Starting phenix.real_space_refine on Sun Jun 15 13:50:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tpw_41495/06_2025/8tpw_41495.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tpw_41495/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tpw_41495/06_2025/8tpw_41495.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tpw_41495/06_2025/8tpw_41495.map" model { file = "/net/cci-nas-00/data/ceres_data/8tpw_41495/06_2025/8tpw_41495.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tpw_41495/06_2025/8tpw_41495.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.043 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.03, per 1000 atoms: 0.99 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: 3.98 Conformation dependent library (CDL) restraints added in 3.7 seconds 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: 2.11 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: 6.94 Time building geometry restraints manager: 4.78 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: 117.270 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: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 50.000 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.020 ------------------------------------------------------------------------------- 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 : 7.30 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 (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: 1.20 (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 TRP 0.013 0.001 TRP A 571 HIS 0.004 0.001 HIS C1475 PHE 0.013 0.001 PHE H 52 TYR 0.008 0.001 TYR B 357 ARG 0.002 0.000 ARG B 520 Details of bonding type rmsd hydrogen bonds : bond 0.15113 ( 778) hydrogen bonds : angle 5.52736 ( 2219) SS BOND : bond 0.00269 ( 4) SS BOND : angle 0.49819 ( 8) covalent geometry : bond 0.00257 (17597) covalent geometry : angle 0.49542 (23942) *********************** 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 : 1.797 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: 0.3069 time to fit residues: 35.0845 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 : 1.876 ------------------------------------------------------------------------------- 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 191 optimal weight: 10.0000 chunk 172 optimal weight: 0.4980 chunk 95 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 177 optimal weight: 0.0060 chunk 68 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- 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 = 0.3156 r_free = 0.3156 target = 0.040325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.025916 restraints weight = 859740.823| |-----------------------------------------------------------------------------| r_work (start): 0.2492 rms_B_bonded: 11.71 r_work: 0.2290 rms_B_bonded: 9.64 restraints_weight: 2.0000 r_work: 0.2408 rms_B_bonded: 6.23 restraints_weight: 4.0000 r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2408 r_free = 0.2408 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 = 0.2408 r_free = 0.2408 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 113 | |-----------------------------------------------------------------------------| r_final: 0.2408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17601 Z= 0.119 Angle : 0.506 9.277 23950 Z= 0.258 Chirality : 0.041 0.135 2694 Planarity : 0.004 0.040 3193 Dihedral : 4.631 56.885 2562 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.51 % Favored : 95.45 % Rotamer: Outliers : 1.35 % Allowed : 9.87 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 1.23 (0.18), residues: 2299 helix: 2.57 (0.19), residues: 798 sheet: 0.73 (0.25), residues: 432 loop : -0.51 (0.20), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 571 HIS 0.003 0.001 HIS C1475 PHE 0.011 0.001 PHE C1473 TYR 0.009 0.001 TYR B 357 ARG 0.004 0.000 ARG A 744 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 778) hydrogen bonds : angle 4.37368 ( 2219) SS BOND : bond 0.00279 ( 4) SS BOND : angle 0.55232 ( 8) covalent geometry : bond 0.00266 (17597) covalent geometry : angle 0.50582 (23942) *********************** 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 73 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.8256 (mmt) cc_final: 0.7701 (mmt) REVERT: A 681 MET cc_start: 0.9398 (tpp) cc_final: 0.9142 (tpp) REVERT: A 690 MET cc_start: 0.8683 (mmt) cc_final: 0.7994 (mmp) REVERT: B 599 MET cc_start: 0.9368 (mmp) cc_final: 0.8825 (mtt) REVERT: B 791 MET cc_start: 0.8830 (ppp) cc_final: 0.8017 (ppp) REVERT: H 33 ASP cc_start: 0.9665 (m-30) cc_final: 0.9376 (p0) REVERT: H 36 MET cc_start: 0.9523 (mmp) cc_final: 0.9269 (mmp) REVERT: C 1422 ASN cc_start: 0.9290 (m110) cc_final: 0.9051 (m110) REVERT: C 1483 GLN cc_start: 0.9585 (mp10) cc_final: 0.9289 (mp10) outliers start: 16 outliers final: 9 residues processed: 73 average time/residue: 0.3082 time to fit residues: 35.7538 Evaluate side-chains 62 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 2.047 ------------------------------------------------------------------------------- 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 123 optimal weight: 3.9990 chunk 196 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 217 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 198 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3145 r_free = 0.3145 target = 0.040000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.025662 restraints weight = 701284.096| |-----------------------------------------------------------------------------| r_work (start): 0.2479 rms_B_bonded: 10.96 r_work: 0.2284 rms_B_bonded: 9.28 restraints_weight: 2.0000 r_work: 0.2404 rms_B_bonded: 5.99 restraints_weight: 4.0000 r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2404 r_free = 0.2404 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 = 0.2404 r_free = 0.2404 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 102 | |-----------------------------------------------------------------------------| r_final: 0.2404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.0971 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= 0.138 Angle : 0.504 8.773 23950 Z= 0.256 Chirality : 0.040 0.135 2694 Planarity : 0.004 0.039 3193 Dihedral : 4.188 56.500 2547 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.51 % Favored : 95.45 % Rotamer: Outliers : 1.63 % Allowed : 9.87 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 1.22 (0.18), residues: 2299 helix: 2.56 (0.19), residues: 801 sheet: 0.62 (0.25), residues: 444 loop : -0.48 (0.20), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 571 HIS 0.004 0.001 HIS A 660 PHE 0.010 0.001 PHE H 52 TYR 0.009 0.001 TYR B 357 ARG 0.002 0.000 ARG A 744 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 778) hydrogen bonds : angle 4.24198 ( 2219) SS BOND : bond 0.00277 ( 4) SS BOND : angle 0.52105 ( 8) covalent geometry : bond 0.00314 (17597) covalent geometry : angle 0.50432 (23942) *********************** 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 75 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.8232 (mmt) cc_final: 0.7696 (mmt) REVERT: A 690 MET cc_start: 0.8623 (mmt) cc_final: 0.7944 (mmp) REVERT: B 791 MET cc_start: 0.8901 (ppp) cc_final: 0.8123 (ppp) REVERT: L 185 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8544 (t) REVERT: C 1483 GLN cc_start: 0.9594 (mp10) cc_final: 0.9332 (mp10) outliers start: 19 outliers final: 10 residues processed: 73 average time/residue: 0.3003 time to fit residues: 34.9793 Evaluate side-chains 61 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 1.802 ------------------------------------------------------------------------------- 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 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 15 optimal weight: 0.9980 chunk 200 optimal weight: 0.0980 chunk 147 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 77 optimal weight: 0.2980 chunk 86 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 118 optimal weight: 0.0770 chunk 18 optimal weight: 1.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 = 0.3170 r_free = 0.3170 target = 0.040720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.026329 restraints weight = 772719.609| |-----------------------------------------------------------------------------| r_work (start): 0.2511 rms_B_bonded: 11.34 r_work: 0.2314 rms_B_bonded: 9.44 restraints_weight: 2.0000 r_work: 0.2434 rms_B_bonded: 6.10 restraints_weight: 4.0000 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2434 r_free = 0.2434 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 = 0.2434 r_free = 0.2434 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 111 | |-----------------------------------------------------------------------------| r_final: 0.2434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17601 Z= 0.086 Angle : 0.484 9.273 23950 Z= 0.243 Chirality : 0.040 0.135 2694 Planarity : 0.003 0.039 3193 Dihedral : 4.038 56.978 2544 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.80 % Favored : 96.16 % Rotamer: Outliers : 1.46 % Allowed : 10.43 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 1.28 (0.18), residues: 2299 helix: 2.63 (0.19), residues: 794 sheet: 0.73 (0.25), residues: 431 loop : -0.48 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 571 HIS 0.002 0.000 HIS B 859 PHE 0.011 0.001 PHE C1473 TYR 0.010 0.001 TYR A 641 ARG 0.007 0.000 ARG C1466 Details of bonding type rmsd hydrogen bonds : bond 0.03009 ( 778) hydrogen bonds : angle 3.99946 ( 2219) SS BOND : bond 0.00202 ( 4) SS BOND : angle 0.38525 ( 8) covalent geometry : bond 0.00192 (17597) covalent geometry : angle 0.48422 (23942) *********************** 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 71 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.8309 (mmt) cc_final: 0.7679 (mmt) REVERT: A 681 MET cc_start: 0.9396 (tpp) cc_final: 0.9158 (tpp) REVERT: A 690 MET cc_start: 0.8650 (mmt) cc_final: 0.8072 (mmp) REVERT: B 599 MET cc_start: 0.9412 (mmp) cc_final: 0.8854 (mtt) REVERT: B 791 MET cc_start: 0.8956 (ppp) cc_final: 0.8095 (ppp) REVERT: H 219 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8007 (mp0) REVERT: L 185 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8522 (t) REVERT: L 207 ASP cc_start: 0.9523 (m-30) cc_final: 0.9215 (p0) REVERT: C 1458 ARG cc_start: 0.9380 (mtp85) cc_final: 0.9115 (mtp-110) REVERT: C 1483 GLN cc_start: 0.9607 (mp10) cc_final: 0.9344 (mp10) outliers start: 16 outliers final: 12 residues processed: 69 average time/residue: 0.3701 time to fit residues: 39.7455 Evaluate side-chains 66 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 2.513 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 41 optimal weight: 0.0010 chunk 206 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- 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 = 0.3158 r_free = 0.3158 target = 0.040293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.025874 restraints weight = 821949.505| |-----------------------------------------------------------------------------| r_work (start): 0.2490 rms_B_bonded: 11.49 r_work: 0.2291 rms_B_bonded: 9.51 restraints_weight: 2.0000 r_work: 0.2409 rms_B_bonded: 6.18 restraints_weight: 4.0000 r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2408 r_free = 0.2408 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 = 0.2408 r_free = 0.2408 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 102 | |-----------------------------------------------------------------------------| r_final: 0.2408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1176 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= 0.115 Angle : 0.494 8.481 23950 Z= 0.247 Chirality : 0.040 0.135 2694 Planarity : 0.003 0.038 3193 Dihedral : 4.046 56.513 2544 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.68 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 (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: 1.31 (0.18), residues: 2299 helix: 2.68 (0.19), residues: 794 sheet: 0.74 (0.25), residues: 431 loop : -0.47 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 571 HIS 0.003 0.001 HIS A 660 PHE 0.009 0.001 PHE H 52 TYR 0.008 0.001 TYR B 357 ARG 0.003 0.000 ARG C1466 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 778) hydrogen bonds : angle 4.01599 ( 2219) SS BOND : bond 0.00235 ( 4) SS BOND : angle 0.45888 ( 8) covalent geometry : bond 0.00261 (17597) covalent geometry : angle 0.49393 (23942) *********************** 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: 19 poor density : 54 time to evaluate : 2.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.8272 (mmt) cc_final: 0.7699 (mmt) REVERT: A 681 MET cc_start: 0.9387 (tpp) cc_final: 0.9105 (tpp) REVERT: A 690 MET cc_start: 0.8553 (mmt) cc_final: 0.7913 (mmp) REVERT: B 599 MET cc_start: 0.9433 (mmp) cc_final: 0.8878 (mtt) REVERT: B 791 MET cc_start: 0.8970 (ppp) cc_final: 0.8468 (ppp) REVERT: C 1458 ARG cc_start: 0.9421 (mtp85) cc_final: 0.9182 (mmm160) REVERT: C 1483 GLN cc_start: 0.9608 (mp10) cc_final: 0.9353 (mp10) outliers start: 19 outliers final: 12 residues processed: 70 average time/residue: 0.3541 time to fit residues: 38.8088 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 : 1.973 ------------------------------------------------------------------------------- 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 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 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 185 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 210 optimal weight: 8.9990 chunk 74 optimal weight: 0.4980 chunk 190 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 146 optimal weight: 2.9990 chunk 203 optimal weight: 0.5980 chunk 160 optimal weight: 0.0970 chunk 222 optimal weight: 5.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN L 146 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.040707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.026293 restraints weight = 732053.098| |-----------------------------------------------------------------------------| r_work (start): 0.2522 rms_B_bonded: 10.63 r_work: 0.2329 rms_B_bonded: 9.14 restraints_weight: 2.0000 r_work: 0.2444 rms_B_bonded: 5.95 restraints_weight: 4.0000 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2444 r_free = 0.2444 target_work(ls_wunit_k1) = 0.024 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 102 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2444 r_free = 0.2444 target_work(ls_wunit_k1) = 0.024 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 111 | |-----------------------------------------------------------------------------| r_final: 0.2444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17601 Z= 0.086 Angle : 0.480 11.155 23950 Z= 0.238 Chirality : 0.040 0.134 2694 Planarity : 0.003 0.038 3193 Dihedral : 3.978 56.278 2544 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.71 % Favored : 96.24 % Rotamer: Outliers : 1.51 % Allowed : 10.76 % 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 (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: 1.34 (0.18), residues: 2299 helix: 2.70 (0.19), residues: 794 sheet: 0.77 (0.25), residues: 430 loop : -0.46 (0.20), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 571 HIS 0.003 0.000 HIS B 859 PHE 0.008 0.001 PHE C1473 TYR 0.006 0.001 TYR B 357 ARG 0.003 0.000 ARG C1456 Details of bonding type rmsd hydrogen bonds : bond 0.02873 ( 778) hydrogen bonds : angle 3.87661 ( 2219) SS BOND : bond 0.00218 ( 4) SS BOND : angle 0.43670 ( 8) covalent geometry : bond 0.00196 (17597) covalent geometry : angle 0.47972 (23942) *********************** 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 70 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.8351 (mmt) cc_final: 0.7709 (mmt) REVERT: A 681 MET cc_start: 0.9383 (tpp) cc_final: 0.9068 (tpp) REVERT: A 690 MET cc_start: 0.8562 (mmt) cc_final: 0.7980 (mmp) REVERT: B 791 MET cc_start: 0.8961 (ppp) cc_final: 0.8509 (ppp) REVERT: L 100 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8251 (mp0) REVERT: L 185 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8515 (t) REVERT: L 207 ASP cc_start: 0.9581 (m-30) cc_final: 0.9275 (p0) REVERT: C 1483 GLN cc_start: 0.9624 (mp10) cc_final: 0.9372 (mp10) outliers start: 17 outliers final: 14 residues processed: 67 average time/residue: 0.3324 time to fit residues: 35.5227 Evaluate side-chains 64 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 2.028 ------------------------------------------------------------------------------- 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 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 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 ************** Weight determination summary: number of chunks: 227 random chunks: chunk 25 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 187 optimal weight: 0.0970 chunk 121 optimal weight: 0.9990 chunk 35 optimal weight: 0.0370 chunk 50 optimal weight: 0.8980 chunk 180 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 223 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.5056 ------------------------------------------------------------------------------- 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 = 0.3175 r_free = 0.3175 target = 0.040784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.026385 restraints weight = 778659.462| |-----------------------------------------------------------------------------| r_work (start): 0.2516 rms_B_bonded: 11.44 r_work: 0.2317 rms_B_bonded: 9.59 restraints_weight: 2.0000 r_work: 0.2433 rms_B_bonded: 6.26 restraints_weight: 4.0000 r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2433 r_free = 0.2433 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 = 0.2433 r_free = 0.2433 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 102 | |-----------------------------------------------------------------------------| r_final: 0.2433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17601 Z= 0.086 Angle : 0.475 10.154 23950 Z= 0.235 Chirality : 0.040 0.134 2694 Planarity : 0.003 0.039 3193 Dihedral : 3.929 55.718 2544 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 1.40 % Allowed : 10.82 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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 (0.18), residues: 2299 helix: 2.78 (0.19), residues: 788 sheet: 0.80 (0.25), residues: 430 loop : -0.40 (0.20), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 571 HIS 0.003 0.000 HIS B 859 PHE 0.007 0.001 PHE L 161 TYR 0.006 0.001 TYR B 357 ARG 0.008 0.000 ARG C1466 Details of bonding type rmsd hydrogen bonds : bond 0.02819 ( 778) hydrogen bonds : angle 3.81709 ( 2219) SS BOND : bond 0.00222 ( 4) SS BOND : angle 0.47079 ( 8) covalent geometry : bond 0.00195 (17597) covalent geometry : angle 0.47543 (23942) *********************** REFINEMENT MACRO_CYCLE 7 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 69 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 3.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.8309 (mmt) cc_final: 0.7694 (mmt) REVERT: A 681 MET cc_start: 0.9399 (tpp) cc_final: 0.9066 (tpp) REVERT: A 690 MET cc_start: 0.8532 (mmt) cc_final: 0.7971 (mmp) REVERT: B 599 MET cc_start: 0.9418 (mmp) cc_final: 0.8904 (mtt) REVERT: B 791 MET cc_start: 0.8987 (ppp) cc_final: 0.8525 (ppp) REVERT: L 185 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8515 (t) REVERT: L 207 ASP cc_start: 0.9600 (m-30) cc_final: 0.9310 (p0) REVERT: C 1483 GLN cc_start: 0.9619 (mp10) cc_final: 0.9373 (mp10) outliers start: 15 outliers final: 13 residues processed: 66 average time/residue: 0.3516 time to fit residues: 37.7689 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 : 2.193 ------------------------------------------------------------------------------- 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 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 C residue 1416 LEU Chi-restraints excluded: chain C residue 1436 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 184 optimal weight: 7.9990 chunk 160 optimal weight: 0.5980 chunk 68 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 114 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 188 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3173 r_free = 0.3173 target = 0.040739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.026356 restraints weight = 725735.740| |-----------------------------------------------------------------------------| r_work (start): 0.2524 rms_B_bonded: 10.59 r_work: 0.2331 rms_B_bonded: 9.16 restraints_weight: 2.0000 r_work: 0.2442 rms_B_bonded: 6.08 restraints_weight: 4.0000 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2442 r_free = 0.2442 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 = 0.2442 r_free = 0.2442 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 111 | |-----------------------------------------------------------------------------| r_final: 0.2442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17601 Z= 0.092 Angle : 0.480 11.248 23950 Z= 0.238 Chirality : 0.040 0.134 2694 Planarity : 0.003 0.038 3193 Dihedral : 3.941 55.126 2544 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.62 % Favored : 96.33 % Rotamer: Outliers : 1.40 % Allowed : 10.93 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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 (0.18), residues: 2299 helix: 2.79 (0.19), residues: 790 sheet: 0.80 (0.25), residues: 430 loop : -0.41 (0.20), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 571 HIS 0.003 0.000 HIS B 859 PHE 0.009 0.001 PHE C1473 TYR 0.007 0.001 TYR B 357 ARG 0.005 0.000 ARG C1458 Details of bonding type rmsd hydrogen bonds : bond 0.02859 ( 778) hydrogen bonds : angle 3.80863 ( 2219) SS BOND : bond 0.00211 ( 4) SS BOND : angle 0.43767 ( 8) covalent geometry : bond 0.00212 (17597) covalent geometry : angle 0.48034 (23942) *********************** REFINEMENT MACRO_CYCLE 8 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 68 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 2.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.8284 (mmt) cc_final: 0.7671 (mmt) REVERT: A 681 MET cc_start: 0.9394 (tpp) cc_final: 0.9045 (tpp) REVERT: A 690 MET cc_start: 0.8515 (mmt) cc_final: 0.7939 (mmp) REVERT: B 599 MET cc_start: 0.9434 (mmp) cc_final: 0.8921 (mtm) REVERT: B 791 MET cc_start: 0.8974 (ppp) cc_final: 0.8483 (ppp) REVERT: L 100 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8302 (mp0) REVERT: L 185 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8533 (t) REVERT: L 207 ASP cc_start: 0.9621 (m-30) cc_final: 0.9387 (p0) REVERT: C 1483 GLN cc_start: 0.9615 (mp10) cc_final: 0.9365 (mp10) outliers start: 15 outliers final: 14 residues processed: 65 average time/residue: 0.5533 time to fit residues: 56.6324 Evaluate side-chains 66 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 2.140 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 197 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.040197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.025615 restraints weight = 841085.849| |-----------------------------------------------------------------------------| r_work (start): 0.2490 rms_B_bonded: 11.08 r_work: 0.2294 rms_B_bonded: 9.33 restraints_weight: 2.0000 r_work: 0.2410 rms_B_bonded: 6.10 restraints_weight: 4.0000 r_work (final): 0.2410 ------------------------------------------------------------------------------- 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: 93 | |-----------------------------------------------------------------------------| r_final: 0.2411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1429 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= 0.135 Angle : 0.516 11.271 23950 Z= 0.257 Chirality : 0.040 0.135 2694 Planarity : 0.003 0.037 3193 Dihedral : 4.059 54.190 2544 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.33 % Favored : 95.63 % Rotamer: Outliers : 1.63 % Allowed : 10.71 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.18), residues: 2299 helix: 2.72 (0.19), residues: 795 sheet: 0.74 (0.25), residues: 437 loop : -0.49 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 571 HIS 0.003 0.001 HIS A 660 PHE 0.010 0.001 PHE H 52 TYR 0.009 0.001 TYR B 357 ARG 0.008 0.000 ARG C1458 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 778) hydrogen bonds : angle 3.95449 ( 2219) SS BOND : bond 0.00258 ( 4) SS BOND : angle 0.52783 ( 8) covalent geometry : bond 0.00310 (17597) covalent geometry : angle 0.51626 (23942) *********************** REFINEMENT MACRO_CYCLE 9 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: 19 poor density : 52 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.8350 (mmt) cc_final: 0.7799 (mmt) REVERT: A 681 MET cc_start: 0.9403 (tpp) cc_final: 0.9071 (tpp) REVERT: A 690 MET cc_start: 0.8488 (mmt) cc_final: 0.7947 (mmp) REVERT: B 599 MET cc_start: 0.9438 (mmp) cc_final: 0.8930 (mtt) REVERT: B 791 MET cc_start: 0.8954 (ppp) cc_final: 0.8463 (ppp) REVERT: L 100 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8403 (mp0) REVERT: L 185 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8520 (t) REVERT: L 207 ASP cc_start: 0.9622 (m-30) cc_final: 0.9321 (p0) REVERT: L 211 HIS cc_start: 0.8618 (OUTLIER) cc_final: 0.7858 (p-80) REVERT: C 1483 GLN cc_start: 0.9635 (mp10) cc_final: 0.9369 (mp10) outliers start: 19 outliers final: 16 residues processed: 68 average time/residue: 0.3207 time to fit residues: 34.5863 Evaluate side-chains 68 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 2.014 ------------------------------------------------------------------------------- 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 B residue 748 ILE Chi-restraints excluded: chain H residue 73 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 197 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3150 r_free = 0.3150 target = 0.040096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.025625 restraints weight = 792099.429| |-----------------------------------------------------------------------------| r_work (start): 0.2490 rms_B_bonded: 10.81 r_work: 0.2294 rms_B_bonded: 9.31 restraints_weight: 2.0000 r_work: 0.2409 rms_B_bonded: 6.11 restraints_weight: 4.0000 r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2409 r_free = 0.2409 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2409 r_free = 0.2409 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 102 | |-----------------------------------------------------------------------------| r_final: 0.2409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17601 Z= 0.140 Angle : 0.524 11.862 23950 Z= 0.261 Chirality : 0.040 0.135 2694 Planarity : 0.004 0.070 3193 Dihedral : 4.124 53.710 2544 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.33 % Favored : 95.63 % Rotamer: Outliers : 1.57 % Allowed : 10.87 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.18), residues: 2299 helix: 2.70 (0.19), residues: 795 sheet: 0.71 (0.25), residues: 437 loop : -0.51 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 571 HIS 0.003 0.001 HIS A 660 PHE 0.009 0.001 PHE H 52 TYR 0.009 0.001 TYR B 357 ARG 0.016 0.000 ARG H 18 Details of bonding type rmsd hydrogen bonds : bond 0.03396 ( 778) hydrogen bonds : angle 3.97664 ( 2219) SS BOND : bond 0.00265 ( 4) SS BOND : angle 0.53492 ( 8) covalent geometry : bond 0.00320 (17597) covalent geometry : angle 0.52446 (23942) ********************** REFINEMENT MACRO_CYCLE 10 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 68 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.8382 (mmt) cc_final: 0.7789 (mmt) REVERT: A 681 MET cc_start: 0.9404 (tpp) cc_final: 0.9202 (tpp) REVERT: A 690 MET cc_start: 0.8482 (mmt) cc_final: 0.7915 (mmp) REVERT: B 599 MET cc_start: 0.9445 (mmp) cc_final: 0.8919 (mtt) REVERT: B 791 MET cc_start: 0.8958 (ppp) cc_final: 0.8450 (ppp) REVERT: L 100 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8387 (mp0) REVERT: L 185 VAL cc_start: 0.8776 (OUTLIER) cc_final: 0.8526 (t) REVERT: L 207 ASP cc_start: 0.9620 (m-30) cc_final: 0.9314 (p0) REVERT: L 211 HIS cc_start: 0.8613 (OUTLIER) cc_final: 0.7854 (p-80) REVERT: C 1483 GLN cc_start: 0.9639 (mp10) cc_final: 0.9358 (mp10) outliers start: 18 outliers final: 16 residues processed: 65 average time/residue: 0.4195 time to fit residues: 44.6514 Evaluate side-chains 68 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 2.071 ------------------------------------------------------------------------------- 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 B residue 748 ILE Chi-restraints excluded: chain H residue 73 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 147 optimal weight: 0.7980 chunk 80 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 162 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3166 r_free = 0.3166 target = 0.040544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.025984 restraints weight = 770266.148| |-----------------------------------------------------------------------------| r_work (start): 0.2508 rms_B_bonded: 10.86 r_work: 0.2315 rms_B_bonded: 9.21 restraints_weight: 2.0000 r_work: 0.2434 rms_B_bonded: 5.98 restraints_weight: 4.0000 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2435 r_free = 0.2435 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 = 0.2435 r_free = 0.2435 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 111 | |-----------------------------------------------------------------------------| r_final: 0.2435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17601 Z= 0.099 Angle : 0.501 10.735 23950 Z= 0.249 Chirality : 0.040 0.133 2694 Planarity : 0.004 0.048 3193 Dihedral : 4.056 53.771 2544 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.98 % Favored : 95.98 % Rotamer: Outliers : 1.57 % Allowed : 10.87 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 1.39 (0.18), residues: 2299 helix: 2.77 (0.19), residues: 789 sheet: 0.76 (0.25), residues: 432 loop : -0.43 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 571 HIS 0.003 0.000 HIS A 660 PHE 0.008 0.001 PHE A 868 TYR 0.007 0.001 TYR B 357 ARG 0.013 0.000 ARG C1466 Details of bonding type rmsd hydrogen bonds : bond 0.02991 ( 778) hydrogen bonds : angle 3.85309 ( 2219) SS BOND : bond 0.00231 ( 4) SS BOND : angle 0.46050 ( 8) covalent geometry : bond 0.00228 (17597) covalent geometry : angle 0.50081 (23942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12458.40 seconds wall clock time: 219 minutes 6.76 seconds (13146.76 seconds total)