final: 0.9014 (m110) REVERT: C 1483 GLN cc_start: 0.9584 (mp10) cc_final: 0.9266 (mp10) outliers start: 16 outliers final: 14 residues processed: 73 average time/residue: 0.1353 time to fit residues: 15.3785 Evaluate side-chains 68 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 703 ARG Chi-restraints excluded: chain H residue 86 GLN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 211 HIS Chi-restraints excluded: chain C residue 1416 LEU Chi-restraints excluded: chain C residue 1436 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 0.0870 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN A 610 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.040215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.025923 restraints weight = 718855.354| |-----------------------------------------------------------------------------| r_work (start): 0.2494 rms_B_bonded: 10.98 r_work: 0.2297 rms_B_bonded: 9.29 restraints_weight: 2.0000 r_work: 0.2418 rms_B_bonded: 5.93 restraints_weight: 4.0000 r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2416 r_free = 0.2416 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2416 r_free = 0.2416 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 113 | |-----------------------------------------------------------------------------| r_final: 0.2416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.0729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17601 Z= 0.128 Angle : 0.510 9.276 23950 Z= 0.261 Chirality : 0.041 0.136 2694 Planarity : 0.004 0.040 3193 Dihedral : 4.644 57.042 2562 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.51 % Favored : 95.45 % Rotamer: Outliers : 1.40 % Allowed : 9.92 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.18), residues: 2299 helix: 2.59 (0.19), residues: 796 sheet: 0.71 (0.25), residues: 432 loop : -0.51 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1466 TYR 0.009 0.001 TYR B 357 PHE 0.011 0.001 PHE C1473 TRP 0.012 0.001 TRP A 571 HIS 0.003 0.001 HIS C1475 Details of bonding type rmsd covalent geometry : bond 0.00287 (17597) covalent geometry : angle 0.51037 (23942) SS BOND : bond 0.00290 ( 4) SS BOND : angle 0.56177 ( 8) hydrogen bonds : bond 0.03843 ( 778) hydrogen bonds : angle 4.41575 ( 2219) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.8257 (mmt) cc_final: 0.7689 (mmt) REVERT: A 681 MET cc_start: 0.9382 (tpp) cc_final: 0.9126 (tpp) REVERT: A 690 MET cc_start: 0.8643 (mmt) cc_final: 0.7900 (mmp) REVERT: B 599 MET cc_start: 0.9364 (mmp) cc_final: 0.8827 (mtt) REVERT: B 791 MET cc_start: 0.8814 (ppp) cc_final: 0.8004 (ppp) REVERT: H 36 MET cc_start: 0.9530 (mmp) cc_final: 0.9278 (mmp) REVERT: C 1483 GLN cc_start: 0.9580 (mp10) cc_final: 0.9278 (mp10) outliers start: 16 outliers final: 9 residues processed: 71 average time/residue: 0.1414 time to fit residues: 15.7502 Evaluate side-chains 61 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 703 ARG Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain C residue 1416 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 3 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 199 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 126 optimal weight: 0.0670 chunk 123 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.040271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.025852 restraints weight = 857721.595| |-----------------------------------------------------------------------------| r_work (start): 0.2488 rms_B_bonded: 11.75 r_work: 0.2289 rms_B_bonded: 9.55 restraints_weight: 2.0000 r_work: 0.2407 rms_B_bonded: 6.24 restraints_weight: 4.0000 r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2406 r_free = 0.2406 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 113 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2406 r_free = 0.2406 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 122 | |-----------------------------------------------------------------------------| r_final: 0.2406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17601 Z= 0.118 Angle : 0.489 8.736 23950 Z= 0.249 Chirality : 0.040 0.135 2694 Planarity : 0.003 0.039 3193 Dihedral : 4.124 56.753 2547 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.02 % Favored : 95.93 % Rotamer: Outliers : 1.57 % Allowed : 10.15 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.18), residues: 2299 helix: 2.57 (0.19), residues: 801 sheet: 0.71 (0.25), residues: 431 loop : -0.49 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 744 TYR 0.008 0.001 TYR B 357 PHE 0.009 0.001 PHE H 52 TRP 0.012 0.001 TRP A 571 HIS 0.003 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00268 (17597) covalent geometry : angle 0.48891 (23942) SS BOND : bond 0.00251 ( 4) SS BOND : angle 0.48382 ( 8) hydrogen bonds : bond 0.03544 ( 778) hydrogen bonds : angle 4.20959 ( 2219) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.8195 (mmt) cc_final: 0.7601 (mmt) REVERT: A 690 MET cc_start: 0.8631 (mmt) cc_final: 0.7959 (mmp) REVERT: B 791 MET cc_start: 0.8914 (ppp) cc_final: 0.8144 (ppp) REVERT: L 185 VAL cc_start: 0.8756 (OUTLIER) cc_final: 0.8515 (t) REVERT: C 1483 GLN cc_start: 0.9598 (mp10) cc_final: 0.9340 (mp10) outliers start: 18 outliers final: 11 residues processed: 71 average time/residue: 0.1362 time to fit residues: 15.0323 Evaluate side-chains 63 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 703 ARG Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain C residue 1416 LEU Chi-restraints excluded: chain C residue 1436 ILE Chi-restraints excluded: chain C residue 1479 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 175 optimal weight: 4.9990 chunk 13 optimal weight: 0.0670 chunk 143 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.9124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN C1415 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.040192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.025817 restraints weight = 868683.946| |-----------------------------------------------------------------------------| r_work (start): 0.2487 rms_B_bonded: 11.72 r_work: 0.2286 rms_B_bonded: 9.58 restraints_weight: 2.0000 r_work: 0.2405 rms_B_bonded: 6.19 restraints_weight: 4.0000 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2405 r_free = 0.2405 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 122 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2405 r_free = 0.2405 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 111 | |-----------------------------------------------------------------------------| r_final: 0.2405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17601 Z= 0.118 Angle : 0.499 9.203 23950 Z= 0.251 Chirality : 0.040 0.135 2694 Planarity : 0.003 0.038 3193 Dihedral : 4.084 56.636 2544 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.24 % Favored : 95.71 % Rotamer: Outliers : 1.63 % Allowed : 10.48 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.18), residues: 2299 helix: 2.63 (0.19), residues: 794 sheet: 0.70 (0.25), residues: 431 loop : -0.49 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 817 TYR 0.009 0.001 TYR A 641 PHE 0.009 0.001 PHE H 52 TRP 0.011 0.001 TRP A 571 HIS 0.003 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00270 (17597) covalent geometry : angle 0.49854 (23942) SS BOND : bond 0.00244 ( 4) SS BOND : angle 0.47453 ( 8) hydrogen bonds : bond 0.03398 ( 778) hydrogen bonds : angle 4.11535 ( 2219) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.8266 (mmt) cc_final: 0.7679 (mmt) REVERT: A 596 MET cc_start: 0.9433 (ppp) cc_final: 0.9228 (ppp) REVERT: A 681 MET cc_start: 0.9394 (tpp) cc_final: 0.9167 (tpp) REVERT: A 690 MET cc_start: 0.8611 (mmt) cc_final: 0.7931 (mmp) REVERT: B 599 MET cc_start: 0.9347 (mmp) cc_final: 0.8910 (mtt) REVERT: B 791 MET cc_start: 0.8934 (ppp) cc_final: 0.8481 (ppp) REVERT: L 185 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8517 (t) REVERT: C 1483 GLN cc_start: 0.9603 (mp10) cc_final: 0.9341 (mp10) outliers start: 19 outliers final: 13 residues processed: 71 average time/residue: 0.1249 time to fit residues: 13.6824 Evaluate side-chains 64 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 703 ARG Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain C residue 1416 LEU Chi-restraints excluded: chain C residue 1436 ILE Chi-restraints excluded: chain C residue 1479 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 123 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 199 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 175 optimal weight: 0.0970 chunk 9 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 166 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.040281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.025835 restraints weight = 792732.987| |-----------------------------------------------------------------------------| r_work (start): 0.2488 rms_B_bonded: 11.44 r_work: 0.2292 rms_B_bonded: 9.43 restraints_weight: 2.0000 r_work: 0.2411 rms_B_bonded: 6.12 restraints_weight: 4.0000 r_work (final): 0.2411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2411 r_free = 0.2411 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 111 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2411 r_free = 0.2411 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 102 | |-----------------------------------------------------------------------------| r_final: 0.2411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17601 Z= 0.112 Angle : 0.495 8.251 23950 Z= 0.247 Chirality : 0.040 0.136 2694 Planarity : 0.003 0.038 3193 Dihedral : 4.071 56.411 2544 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.07 % Favored : 95.89 % Rotamer: Outliers : 1.68 % Allowed : 10.59 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.18), residues: 2299 helix: 2.66 (0.19), residues: 794 sheet: 0.70 (0.25), residues: 437 loop : -0.49 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 703 TYR 0.007 0.001 TYR B 357 PHE 0.008 0.001 PHE H 52 TRP 0.012 0.001 TRP A 571 HIS 0.003 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00256 (17597) covalent geometry : angle 0.49462 (23942) SS BOND : bond 0.00232 ( 4) SS BOND : angle 0.42419 ( 8) hydrogen bonds : bond 0.03261 ( 778) hydrogen bonds : angle 4.02202 ( 2219) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.8265 (mmt) cc_final: 0.7682 (mmt) REVERT: A 681 MET cc_start: 0.9373 (tpp) cc_final: 0.9097 (tpp) REVERT: A 690 MET cc_start: 0.8548 (mmt) cc_final: 0.7920 (mmp) REVERT: B 599 MET cc_start: 0.9352 (mmp) cc_final: 0.8867 (mtt) REVERT: B 791 MET cc_start: 0.8928 (ppp) cc_final: 0.8434 (ppp) REVERT: L 185 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8505 (t) REVERT: L 207 ASP cc_start: 0.9538 (m-30) cc_final: 0.9232 (p0) REVERT: C 1483 GLN cc_start: 0.9607 (mp10) cc_final: 0.9350 (mp10) outliers start: 20 outliers final: 13 residues processed: 70 average time/residue: 0.1426 time to fit residues: 15.5121 Evaluate side-chains 63 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 703 ARG Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain C residue 1416 LEU Chi-restraints excluded: chain C residue 1436 ILE Chi-restraints excluded: chain C residue 1479 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 153 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 224 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.039694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.025242 restraints weight = 743042.840| |-----------------------------------------------------------------------------| r_work (start): 0.2472 rms_B_bonded: 10.51 r_work: 0.2280 rms_B_bonded: 9.02 restraints_weight: 2.0000 r_work: 0.2395 rms_B_bonded: 5.91 restraints_weight: 4.0000 r_work (final): 0.2395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2395 r_free = 0.2395 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 102 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2395 r_free = 0.2395 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 102 | |-----------------------------------------------------------------------------| r_final: 0.2395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17601 Z= 0.167 Angle : 0.536 11.239 23950 Z= 0.268 Chirality : 0.041 0.134 2694 Planarity : 0.004 0.037 3193 Dihedral : 4.221 55.536 2544 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.95 % Favored : 95.01 % Rotamer: Outliers : 1.46 % Allowed : 11.21 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.18), residues: 2299 helix: 2.61 (0.19), residues: 795 sheet: 0.61 (0.25), residues: 437 loop : -0.52 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 520 TYR 0.011 0.001 TYR B 357 PHE 0.011 0.001 PHE H 52 TRP 0.010 0.001 TRP A 571 HIS 0.004 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00379 (17597) covalent geometry : angle 0.53585 (23942) SS BOND : bond 0.00302 ( 4) SS BOND : angle 0.57597 ( 8) hydrogen bonds : bond 0.03840 ( 778) hydrogen bonds : angle 4.17519 ( 2219) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.8209 (mmt) cc_final: 0.7725 (mmt) REVERT: A 681 MET cc_start: 0.9351 (tpp) cc_final: 0.9059 (tpp) REVERT: B 599 MET cc_start: 0.9393 (mmp) cc_final: 0.8925 (mtt) REVERT: B 791 MET cc_start: 0.8897 (ppp) cc_final: 0.8367 (ppp) REVERT: L 100 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8249 (mp0) REVERT: L 185 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8501 (t) REVERT: L 211 HIS cc_start: 0.8719 (OUTLIER) cc_final: 0.7909 (p-80) REVERT: C 1483 GLN cc_start: 0.9629 (mp10) cc_final: 0.9376 (mp10) outliers start: 16 outliers final: 11 residues processed: 65 average time/residue: 0.1332 time to fit residues: 13.0730 Evaluate side-chains 63 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 703 ARG Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 211 HIS Chi-restraints excluded: chain C residue 1416 LEU Chi-restraints excluded: chain C residue 1436 ILE Chi-restraints excluded: chain C residue 1479 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.6072 > 50: distance: 17 - 32: 10.471 distance: 22 - 40: 14.904 distance: 26 - 49: 8.656 distance: 29 - 32: 9.763 distance: 30 - 55: 8.090 distance: 32 - 33: 14.981 distance: 33 - 34: 6.053 distance: 33 - 36: 5.066 distance: 34 - 35: 12.809 distance: 34 - 40: 4.445 distance: 35 - 61: 12.272 distance: 36 - 37: 9.873 distance: 37 - 38: 16.944 distance: 37 - 39: 8.936 distance: 40 - 41: 4.232 distance: 41 - 42: 9.584 distance: 41 - 44: 14.324 distance: 42 - 43: 12.000 distance: 42 - 49: 5.459 distance: 44 - 45: 13.626 distance: 45 - 46: 4.077 distance: 46 - 47: 4.595 distance: 46 - 48: 14.479 distance: 49 - 50: 9.856 distance: 50 - 51: 13.810 distance: 50 - 53: 5.971 distance: 51 - 52: 26.063 distance: 51 - 55: 14.963 distance: 53 - 54: 16.440 distance: 55 - 56: 8.520 distance: 56 - 57: 11.739 distance: 56 - 59: 11.272 distance: 57 - 58: 8.829 distance: 57 - 61: 5.120 distance: 59 - 60: 21.245 distance: 61 - 62: 28.956 distance: 62 - 63: 19.952 distance: 63 - 64: 21.086 distance: 63 - 65: 26.622 distance: 65 - 66: 19.585 distance: 66 - 67: 33.553 distance: 66 - 69: 8.184 distance: 67 - 68: 34.387 distance: 67 - 73: 23.648 distance: 69 - 70: 8.018 distance: 70 - 71: 16.861 distance: 70 - 72: 30.323 distance: 73 - 74: 26.763 distance: 74 - 75: 3.792 distance: 74 - 77: 44.220 distance: 75 - 76: 10.286 distance: 75 - 82: 25.426 distance: 77 - 78: 15.617 distance: 78 - 79: 23.857 distance: 79 - 80: 20.756 distance: 79 - 81: 18.162 distance: 82 - 83: 6.983 distance: 82 - 88: 9.372 distance: 83 - 84: 11.740 distance: 83 - 86: 11.132 distance: 84 - 85: 22.427 distance: 84 - 89: 16.065 distance: 86 - 87: 28.278 distance: 87 - 88: 16.240 distance: 89 - 90: 37.415 distance: 90 - 91: 19.673 distance: 91 - 92: 25.180 distance: 91 - 93: 14.006 distance: 93 - 94: 11.679 distance: 94 - 95: 14.288 distance: 94 - 97: 18.130 distance: 95 - 96: 18.489 distance: 95 - 101: 5.203 distance: 97 - 98: 9.888 distance: 98 - 99: 8.503 distance: 98 - 100: 8.808