Starting phenix.real_space_refine on Thu Aug 6 20:24:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wuc_66257/08_2026/9wuc_66257.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wuc_66257/08_2026/9wuc_66257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wuc_66257/08_2026/9wuc_66257.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wuc_66257/08_2026/9wuc_66257.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wuc_66257/08_2026/9wuc_66257.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wuc_66257/08_2026/9wuc_66257.map" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.027 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: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 P 6 5.49 5 S 68 5.16 5 C 10536 2.51 5 N 2859 2.21 5 O 3157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16628 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 8178 Classifications: {'peptide': 1024} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 972} Chain breaks: 1 Chain: "B" Number of atoms: 8194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8194 Classifications: {'peptide': 1026} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 974} Chain breaks: 1 Chain: "A" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 127 Unusual residues: {'FAD': 1, 'FMN': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 127 Unusual residues: {'FAD': 1, 'FMN': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3259 SG CYS A 404 39.949 25.265 44.775 1.00 17.43 S ATOM 11437 SG CYS B 404 32.833 80.318 86.799 1.00 36.95 S Time building chain proxies: 3.54, per 1000 atoms: 0.21 Number of scatterers: 16628 At special positions: 0 Unit cell: (112.53, 109.74, 133.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 68 16.00 P 6 15.00 O 3157 8.00 N 2859 7.00 C 10536 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 699.6 milliseconds 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3812 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 22 sheets defined 50.7% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 13 through 17 Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 26 through 39 removed outlier: 3.862A pdb=" N SER A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 75 through 85 removed outlier: 4.453A pdb=" N ALA A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N PHE A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 106 removed outlier: 3.659A pdb=" N ARG A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 110 removed outlier: 3.711A pdb=" N SER A 110 " --> pdb=" O PRO A 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 107 through 110' Processing helix chain 'A' and resid 111 through 115 removed outlier: 4.000A pdb=" N LYS A 115 " --> pdb=" O ARG A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 135 Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 173 through 191 removed outlier: 3.589A pdb=" N THR A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN A 191 " --> pdb=" O MET A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 200 through 227 Processing helix chain 'A' and resid 235 through 243 Processing helix chain 'A' and resid 253 through 282 removed outlier: 4.575A pdb=" N GLU A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 Processing helix chain 'A' and resid 307 through 313 Processing helix chain 'A' and resid 314 through 328 Processing helix chain 'A' and resid 361 through 365 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 379 through 384 removed outlier: 3.645A pdb=" N ARG A 382 " --> pdb=" O ARG A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 399 through 403 removed outlier: 3.758A pdb=" N ARG A 402 " --> pdb=" O ASN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 424 Processing helix chain 'A' and resid 508 through 524 Processing helix chain 'A' and resid 534 through 536 No H-bonds generated for 'chain 'A' and resid 534 through 536' Processing helix chain 'A' and resid 561 through 571 Processing helix chain 'A' and resid 596 through 609 Processing helix chain 'A' and resid 625 through 645 removed outlier: 4.086A pdb=" N GLU A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 696 removed outlier: 4.206A pdb=" N GLY A 696 " --> pdb=" O PRO A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 736 Processing helix chain 'A' and resid 764 through 771 Processing helix chain 'A' and resid 779 through 789 Processing helix chain 'A' and resid 792 through 801 Processing helix chain 'A' and resid 802 through 804 No H-bonds generated for 'chain 'A' and resid 802 through 804' Processing helix chain 'A' and resid 806 through 812 Processing helix chain 'A' and resid 818 through 826 Processing helix chain 'A' and resid 832 through 840 Processing helix chain 'A' and resid 881 through 889 Processing helix chain 'A' and resid 922 through 925 Processing helix chain 'A' and resid 926 through 942 removed outlier: 3.657A pdb=" N GLY A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 973 Processing helix chain 'A' and resid 992 through 1000 removed outlier: 3.570A pdb=" N VAL A 996 " --> pdb=" O TYR A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1011 Processing helix chain 'A' and resid 1022 through 1040 removed outlier: 3.698A pdb=" N GLU A1026 " --> pdb=" O ARG A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1056 Processing helix chain 'B' and resid 13 through 17 Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 26 through 38 removed outlier: 3.604A pdb=" N SER B 30 " --> pdb=" O LYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 64 Processing helix chain 'B' and resid 75 through 85 removed outlier: 3.556A pdb=" N LYS B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N PHE B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 106 removed outlier: 3.518A pdb=" N ARG B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 110 removed outlier: 3.858A pdb=" N SER B 110 " --> pdb=" O PRO B 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 107 through 110' Processing helix chain 'B' and resid 111 through 115 removed outlier: 4.377A pdb=" N LYS B 115 " --> pdb=" O ARG B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 134 removed outlier: 3.843A pdb=" N ILE B 124 " --> pdb=" O MET B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 161 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 173 through 191 removed outlier: 3.735A pdb=" N GLN B 191 " --> pdb=" O MET B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 200 through 227 Processing helix chain 'B' and resid 235 through 243 Processing helix chain 'B' and resid 253 through 282 removed outlier: 4.359A pdb=" N GLU B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N THR B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 Processing helix chain 'B' and resid 307 through 313 Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 379 through 384 removed outlier: 3.545A pdb=" N GLU B 384 " --> pdb=" O GLU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 403 removed outlier: 3.664A pdb=" N ARG B 402 " --> pdb=" O ASN B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 424 Processing helix chain 'B' and resid 508 through 524 Processing helix chain 'B' and resid 534 through 537 removed outlier: 3.939A pdb=" N ILE B 537 " --> pdb=" O ASN B 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 534 through 537' Processing helix chain 'B' and resid 561 through 571 Processing helix chain 'B' and resid 588 through 595 removed outlier: 3.507A pdb=" N ALA B 592 " --> pdb=" O HIS B 589 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N SER B 593 " --> pdb=" O ASN B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 609 Processing helix chain 'B' and resid 625 through 645 removed outlier: 3.828A pdb=" N GLU B 643 " --> pdb=" O SER B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 655 removed outlier: 3.550A pdb=" N LYS B 655 " --> pdb=" O ASP B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 696 removed outlier: 4.078A pdb=" N GLY B 696 " --> pdb=" O PRO B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 736 Processing helix chain 'B' and resid 764 through 771 Processing helix chain 'B' and resid 779 through 789 Processing helix chain 'B' and resid 792 through 802 removed outlier: 3.583A pdb=" N LEU B 802 " --> pdb=" O GLU B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 812 Processing helix chain 'B' and resid 818 through 826 Processing helix chain 'B' and resid 832 through 838 Processing helix chain 'B' and resid 881 through 889 Processing helix chain 'B' and resid 922 through 925 Processing helix chain 'B' and resid 926 through 943 Processing helix chain 'B' and resid 963 through 974 removed outlier: 3.521A pdb=" N GLY B 974 " --> pdb=" O TYR B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 999 Processing helix chain 'B' and resid 1000 through 1011 Processing helix chain 'B' and resid 1023 through 1040 Processing helix chain 'B' and resid 1044 through 1057 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 46 removed outlier: 7.144A pdb=" N SER A 50 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N THR A 358 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ILE A 52 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 360 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL A 54 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE A 334 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 141 through 142 removed outlier: 3.581A pdb=" N GLN A 451 " --> pdb=" O ILE A 428 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 342 through 344 removed outlier: 3.505A pdb=" N THR A 342 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 437 through 439 Processing sheet with id=AA5, first strand: chain 'A' and resid 528 through 532 removed outlier: 6.350A pdb=" N VAL A 546 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N PHE A 584 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ILE A 548 " --> pdb=" O PHE A 584 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N CYS A 586 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR A 550 " --> pdb=" O CYS A 586 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 528 through 532 removed outlier: 6.350A pdb=" N VAL A 546 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N PHE A 584 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ILE A 548 " --> pdb=" O PHE A 584 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N CYS A 586 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR A 550 " --> pdb=" O CYS A 586 " (cutoff:3.500A) removed outlier: 9.504A pdb=" N GLY A 618 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 583 " --> pdb=" O GLY A 618 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N GLY A 620 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY A 585 " --> pdb=" O GLY A 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 660 through 661 Processing sheet with id=AA8, first strand: chain 'A' and resid 664 through 665 removed outlier: 4.311A pdb=" N GLN B 743 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 717 through 720 removed outlier: 3.717A pdb=" N LYS A 683 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLU A 703 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN A 687 " --> pdb=" O HIS A 701 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N HIS A 701 " --> pdb=" O ASN A 687 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLU A 689 " --> pdb=" O THR A 699 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N THR A 699 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER A 698 " --> pdb=" O VAL A 867 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 761 through 763 removed outlier: 4.497A pdb=" N GLN A 743 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 772 through 773 removed outlier: 4.355A pdb=" N HIS A 841 " --> pdb=" O GLU A 773 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 869 through 871 Processing sheet with id=AB4, first strand: chain 'A' and resid 976 through 982 removed outlier: 6.873A pdb=" N ALA A 949 " --> pdb=" O THR A 977 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N TYR A 979 " --> pdb=" O ALA A 949 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU A 951 " --> pdb=" O TYR A 979 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ALA A 981 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE A 953 " --> pdb=" O ALA A 981 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE A 918 " --> pdb=" O TYR A1015 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N CYS A1017 " --> pdb=" O ILE A 918 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL A 920 " --> pdb=" O CYS A1017 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ASP A1019 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A1014 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ASP A1062 " --> pdb=" O LEU A1014 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE A1016 " --> pdb=" O ASP A1062 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TRP A1064 " --> pdb=" O ILE A1016 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY A1018 " --> pdb=" O TRP A1064 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 41 through 45 removed outlier: 4.413A pdb=" N ARG B 356 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE B 334 " --> pdb=" O VAL B 359 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 141 through 142 Processing sheet with id=AB7, first strand: chain 'B' and resid 342 through 344 Processing sheet with id=AB8, first strand: chain 'B' and resid 437 through 439 Processing sheet with id=AB9, first strand: chain 'B' and resid 528 through 532 removed outlier: 6.829A pdb=" N LEU B 500 " --> pdb=" O LEU B 547 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N VAL B 549 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU B 502 " --> pdb=" O VAL B 549 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N SER B 551 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLY B 504 " --> pdb=" O SER B 551 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 546 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N PHE B 584 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 548 " --> pdb=" O PHE B 584 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N CYS B 586 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR B 550 " --> pdb=" O CYS B 586 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N GLY B 618 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL B 583 " --> pdb=" O GLY B 618 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N GLY B 620 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLY B 585 " --> pdb=" O GLY B 620 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 717 through 720 removed outlier: 3.823A pdb=" N LYS B 683 " --> pdb=" O THR B 705 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU B 703 " --> pdb=" O VAL B 685 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN B 687 " --> pdb=" O HIS B 701 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N HIS B 701 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLU B 689 " --> pdb=" O THR B 699 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N THR B 699 " --> pdb=" O GLU B 689 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER B 698 " --> pdb=" O VAL B 867 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 772 through 773 removed outlier: 4.393A pdb=" N HIS B 841 " --> pdb=" O GLU B 773 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 869 through 871 Processing sheet with id=AC4, first strand: chain 'B' and resid 977 through 980 removed outlier: 6.912A pdb=" N ALA B 949 " --> pdb=" O THR B 977 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N TYR B 979 " --> pdb=" O ALA B 949 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU B 951 " --> pdb=" O TYR B 979 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE B 917 " --> pdb=" O TYR B 950 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N TYR B 952 " --> pdb=" O ILE B 917 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N MET B 919 " --> pdb=" O TYR B 952 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE B 918 " --> pdb=" O TYR B1015 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N CYS B1017 " --> pdb=" O ILE B 918 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL B 920 " --> pdb=" O CYS B1017 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ASP B1019 " --> pdb=" O VAL B 920 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU B1014 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ASP B1062 " --> pdb=" O LEU B1014 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE B1016 " --> pdb=" O ASP B1062 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TRP B1064 " --> pdb=" O ILE B1016 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY B1018 " --> pdb=" O TRP B1064 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 779 hydrogen bonds defined for protein. 2217 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: 3.86 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 6047 1.38 - 1.55: 10808 1.55 - 1.71: 29 1.71 - 1.88: 118 1.88 - 2.05: 8 Bond restraints: 17010 Sorted by residual: bond pdb=" C4 FMN B1103 " pdb=" C4A FMN B1103 " ideal model delta sigma weight residual 1.485 1.383 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C4 FMN A1102 " pdb=" C4A FMN A1102 " ideal model delta sigma weight residual 1.485 1.388 0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C4A FMN A1102 " pdb=" N5 FMN A1102 " ideal model delta sigma weight residual 1.300 1.379 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C4A FMN B1103 " pdb=" N5 FMN B1103 " ideal model delta sigma weight residual 1.300 1.377 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" O5' FMN A1102 " pdb=" P FMN A1102 " ideal model delta sigma weight residual 1.676 1.601 0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 17005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 22663 1.93 - 3.85: 327 3.85 - 5.78: 58 5.78 - 7.71: 17 7.71 - 9.63: 3 Bond angle restraints: 23068 Sorted by residual: angle pdb=" C ASP A 597 " pdb=" N VAL A 598 " pdb=" CA VAL A 598 " ideal model delta sigma weight residual 120.33 122.90 -2.57 8.00e-01 1.56e+00 1.03e+01 angle pdb=" C ASN A1000 " pdb=" N ALA A1001 " pdb=" CA ALA A1001 " ideal model delta sigma weight residual 120.82 125.22 -4.40 1.50e+00 4.44e-01 8.61e+00 angle pdb=" C ASP B 436 " pdb=" CA ASP B 436 " pdb=" CB ASP B 436 " ideal model delta sigma weight residual 109.37 114.45 -5.08 1.83e+00 2.99e-01 7.70e+00 angle pdb=" N ALA A1001 " pdb=" CA ALA A1001 " pdb=" C ALA A1001 " ideal model delta sigma weight residual 111.37 115.66 -4.29 1.65e+00 3.67e-01 6.77e+00 angle pdb=" O3P FMN B1103 " pdb=" P FMN B1103 " pdb=" O5' FMN B1103 " ideal model delta sigma weight residual 102.33 110.11 -7.78 3.00e+00 1.11e-01 6.73e+00 ... (remaining 23063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8743 17.94 - 35.89: 1065 35.89 - 53.83: 371 53.83 - 71.77: 61 71.77 - 89.72: 32 Dihedral angle restraints: 10272 sinusoidal: 4334 harmonic: 5938 Sorted by residual: dihedral pdb=" CA LYS B1061 " pdb=" C LYS B1061 " pdb=" N ASP B1062 " pdb=" CA ASP B1062 " ideal model delta harmonic sigma weight residual 180.00 161.20 18.80 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA GLN B 657 " pdb=" C GLN B 657 " pdb=" N ASN B 658 " pdb=" CA ASN B 658 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA MET A 898 " pdb=" C MET A 898 " pdb=" N PHE A 899 " pdb=" CA PHE A 899 " ideal model delta harmonic sigma weight residual 180.00 162.38 17.62 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 10269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1366 0.027 - 0.055: 717 0.055 - 0.082: 208 0.082 - 0.110: 140 0.110 - 0.137: 36 Chirality restraints: 2467 Sorted by residual: chirality pdb=" CA ILE A 918 " pdb=" N ILE A 918 " pdb=" C ILE A 918 " pdb=" CB ILE A 918 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CB ILE B 642 " pdb=" CA ILE B 642 " pdb=" CG1 ILE B 642 " pdb=" CG2 ILE B 642 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA GLN B 260 " pdb=" N GLN B 260 " pdb=" C GLN B 260 " pdb=" CB GLN B 260 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 2464 not shown) Planarity restraints: 2987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 921 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO A 922 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 922 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 922 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 371 " 0.012 2.00e-02 2.50e+03 1.17e-02 3.43e+00 pdb=" CG TRP B 371 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP B 371 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 371 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 371 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 371 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 371 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 371 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 371 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 371 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 792 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO A 793 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 793 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 793 " -0.022 5.00e-02 4.00e+02 ... (remaining 2984 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 8029 2.98 - 3.46: 17049 3.46 - 3.94: 29384 3.94 - 4.42: 34869 4.42 - 4.90: 55472 Nonbonded interactions: 144803 Sorted by model distance: nonbonded pdb=" C3' FAD A1103 " pdb=" O5' FAD A1103 " model vdw 2.503 2.776 nonbonded pdb=" O2B FAD B1102 " pdb=" O3B FAD B1102 " model vdw 2.516 2.432 nonbonded pdb=" N THR B 779 " pdb=" OG1 THR B 779 " model vdw 2.590 2.496 nonbonded pdb=" N ASP A 253 " pdb=" OD1 ASP A 253 " model vdw 2.593 3.120 nonbonded pdb=" N LEU B 441 " pdb=" N THR B 442 " model vdw 2.609 2.560 ... (remaining 144798 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 5 through 1101) selection = (chain 'B' and (resid 5 through 456 or resid 496 through 1101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.940 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 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 : 0.004 0.102 17012 Z= 0.175 Angle : 0.607 9.634 23068 Z= 0.297 Chirality : 0.041 0.137 2467 Planarity : 0.004 0.052 2987 Dihedral : 17.963 89.718 6460 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.45 % Allowed : 26.30 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.19), residues: 2042 helix: 1.02 (0.17), residues: 912 sheet: -0.99 (0.29), residues: 290 loop : -0.38 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 497 TYR 0.016 0.001 TYR A 736 PHE 0.019 0.002 PHE B 160 TRP 0.031 0.002 TRP B 371 HIS 0.007 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (17010) covalent geometry : angle 0.60746 / 0.30 (23068) hydrogen bonds : bond 0.13697 / 8.31 ( 769) hydrogen bonds : angle 6.51735 / 4.74 ( 2217) Misc. bond : bond 0.01830 / 0.91 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 241 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7446 (ttpt) cc_final: 0.7164 (ttpp) REVERT: A 74 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6579 (mm-30) REVERT: A 99 ARG cc_start: 0.6846 (tpp-160) cc_final: 0.6413 (tpp-160) REVERT: A 184 ASP cc_start: 0.8061 (t70) cc_final: 0.7827 (m-30) REVERT: A 270 GLU cc_start: 0.6412 (pt0) cc_final: 0.5781 (mm-30) REVERT: A 296 GLU cc_start: 0.8205 (tp30) cc_final: 0.7424 (tm-30) REVERT: A 299 GLN cc_start: 0.6766 (mt0) cc_final: 0.5909 (tm130) REVERT: A 307 THR cc_start: 0.7935 (p) cc_final: 0.7544 (t) REVERT: A 309 LYS cc_start: 0.6793 (mtmt) cc_final: 0.6577 (mtpp) REVERT: A 399 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.7977 (t0) REVERT: A 453 GLN cc_start: 0.7737 (mt0) cc_final: 0.7286 (mt0) REVERT: A 529 GLU cc_start: 0.7571 (mp0) cc_final: 0.7339 (tt0) REVERT: A 627 GLU cc_start: 0.7724 (tt0) cc_final: 0.5942 (mp0) REVERT: A 636 LYS cc_start: 0.8177 (tppp) cc_final: 0.7920 (tptp) REVERT: A 675 ARG cc_start: 0.7390 (mmp-170) cc_final: 0.6841 (mtm110) REVERT: A 730 HIS cc_start: 0.7518 (t70) cc_final: 0.6418 (m-70) REVERT: A 734 GLN cc_start: 0.7697 (mm110) cc_final: 0.7266 (pt0) REVERT: A 804 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6907 (mp0) REVERT: A 814 LYS cc_start: 0.7585 (mptt) cc_final: 0.6877 (tptt) REVERT: A 880 ARG cc_start: 0.8738 (mmm-85) cc_final: 0.8499 (mtp-110) REVERT: A 937 ASP cc_start: 0.7642 (m-30) cc_final: 0.7008 (t70) REVERT: A 977 THR cc_start: 0.7825 (m) cc_final: 0.7124 (t) REVERT: A 984 ARG cc_start: 0.6679 (mtt-85) cc_final: 0.6041 (mtp180) REVERT: B 24 LYS cc_start: 0.7247 (mtpp) cc_final: 0.6659 (ptmm) REVERT: B 25 ASP cc_start: 0.7348 (m-30) cc_final: 0.7027 (m-30) REVERT: B 78 GLU cc_start: 0.7936 (tt0) cc_final: 0.7685 (tm-30) REVERT: B 170 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6789 (mm-30) REVERT: B 191 GLN cc_start: 0.7739 (pt0) cc_final: 0.7389 (pt0) REVERT: B 204 LYS cc_start: 0.7868 (mtmt) cc_final: 0.7367 (tppt) REVERT: B 219 ASP cc_start: 0.8200 (m-30) cc_final: 0.7972 (m-30) REVERT: B 343 ILE cc_start: 0.7464 (mt) cc_final: 0.7049 (tt) REVERT: B 425 PHE cc_start: 0.7113 (m-80) cc_final: 0.6717 (m-80) REVERT: B 441 LEU cc_start: 0.6210 (OUTLIER) cc_final: 0.5719 (tp) REVERT: B 542 LYS cc_start: 0.7014 (mtmp) cc_final: 0.6502 (mmtt) REVERT: B 543 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6464 (tm-30) REVERT: B 572 GLN cc_start: 0.6889 (mm-40) cc_final: 0.6622 (mm-40) REVERT: B 628 GLU cc_start: 0.7182 (tt0) cc_final: 0.6851 (tp30) REVERT: B 632 GLN cc_start: 0.6853 (mm110) cc_final: 0.6580 (mt0) REVERT: B 643 GLU cc_start: 0.6622 (pt0) cc_final: 0.6239 (mp0) REVERT: B 726 LYS cc_start: 0.6948 (ptmm) cc_final: 0.6619 (ptmm) REVERT: B 739 ASN cc_start: 0.7549 (m-40) cc_final: 0.6996 (t0) REVERT: B 760 GLN cc_start: 0.7526 (tt0) cc_final: 0.7203 (tm-30) REVERT: B 814 LYS cc_start: 0.6885 (mptt) cc_final: 0.6181 (tttp) REVERT: B 844 LYS cc_start: 0.7724 (mtmt) cc_final: 0.7248 (mtmt) REVERT: B 880 ARG cc_start: 0.7247 (mtp180) cc_final: 0.6187 (mtp-110) REVERT: B 895 ASP cc_start: 0.7753 (p0) cc_final: 0.7543 (p0) REVERT: B 973 ASN cc_start: 0.6785 (t0) cc_final: 0.6579 (t0) REVERT: B 1051 GLU cc_start: 0.6353 (tt0) cc_final: 0.6046 (mp0) outliers start: 8 outliers final: 0 residues processed: 246 average time/residue: 0.7018 time to fit residues: 189.6827 Evaluate side-chains 230 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 228 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain B residue 441 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 HIS A 527 HIS A 741 ASN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 HIS ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 885 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.184261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.155419 restraints weight = 16850.895| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.46 r_work: 0.3624 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17012 Z= 0.220 Angle : 0.649 10.608 23068 Z= 0.319 Chirality : 0.044 0.161 2467 Planarity : 0.005 0.048 2987 Dihedral : 7.825 84.285 2376 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.59 % Allowed : 21.32 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.19), residues: 2042 helix: 0.79 (0.17), residues: 924 sheet: -1.03 (0.29), residues: 276 loop : -0.40 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 700 TYR 0.021 0.002 TYR A 736 PHE 0.024 0.002 PHE B 160 TRP 0.017 0.002 TRP A 98 HIS 0.008 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 (17010) covalent geometry : angle 0.64885 / 0.32 (23068) hydrogen bonds : bond 0.04618 / 3.05 ( 769) hydrogen bonds : angle 5.18367 / 3.75 ( 2217) Misc. bond : bond 0.04218 / 2.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 239 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7315 (ttpt) cc_final: 0.7011 (ttpp) REVERT: A 99 ARG cc_start: 0.6841 (tpp-160) cc_final: 0.6378 (tpp-160) REVERT: A 184 ASP cc_start: 0.7841 (t70) cc_final: 0.7537 (m-30) REVERT: A 270 GLU cc_start: 0.6230 (pt0) cc_final: 0.5588 (mm-30) REVERT: A 299 GLN cc_start: 0.6640 (mt0) cc_final: 0.5957 (tm-30) REVERT: A 301 LEU cc_start: 0.7307 (mp) cc_final: 0.7032 (mt) REVERT: A 307 THR cc_start: 0.7858 (p) cc_final: 0.7399 (t) REVERT: A 309 LYS cc_start: 0.6742 (mtmt) cc_final: 0.6486 (mtpp) REVERT: A 453 GLN cc_start: 0.7483 (mt0) cc_final: 0.7026 (mt0) REVERT: A 597 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7150 (t70) REVERT: A 619 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8059 (mm-30) REVERT: A 627 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7607 (tt0) REVERT: A 636 LYS cc_start: 0.8120 (tppp) cc_final: 0.7809 (tptp) REVERT: A 675 ARG cc_start: 0.7423 (mmp-170) cc_final: 0.6948 (mtm110) REVERT: A 730 HIS cc_start: 0.7200 (t70) cc_final: 0.6182 (m-70) REVERT: A 804 GLU cc_start: 0.7269 (mm-30) cc_final: 0.7027 (mp0) REVERT: A 814 LYS cc_start: 0.7457 (mptt) cc_final: 0.6833 (tptt) REVERT: A 856 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.6618 (mp) REVERT: A 937 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7151 (t70) REVERT: A 948 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6820 (tm-30) REVERT: A 976 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7360 (ptt) REVERT: A 984 ARG cc_start: 0.6760 (mtt-85) cc_final: 0.6027 (mtp180) REVERT: A 1007 ILE cc_start: 0.6388 (OUTLIER) cc_final: 0.5988 (mt) REVERT: B 24 LYS cc_start: 0.7321 (mtpp) cc_final: 0.6711 (pttp) REVERT: B 25 ASP cc_start: 0.7577 (m-30) cc_final: 0.7375 (m-30) REVERT: B 78 GLU cc_start: 0.7936 (tt0) cc_final: 0.7729 (tm-30) REVERT: B 170 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6686 (mm-30) REVERT: B 191 GLN cc_start: 0.7945 (pt0) cc_final: 0.7715 (pt0) REVERT: B 204 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7539 (tppt) REVERT: B 219 ASP cc_start: 0.8172 (m-30) cc_final: 0.7931 (m-30) REVERT: B 291 LYS cc_start: 0.6146 (mtmm) cc_final: 0.5525 (ptpt) REVERT: B 368 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6753 (mmtt) REVERT: B 441 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.6112 (mp) REVERT: B 451 GLN cc_start: 0.7250 (mt0) cc_final: 0.7049 (mt0) REVERT: B 542 LYS cc_start: 0.7087 (mtmp) cc_final: 0.6596 (mmtt) REVERT: B 543 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6527 (tm-30) REVERT: B 572 GLN cc_start: 0.7088 (mm-40) cc_final: 0.6853 (mm-40) REVERT: B 628 GLU cc_start: 0.7123 (tt0) cc_final: 0.6874 (tp30) REVERT: B 632 GLN cc_start: 0.6884 (mm110) cc_final: 0.6657 (mt0) REVERT: B 643 GLU cc_start: 0.6658 (pt0) cc_final: 0.6372 (mp0) REVERT: B 726 LYS cc_start: 0.7231 (ptmm) cc_final: 0.6896 (ptmm) REVERT: B 739 ASN cc_start: 0.7781 (m-40) cc_final: 0.7220 (t0) REVERT: B 760 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7274 (tm-30) REVERT: B 814 LYS cc_start: 0.6862 (OUTLIER) cc_final: 0.6228 (tttp) REVERT: B 844 LYS cc_start: 0.7967 (mtmt) cc_final: 0.7584 (mtmt) REVERT: B 880 ARG cc_start: 0.7715 (mtp180) cc_final: 0.6620 (mtp-110) REVERT: B 973 ASN cc_start: 0.6968 (t0) cc_final: 0.6740 (t0) outliers start: 81 outliers final: 23 residues processed: 293 average time/residue: 0.5997 time to fit residues: 193.6795 Evaluate side-chains 268 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 232 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 688 ARG Chi-restraints excluded: chain B residue 760 GLN Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain B residue 956 ARG Chi-restraints excluded: chain B residue 993 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 82 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 ASN A 524 HIS A 527 HIS A 741 ASN A 775 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 713 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.187445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.158930 restraints weight = 17094.948| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.46 r_work: 0.3624 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17012 Z= 0.128 Angle : 0.539 9.554 23068 Z= 0.268 Chirality : 0.040 0.138 2467 Planarity : 0.004 0.052 2987 Dihedral : 7.538 86.044 2376 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.17 % Allowed : 23.07 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.19), residues: 2042 helix: 1.01 (0.17), residues: 930 sheet: -1.09 (0.29), residues: 280 loop : -0.42 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 700 TYR 0.017 0.001 TYR A 736 PHE 0.014 0.001 PHE B 160 TRP 0.016 0.001 TRP B 98 HIS 0.004 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (17010) covalent geometry : angle 0.53937 / 0.27 (23068) hydrogen bonds : bond 0.03883 / 2.54 ( 769) hydrogen bonds : angle 4.79486 / 3.47 ( 2217) Misc. bond : bond 0.02116 / 1.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 241 time to evaluate : 0.543 Fit side-chains REVERT: A 61 LYS cc_start: 0.7346 (ttpt) cc_final: 0.7019 (ttpp) REVERT: A 99 ARG cc_start: 0.6753 (tpp-160) cc_final: 0.6273 (tpp-160) REVERT: A 184 ASP cc_start: 0.7763 (t70) cc_final: 0.7452 (m-30) REVERT: A 191 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7147 (mp10) REVERT: A 270 GLU cc_start: 0.6061 (pt0) cc_final: 0.5398 (mm-30) REVERT: A 299 GLN cc_start: 0.6552 (mt0) cc_final: 0.5815 (tm130) REVERT: A 301 LEU cc_start: 0.7224 (mp) cc_final: 0.6925 (mt) REVERT: A 307 THR cc_start: 0.7743 (p) cc_final: 0.7274 (t) REVERT: A 309 LYS cc_start: 0.6662 (mtmt) cc_final: 0.6394 (mtpp) REVERT: A 354 GLN cc_start: 0.6336 (mm-40) cc_final: 0.6039 (mp10) REVERT: A 369 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6020 (mp0) REVERT: A 453 GLN cc_start: 0.7455 (mt0) cc_final: 0.7008 (mt0) REVERT: A 529 GLU cc_start: 0.7294 (mp0) cc_final: 0.6636 (mp0) REVERT: A 588 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.7921 (OUTLIER) REVERT: A 597 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.7066 (t70) REVERT: A 619 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7902 (mm-30) REVERT: A 636 LYS cc_start: 0.8071 (tppp) cc_final: 0.7767 (tptp) REVERT: A 675 ARG cc_start: 0.7303 (mmp-170) cc_final: 0.6834 (mtm110) REVERT: A 730 HIS cc_start: 0.7141 (t70) cc_final: 0.6121 (m-70) REVERT: A 804 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6946 (mp0) REVERT: A 814 LYS cc_start: 0.7462 (mptt) cc_final: 0.6806 (tptt) REVERT: A 856 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6540 (mp) REVERT: A 880 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8421 (mtp180) REVERT: A 904 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7394 (mp0) REVERT: A 937 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7120 (t70) REVERT: A 976 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7582 (ptt) REVERT: A 984 ARG cc_start: 0.6674 (mtt-85) cc_final: 0.5936 (mtp180) REVERT: A 997 MET cc_start: 0.6973 (mmm) cc_final: 0.6379 (mtm) REVERT: A 1007 ILE cc_start: 0.6249 (OUTLIER) cc_final: 0.5809 (mt) REVERT: A 1053 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7383 (mp) REVERT: A 1055 LYS cc_start: 0.7740 (mptt) cc_final: 0.7423 (mmtt) REVERT: B 24 LYS cc_start: 0.7251 (mtpp) cc_final: 0.6626 (pttp) REVERT: B 25 ASP cc_start: 0.7560 (m-30) cc_final: 0.7262 (m-30) REVERT: B 45 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7025 (mm110) REVERT: B 170 GLU cc_start: 0.6940 (mm-30) cc_final: 0.6615 (mm-30) REVERT: B 191 GLN cc_start: 0.7858 (pt0) cc_final: 0.7564 (pt0) REVERT: B 204 LYS cc_start: 0.7903 (mtmt) cc_final: 0.7468 (tppt) REVERT: B 219 ASP cc_start: 0.8047 (m-30) cc_final: 0.7847 (m-30) REVERT: B 291 LYS cc_start: 0.6074 (mtmm) cc_final: 0.5486 (ptpt) REVERT: B 368 LYS cc_start: 0.6941 (OUTLIER) cc_final: 0.6689 (mmtt) REVERT: B 441 LEU cc_start: 0.6281 (OUTLIER) cc_final: 0.5987 (tp) REVERT: B 539 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7324 (pt0) REVERT: B 542 LYS cc_start: 0.7026 (mtmp) cc_final: 0.6526 (mmtt) REVERT: B 543 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6485 (tm-30) REVERT: B 572 GLN cc_start: 0.7004 (mm-40) cc_final: 0.6799 (mm-40) REVERT: B 628 GLU cc_start: 0.7068 (tt0) cc_final: 0.6826 (tp30) REVERT: B 643 GLU cc_start: 0.6614 (pt0) cc_final: 0.6325 (mp0) REVERT: B 726 LYS cc_start: 0.7225 (ptmm) cc_final: 0.6895 (ptmm) REVERT: B 739 ASN cc_start: 0.7710 (m-40) cc_final: 0.7126 (t0) REVERT: B 760 GLN cc_start: 0.7533 (tt0) cc_final: 0.7214 (tm-30) REVERT: B 814 LYS cc_start: 0.6771 (mptt) cc_final: 0.6109 (tttp) REVERT: B 844 LYS cc_start: 0.7849 (mtmt) cc_final: 0.7410 (mtmt) REVERT: B 880 ARG cc_start: 0.7546 (mtp180) cc_final: 0.6572 (mtp-110) REVERT: B 939 MET cc_start: 0.6568 (ptp) cc_final: 0.6148 (ptp) REVERT: B 1037 GLU cc_start: 0.6128 (OUTLIER) cc_final: 0.5872 (pt0) outliers start: 56 outliers final: 12 residues processed: 272 average time/residue: 0.5861 time to fit residues: 175.3875 Evaluate side-chains 257 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 229 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 880 ARG Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 688 ARG Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain B residue 956 ARG Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 1037 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 123 optimal weight: 0.1980 chunk 180 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 181 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 138 optimal weight: 0.0770 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 HIS A 527 HIS A 739 ASN A 741 ASN A 775 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 GLN ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 713 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.190270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.162231 restraints weight = 16819.396| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.44 r_work: 0.3708 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17012 Z= 0.115 Angle : 0.518 9.008 23068 Z= 0.257 Chirality : 0.040 0.130 2467 Planarity : 0.004 0.054 2987 Dihedral : 7.346 88.972 2374 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.80 % Allowed : 22.22 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.19), residues: 2042 helix: 1.18 (0.17), residues: 924 sheet: -1.06 (0.29), residues: 280 loop : -0.37 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 956 TYR 0.015 0.001 TYR A 736 PHE 0.014 0.001 PHE B 160 TRP 0.014 0.001 TRP B 98 HIS 0.003 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 (17010) covalent geometry : angle 0.51826 / 0.26 (23068) hydrogen bonds : bond 0.03583 / 2.35 ( 769) hydrogen bonds : angle 4.58985 / 3.32 ( 2217) Misc. bond : bond 0.01949 / 0.93 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 240 time to evaluate : 0.647 Fit side-chains REVERT: A 33 LYS cc_start: 0.6906 (mtpp) cc_final: 0.6522 (tmtt) REVERT: A 61 LYS cc_start: 0.7364 (ttpt) cc_final: 0.7043 (ttpp) REVERT: A 99 ARG cc_start: 0.6781 (tpp-160) cc_final: 0.6296 (tpp-160) REVERT: A 184 ASP cc_start: 0.7788 (t70) cc_final: 0.7513 (m-30) REVERT: A 191 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7198 (mp10) REVERT: A 251 LYS cc_start: 0.6418 (OUTLIER) cc_final: 0.6206 (mtmt) REVERT: A 270 GLU cc_start: 0.6139 (pt0) cc_final: 0.5534 (mm-30) REVERT: A 299 GLN cc_start: 0.6612 (mt0) cc_final: 0.5856 (tm130) REVERT: A 307 THR cc_start: 0.7803 (p) cc_final: 0.7326 (t) REVERT: A 309 LYS cc_start: 0.6716 (mtmt) cc_final: 0.6469 (mtpp) REVERT: A 354 GLN cc_start: 0.6455 (mm-40) cc_final: 0.6180 (mp10) REVERT: A 369 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6171 (mp0) REVERT: A 453 GLN cc_start: 0.7378 (mt0) cc_final: 0.6976 (mt0) REVERT: A 529 GLU cc_start: 0.7362 (mp0) cc_final: 0.6684 (mp0) REVERT: A 588 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.7867 (OUTLIER) REVERT: A 597 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7106 (t70) REVERT: A 619 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7878 (mm-30) REVERT: A 636 LYS cc_start: 0.8049 (tppp) cc_final: 0.7774 (tptp) REVERT: A 675 ARG cc_start: 0.7267 (mmp-170) cc_final: 0.6916 (mtm110) REVERT: A 730 HIS cc_start: 0.7216 (t70) cc_final: 0.6195 (m-70) REVERT: A 734 GLN cc_start: 0.7424 (mm110) cc_final: 0.6999 (pt0) REVERT: A 804 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6950 (mp0) REVERT: A 814 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.6848 (tptt) REVERT: A 904 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7490 (mp0) REVERT: A 937 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.7000 (t70) REVERT: A 976 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7711 (ptt) REVERT: A 984 ARG cc_start: 0.6691 (mtt-85) cc_final: 0.5974 (mtp180) REVERT: A 997 MET cc_start: 0.6882 (mmm) cc_final: 0.6397 (mtm) REVERT: A 1007 ILE cc_start: 0.6123 (OUTLIER) cc_final: 0.5633 (mt) REVERT: A 1053 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7485 (mp) REVERT: A 1055 LYS cc_start: 0.7767 (mptt) cc_final: 0.7452 (mmtt) REVERT: B 24 LYS cc_start: 0.7259 (mtpp) cc_final: 0.6651 (pttp) REVERT: B 25 ASP cc_start: 0.7610 (m-30) cc_final: 0.7347 (m-30) REVERT: B 45 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7053 (mm110) REVERT: B 170 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6731 (mm-30) REVERT: B 191 GLN cc_start: 0.7906 (pt0) cc_final: 0.7622 (pt0) REVERT: B 204 LYS cc_start: 0.7907 (mtmt) cc_final: 0.7527 (tppt) REVERT: B 368 LYS cc_start: 0.6937 (OUTLIER) cc_final: 0.6717 (mmtt) REVERT: B 441 LEU cc_start: 0.6286 (OUTLIER) cc_final: 0.6080 (tp) REVERT: B 452 VAL cc_start: 0.7480 (OUTLIER) cc_final: 0.7261 (m) REVERT: B 542 LYS cc_start: 0.7059 (mtmp) cc_final: 0.6578 (mmtt) REVERT: B 543 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6570 (tm-30) REVERT: B 604 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.7058 (tttp) REVERT: B 628 GLU cc_start: 0.7193 (tt0) cc_final: 0.6926 (tp30) REVERT: B 643 GLU cc_start: 0.6601 (pt0) cc_final: 0.6355 (mp0) REVERT: B 726 LYS cc_start: 0.7186 (ptmm) cc_final: 0.6960 (ptmm) REVERT: B 739 ASN cc_start: 0.7765 (m-40) cc_final: 0.7197 (t0) REVERT: B 760 GLN cc_start: 0.7492 (tt0) cc_final: 0.7232 (tm-30) REVERT: B 814 LYS cc_start: 0.6792 (mptt) cc_final: 0.6170 (tttp) REVERT: B 844 LYS cc_start: 0.7824 (mtmt) cc_final: 0.7461 (mtmt) REVERT: B 904 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7866 (mt-10) REVERT: B 939 MET cc_start: 0.6517 (ptp) cc_final: 0.6083 (ptp) REVERT: B 1037 GLU cc_start: 0.5982 (OUTLIER) cc_final: 0.5781 (pt0) outliers start: 67 outliers final: 21 residues processed: 283 average time/residue: 0.5871 time to fit residues: 183.6264 Evaluate side-chains 259 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 220 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 604 LYS Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 688 ARG Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain B residue 956 ARG Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 1037 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 31 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 153 optimal weight: 0.0980 chunk 23 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 HIS A 741 ASN A 775 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 713 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.191038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.162953 restraints weight = 16848.453| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.44 r_work: 0.3716 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17012 Z= 0.111 Angle : 0.513 9.102 23068 Z= 0.254 Chirality : 0.039 0.128 2467 Planarity : 0.004 0.054 2987 Dihedral : 7.285 88.340 2374 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.97 % Allowed : 22.22 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.19), residues: 2042 helix: 1.30 (0.17), residues: 914 sheet: -1.02 (0.30), residues: 280 loop : -0.29 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 239 TYR 0.015 0.001 TYR A 736 PHE 0.014 0.001 PHE B 160 TRP 0.014 0.001 TRP A 98 HIS 0.004 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (17010) covalent geometry : angle 0.51289 / 0.25 (23068) hydrogen bonds : bond 0.03482 / 2.29 ( 769) hydrogen bonds : angle 4.50345 / 3.25 ( 2217) Misc. bond : bond 0.01870 / 0.90 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 234 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.6890 (mtpp) cc_final: 0.6523 (tmtt) REVERT: A 61 LYS cc_start: 0.7385 (ttpt) cc_final: 0.7060 (ttpp) REVERT: A 99 ARG cc_start: 0.6719 (tpp-160) cc_final: 0.6224 (tpp-160) REVERT: A 161 ASN cc_start: 0.8099 (OUTLIER) cc_final: 0.7761 (m-40) REVERT: A 184 ASP cc_start: 0.7787 (t70) cc_final: 0.7510 (m-30) REVERT: A 251 LYS cc_start: 0.6434 (OUTLIER) cc_final: 0.6156 (mtmt) REVERT: A 270 GLU cc_start: 0.6175 (pt0) cc_final: 0.5585 (mm-30) REVERT: A 299 GLN cc_start: 0.6633 (mt0) cc_final: 0.5799 (tm130) REVERT: A 307 THR cc_start: 0.7780 (p) cc_final: 0.7296 (t) REVERT: A 309 LYS cc_start: 0.6788 (mtmt) cc_final: 0.6542 (mtpp) REVERT: A 369 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6161 (mp0) REVERT: A 407 MET cc_start: 0.8487 (ttt) cc_final: 0.8285 (ttt) REVERT: A 453 GLN cc_start: 0.7260 (mt0) cc_final: 0.6853 (mt0) REVERT: A 529 GLU cc_start: 0.7457 (mp0) cc_final: 0.7118 (tt0) REVERT: A 588 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.7848 (OUTLIER) REVERT: A 597 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7107 (t70) REVERT: A 619 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7856 (mm-30) REVERT: A 636 LYS cc_start: 0.8033 (tppp) cc_final: 0.7664 (tptt) REVERT: A 675 ARG cc_start: 0.7297 (mmp-170) cc_final: 0.6894 (mtm110) REVERT: A 726 LYS cc_start: 0.7116 (mtpp) cc_final: 0.6856 (ttmt) REVERT: A 730 HIS cc_start: 0.7299 (t70) cc_final: 0.6296 (m-70) REVERT: A 734 GLN cc_start: 0.7433 (mm110) cc_final: 0.7040 (pt0) REVERT: A 798 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6089 (tp30) REVERT: A 814 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.6822 (tptt) REVERT: A 937 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7016 (t70) REVERT: A 976 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7655 (ptt) REVERT: A 984 ARG cc_start: 0.6680 (mtt-85) cc_final: 0.5961 (mtp180) REVERT: A 997 MET cc_start: 0.6810 (mmm) cc_final: 0.6527 (mtm) REVERT: A 1007 ILE cc_start: 0.6039 (OUTLIER) cc_final: 0.5552 (mt) REVERT: A 1053 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7491 (mp) REVERT: A 1055 LYS cc_start: 0.7818 (mptt) cc_final: 0.7499 (mmtt) REVERT: B 24 LYS cc_start: 0.7300 (mtpp) cc_final: 0.6660 (pttp) REVERT: B 25 ASP cc_start: 0.7628 (m-30) cc_final: 0.7371 (m-30) REVERT: B 33 LYS cc_start: 0.6880 (pttt) cc_final: 0.6466 (ptpp) REVERT: B 170 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6732 (mm-30) REVERT: B 191 GLN cc_start: 0.7902 (pt0) cc_final: 0.7617 (pt0) REVERT: B 204 LYS cc_start: 0.7894 (mtmt) cc_final: 0.7527 (tppt) REVERT: B 219 ASP cc_start: 0.7423 (m-30) cc_final: 0.7160 (m-30) REVERT: B 368 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6825 (mmtt) REVERT: B 542 LYS cc_start: 0.7042 (mtmp) cc_final: 0.6587 (mmtt) REVERT: B 543 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6587 (tm-30) REVERT: B 628 GLU cc_start: 0.7178 (tt0) cc_final: 0.6909 (tp30) REVERT: B 643 GLU cc_start: 0.6603 (pt0) cc_final: 0.6343 (mp0) REVERT: B 726 LYS cc_start: 0.7179 (ptmm) cc_final: 0.6957 (ptmm) REVERT: B 739 ASN cc_start: 0.7763 (m-40) cc_final: 0.7206 (t0) REVERT: B 760 GLN cc_start: 0.7491 (tt0) cc_final: 0.7230 (tm-30) REVERT: B 814 LYS cc_start: 0.6783 (mptt) cc_final: 0.6157 (tttp) REVERT: B 844 LYS cc_start: 0.7840 (mtmt) cc_final: 0.7473 (mtmt) REVERT: B 904 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: B 1037 GLU cc_start: 0.5930 (OUTLIER) cc_final: 0.5712 (pt0) REVERT: B 1051 GLU cc_start: 0.6288 (mt-10) cc_final: 0.5911 (mp0) outliers start: 70 outliers final: 23 residues processed: 283 average time/residue: 0.5301 time to fit residues: 166.1985 Evaluate side-chains 263 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 227 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 688 ARG Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 1037 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 137 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 159 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 164 optimal weight: 0.5980 chunk 168 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN A 527 HIS A 741 ASN A 775 GLN B 209 HIS ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 713 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.190010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.161813 restraints weight = 16786.077| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.44 r_work: 0.3704 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17012 Z= 0.126 Angle : 0.532 9.207 23068 Z= 0.262 Chirality : 0.040 0.245 2467 Planarity : 0.004 0.053 2987 Dihedral : 7.225 84.720 2372 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.40 % Allowed : 23.24 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.19), residues: 2042 helix: 1.27 (0.17), residues: 915 sheet: -1.02 (0.30), residues: 280 loop : -0.30 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 239 TYR 0.016 0.001 TYR A 736 PHE 0.016 0.001 PHE B 160 TRP 0.014 0.001 TRP A 98 HIS 0.004 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (17010) covalent geometry : angle 0.53154 / 0.26 (23068) hydrogen bonds : bond 0.03588 / 2.37 ( 769) hydrogen bonds : angle 4.50853 / 3.25 ( 2217) Misc. bond : bond 0.02251 / 1.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 231 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.6907 (OUTLIER) cc_final: 0.6539 (tmtt) REVERT: A 61 LYS cc_start: 0.7391 (ttpt) cc_final: 0.7065 (ttpp) REVERT: A 99 ARG cc_start: 0.6680 (tpp-160) cc_final: 0.6206 (tpp-160) REVERT: A 161 ASN cc_start: 0.8093 (OUTLIER) cc_final: 0.7791 (m-40) REVERT: A 184 ASP cc_start: 0.7835 (t70) cc_final: 0.7533 (m-30) REVERT: A 251 LYS cc_start: 0.6452 (OUTLIER) cc_final: 0.6193 (mtmt) REVERT: A 270 GLU cc_start: 0.6166 (pt0) cc_final: 0.5556 (mm-30) REVERT: A 299 GLN cc_start: 0.6604 (mt0) cc_final: 0.5851 (tm130) REVERT: A 307 THR cc_start: 0.7817 (p) cc_final: 0.7341 (t) REVERT: A 309 LYS cc_start: 0.6786 (mtmt) cc_final: 0.6527 (mtpp) REVERT: A 318 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.7045 (tpt170) REVERT: A 369 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6158 (mp0) REVERT: A 407 MET cc_start: 0.8555 (ttt) cc_final: 0.8346 (ttt) REVERT: A 453 GLN cc_start: 0.7315 (mt0) cc_final: 0.6899 (mt0) REVERT: A 523 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6626 (mp) REVERT: A 529 GLU cc_start: 0.7443 (mp0) cc_final: 0.7112 (tt0) REVERT: A 588 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.7870 (m-30) REVERT: A 597 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.7072 (t70) REVERT: A 636 LYS cc_start: 0.8041 (tppp) cc_final: 0.7676 (tptt) REVERT: A 675 ARG cc_start: 0.7381 (mmp-170) cc_final: 0.6831 (mtm-85) REVERT: A 726 LYS cc_start: 0.7134 (mtpp) cc_final: 0.6880 (ttmt) REVERT: A 730 HIS cc_start: 0.7332 (t70) cc_final: 0.6285 (m-70) REVERT: A 734 GLN cc_start: 0.7449 (mm110) cc_final: 0.7046 (pt0) REVERT: A 798 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6092 (tp30) REVERT: A 814 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.6814 (tptt) REVERT: A 904 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: A 937 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7059 (t70) REVERT: A 976 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7646 (ptt) REVERT: A 984 ARG cc_start: 0.6710 (mtt-85) cc_final: 0.5992 (mtp180) REVERT: A 1007 ILE cc_start: 0.6127 (OUTLIER) cc_final: 0.5637 (mt) REVERT: A 1053 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7511 (mp) REVERT: B 24 LYS cc_start: 0.7359 (mtpp) cc_final: 0.6702 (pttp) REVERT: B 25 ASP cc_start: 0.7635 (m-30) cc_final: 0.7406 (m-30) REVERT: B 33 LYS cc_start: 0.6810 (pttt) cc_final: 0.6444 (ptpp) REVERT: B 170 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6737 (mm-30) REVERT: B 187 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7027 (mmt) REVERT: B 191 GLN cc_start: 0.7914 (pt0) cc_final: 0.7660 (pt0) REVERT: B 204 LYS cc_start: 0.7901 (mtmt) cc_final: 0.7521 (tppt) REVERT: B 368 LYS cc_start: 0.6982 (OUTLIER) cc_final: 0.6755 (mmtt) REVERT: B 416 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.6307 (tt) REVERT: B 542 LYS cc_start: 0.7059 (mtmp) cc_final: 0.6599 (mmtt) REVERT: B 543 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6575 (tt0) REVERT: B 628 GLU cc_start: 0.7222 (tt0) cc_final: 0.6928 (tp30) REVERT: B 643 GLU cc_start: 0.6602 (pt0) cc_final: 0.6331 (mp0) REVERT: B 726 LYS cc_start: 0.7225 (ptmm) cc_final: 0.7004 (ptmm) REVERT: B 739 ASN cc_start: 0.7762 (m-40) cc_final: 0.7244 (t0) REVERT: B 760 GLN cc_start: 0.7521 (tt0) cc_final: 0.7228 (tm-30) REVERT: B 814 LYS cc_start: 0.6840 (mptt) cc_final: 0.6179 (tttp) REVERT: B 815 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6654 (mptt) REVERT: B 844 LYS cc_start: 0.7831 (mtmt) cc_final: 0.7451 (mtmt) REVERT: B 904 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7880 (mt-10) REVERT: B 939 MET cc_start: 0.6438 (ptp) cc_final: 0.6073 (ptp) REVERT: B 1051 GLU cc_start: 0.6356 (mt-10) cc_final: 0.5988 (mp0) outliers start: 60 outliers final: 23 residues processed: 272 average time/residue: 0.5732 time to fit residues: 172.4526 Evaluate side-chains 266 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 815 LYS Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain B residue 956 ARG Chi-restraints excluded: chain B residue 993 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 46 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 191 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 HIS A 741 ASN A 775 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 713 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.189540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.161407 restraints weight = 16785.681| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.43 r_work: 0.3698 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17012 Z= 0.134 Angle : 0.545 10.907 23068 Z= 0.268 Chirality : 0.041 0.220 2467 Planarity : 0.004 0.054 2987 Dihedral : 7.253 83.731 2372 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.46 % Allowed : 23.53 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.19), residues: 2042 helix: 1.27 (0.17), residues: 915 sheet: -1.01 (0.30), residues: 280 loop : -0.31 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 239 TYR 0.017 0.001 TYR A 736 PHE 0.016 0.001 PHE B 160 TRP 0.014 0.001 TRP A 98 HIS 0.004 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (17010) covalent geometry : angle 0.54531 / 0.27 (23068) hydrogen bonds : bond 0.03647 / 2.40 ( 769) hydrogen bonds : angle 4.50656 / 3.25 ( 2217) Misc. bond : bond 0.02370 / 1.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 228 time to evaluate : 0.470 Fit side-chains REVERT: A 33 LYS cc_start: 0.6932 (mtpp) cc_final: 0.6560 (tmtt) REVERT: A 61 LYS cc_start: 0.7467 (ttpt) cc_final: 0.7111 (ttpp) REVERT: A 99 ARG cc_start: 0.6666 (tpp-160) cc_final: 0.6175 (tpp-160) REVERT: A 170 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7482 (tp30) REVERT: A 184 ASP cc_start: 0.7832 (t70) cc_final: 0.7519 (m-30) REVERT: A 198 LYS cc_start: 0.7638 (pttm) cc_final: 0.7112 (pptt) REVERT: A 251 LYS cc_start: 0.6421 (OUTLIER) cc_final: 0.6125 (mtmt) REVERT: A 270 GLU cc_start: 0.6132 (pt0) cc_final: 0.5508 (mm-30) REVERT: A 299 GLN cc_start: 0.6602 (mt0) cc_final: 0.5835 (tm130) REVERT: A 307 THR cc_start: 0.7827 (p) cc_final: 0.7349 (t) REVERT: A 309 LYS cc_start: 0.6799 (mtmt) cc_final: 0.6540 (mtpp) REVERT: A 318 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.7054 (tpt170) REVERT: A 369 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6281 (mp0) REVERT: A 407 MET cc_start: 0.8574 (ttt) cc_final: 0.8363 (ttt) REVERT: A 453 GLN cc_start: 0.7320 (mt0) cc_final: 0.6898 (mt0) REVERT: A 523 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6543 (mp) REVERT: A 529 GLU cc_start: 0.7446 (mp0) cc_final: 0.7107 (tt0) REVERT: A 588 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.7873 (m-30) REVERT: A 597 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.7158 (t70) REVERT: A 636 LYS cc_start: 0.8077 (tppp) cc_final: 0.7705 (tptt) REVERT: A 675 ARG cc_start: 0.7413 (mmp-170) cc_final: 0.6847 (mtm-85) REVERT: A 726 LYS cc_start: 0.7143 (mtpp) cc_final: 0.6892 (ttmt) REVERT: A 730 HIS cc_start: 0.7368 (t70) cc_final: 0.6307 (m-70) REVERT: A 734 GLN cc_start: 0.7462 (mm110) cc_final: 0.7066 (pt0) REVERT: A 798 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6102 (tp30) REVERT: A 805 GLU cc_start: 0.7159 (mp0) cc_final: 0.6568 (tm-30) REVERT: A 814 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.6829 (tptt) REVERT: A 904 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: A 937 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.6982 (t70) REVERT: A 975 ILE cc_start: 0.6751 (OUTLIER) cc_final: 0.6244 (mp) REVERT: A 976 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7653 (ptt) REVERT: A 984 ARG cc_start: 0.6733 (mtt-85) cc_final: 0.6014 (mtp180) REVERT: A 1007 ILE cc_start: 0.6190 (OUTLIER) cc_final: 0.5702 (mt) REVERT: A 1026 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6717 (mm-30) REVERT: A 1053 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7509 (mp) REVERT: B 24 LYS cc_start: 0.7382 (mtpp) cc_final: 0.6720 (pttp) REVERT: B 33 LYS cc_start: 0.6831 (pttt) cc_final: 0.6461 (ptpp) REVERT: B 45 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7115 (mm110) REVERT: B 170 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6702 (mm-30) REVERT: B 187 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7032 (mmt) REVERT: B 191 GLN cc_start: 0.7923 (pt0) cc_final: 0.7664 (pt0) REVERT: B 204 LYS cc_start: 0.7913 (mtmt) cc_final: 0.7528 (tppt) REVERT: B 219 ASP cc_start: 0.7418 (m-30) cc_final: 0.7175 (m-30) REVERT: B 368 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6633 (mmtt) REVERT: B 416 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.6340 (tt) REVERT: B 542 LYS cc_start: 0.7083 (mtmp) cc_final: 0.6594 (mmtt) REVERT: B 543 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6559 (tt0) REVERT: B 628 GLU cc_start: 0.7214 (tt0) cc_final: 0.6935 (tp30) REVERT: B 643 GLU cc_start: 0.6657 (pt0) cc_final: 0.6329 (mp0) REVERT: B 726 LYS cc_start: 0.7255 (ptmm) cc_final: 0.7032 (ptmm) REVERT: B 739 ASN cc_start: 0.7768 (m-40) cc_final: 0.7241 (t0) REVERT: B 760 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7254 (tm-30) REVERT: B 814 LYS cc_start: 0.6884 (mptt) cc_final: 0.6230 (tttp) REVERT: B 815 LYS cc_start: 0.7094 (OUTLIER) cc_final: 0.6636 (mptt) REVERT: B 844 LYS cc_start: 0.7846 (mtmt) cc_final: 0.7470 (mtmt) REVERT: B 939 MET cc_start: 0.6435 (ptp) cc_final: 0.6058 (ptp) REVERT: B 1051 GLU cc_start: 0.6373 (mt-10) cc_final: 0.6018 (mp0) outliers start: 61 outliers final: 27 residues processed: 268 average time/residue: 0.6064 time to fit residues: 179.1676 Evaluate side-chains 273 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 226 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 760 GLN Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 815 LYS Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain B residue 956 ARG Chi-restraints excluded: chain B residue 993 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 62 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 198 optimal weight: 0.3980 chunk 150 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 HIS A 741 ASN A 775 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 713 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.188922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.160654 restraints weight = 16862.351| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.45 r_work: 0.3691 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17012 Z= 0.138 Angle : 0.551 9.891 23068 Z= 0.272 Chirality : 0.041 0.216 2467 Planarity : 0.004 0.055 2987 Dihedral : 7.301 84.227 2372 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.06 % Allowed : 24.21 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.19), residues: 2042 helix: 1.23 (0.17), residues: 915 sheet: -1.04 (0.30), residues: 280 loop : -0.33 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 382 TYR 0.017 0.001 TYR A 736 PHE 0.033 0.002 PHE B 425 TRP 0.014 0.001 TRP B 98 HIS 0.005 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (17010) covalent geometry : angle 0.55150 / 0.27 (23068) hydrogen bonds : bond 0.03717 / 2.45 ( 769) hydrogen bonds : angle 4.52832 / 3.27 ( 2217) Misc. bond : bond 0.02450 / 1.17 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 234 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7474 (ttpt) cc_final: 0.7124 (ttpp) REVERT: A 99 ARG cc_start: 0.6680 (tpp-160) cc_final: 0.6337 (tpp-160) REVERT: A 161 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7823 (m-40) REVERT: A 170 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7504 (tp30) REVERT: A 184 ASP cc_start: 0.7809 (t70) cc_final: 0.7504 (m-30) REVERT: A 198 LYS cc_start: 0.7647 (pttm) cc_final: 0.7098 (pptt) REVERT: A 251 LYS cc_start: 0.6429 (OUTLIER) cc_final: 0.6190 (mtmt) REVERT: A 270 GLU cc_start: 0.6142 (pt0) cc_final: 0.5524 (mm-30) REVERT: A 299 GLN cc_start: 0.6579 (mt0) cc_final: 0.5836 (tm130) REVERT: A 307 THR cc_start: 0.7845 (p) cc_final: 0.7375 (t) REVERT: A 309 LYS cc_start: 0.6801 (mtmt) cc_final: 0.6559 (mtpp) REVERT: A 318 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.7036 (tpt170) REVERT: A 369 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6310 (mp0) REVERT: A 407 MET cc_start: 0.8567 (ttt) cc_final: 0.8355 (ttt) REVERT: A 453 GLN cc_start: 0.7334 (mt0) cc_final: 0.6908 (mt0) REVERT: A 523 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6577 (mp) REVERT: A 529 GLU cc_start: 0.7459 (mp0) cc_final: 0.7120 (tt0) REVERT: A 588 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.7895 (m-30) REVERT: A 597 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7160 (t70) REVERT: A 636 LYS cc_start: 0.8077 (tppp) cc_final: 0.7701 (tptt) REVERT: A 675 ARG cc_start: 0.7491 (mmp-170) cc_final: 0.6899 (mtm-85) REVERT: A 726 LYS cc_start: 0.7152 (mtpp) cc_final: 0.6902 (ttmt) REVERT: A 730 HIS cc_start: 0.7380 (t70) cc_final: 0.6283 (m-70) REVERT: A 734 GLN cc_start: 0.7482 (mm110) cc_final: 0.7086 (pt0) REVERT: A 798 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6159 (tp30) REVERT: A 805 GLU cc_start: 0.7173 (mp0) cc_final: 0.6550 (tm-30) REVERT: A 814 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.6814 (tptt) REVERT: A 904 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: A 937 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.6953 (t70) REVERT: A 976 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7754 (ptt) REVERT: A 984 ARG cc_start: 0.6737 (mtt-85) cc_final: 0.5955 (mtp180) REVERT: A 1007 ILE cc_start: 0.6187 (OUTLIER) cc_final: 0.5707 (mt) REVERT: A 1026 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6731 (mm-30) REVERT: A 1053 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7524 (mp) REVERT: B 24 LYS cc_start: 0.7384 (mtpp) cc_final: 0.6716 (pttp) REVERT: B 33 LYS cc_start: 0.6882 (pttt) cc_final: 0.6504 (ptpp) REVERT: B 45 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7144 (mm110) REVERT: B 170 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6710 (mm-30) REVERT: B 187 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7046 (mmt) REVERT: B 191 GLN cc_start: 0.7925 (pt0) cc_final: 0.7678 (pt0) REVERT: B 204 LYS cc_start: 0.7925 (mtmt) cc_final: 0.7534 (tppt) REVERT: B 219 ASP cc_start: 0.7464 (m-30) cc_final: 0.7217 (m-30) REVERT: B 368 LYS cc_start: 0.6848 (OUTLIER) cc_final: 0.6617 (mmtt) REVERT: B 542 LYS cc_start: 0.7094 (mtmp) cc_final: 0.6597 (mmtt) REVERT: B 543 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6560 (tm-30) REVERT: B 628 GLU cc_start: 0.7207 (tt0) cc_final: 0.6915 (tp30) REVERT: B 643 GLU cc_start: 0.6663 (pt0) cc_final: 0.6292 (mp0) REVERT: B 726 LYS cc_start: 0.7254 (ptmm) cc_final: 0.7032 (ptmm) REVERT: B 739 ASN cc_start: 0.7774 (m-40) cc_final: 0.7236 (t0) REVERT: B 760 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7270 (tm-30) REVERT: B 814 LYS cc_start: 0.6979 (mptt) cc_final: 0.6325 (tttp) REVERT: B 815 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6652 (mptt) REVERT: B 844 LYS cc_start: 0.7845 (mtmt) cc_final: 0.7479 (mtmt) REVERT: B 939 MET cc_start: 0.6416 (ptp) cc_final: 0.6021 (ptp) outliers start: 54 outliers final: 28 residues processed: 268 average time/residue: 0.5844 time to fit residues: 172.7428 Evaluate side-chains 274 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 227 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 760 GLN Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 815 LYS Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain B residue 956 ARG Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 993 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 120 optimal weight: 4.9990 chunk 118 optimal weight: 0.0770 chunk 141 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 HIS A 741 ASN A 775 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 713 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.187569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.159183 restraints weight = 16795.023| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.45 r_work: 0.3679 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17012 Z= 0.154 Angle : 0.569 9.797 23068 Z= 0.280 Chirality : 0.041 0.204 2467 Planarity : 0.004 0.056 2987 Dihedral : 7.387 84.536 2372 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.51 % Allowed : 23.70 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.19), residues: 2042 helix: 1.17 (0.17), residues: 916 sheet: -1.04 (0.30), residues: 280 loop : -0.33 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 423 TYR 0.017 0.001 TYR A 736 PHE 0.018 0.002 PHE B 160 TRP 0.014 0.001 TRP B 371 HIS 0.005 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (17010) covalent geometry : angle 0.56931 / 0.28 (23068) hydrogen bonds : bond 0.03841 / 2.54 ( 769) hydrogen bonds : angle 4.58358 / 3.31 ( 2217) Misc. bond : bond 0.02721 / 1.31 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 228 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7429 (ttpt) cc_final: 0.7083 (ttpp) REVERT: A 99 ARG cc_start: 0.6659 (tpp-160) cc_final: 0.6299 (tpp-160) REVERT: A 170 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7259 (tt0) REVERT: A 184 ASP cc_start: 0.7773 (t70) cc_final: 0.7442 (m-30) REVERT: A 198 LYS cc_start: 0.7729 (pttm) cc_final: 0.7106 (pptt) REVERT: A 251 LYS cc_start: 0.6393 (OUTLIER) cc_final: 0.6138 (mtmt) REVERT: A 270 GLU cc_start: 0.6132 (pt0) cc_final: 0.5474 (mm-30) REVERT: A 299 GLN cc_start: 0.6556 (mt0) cc_final: 0.5780 (tm130) REVERT: A 301 LEU cc_start: 0.7206 (mp) cc_final: 0.6972 (mt) REVERT: A 307 THR cc_start: 0.7798 (p) cc_final: 0.7322 (t) REVERT: A 309 LYS cc_start: 0.6769 (mtmt) cc_final: 0.6514 (mtpp) REVERT: A 318 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6995 (tpt170) REVERT: A 369 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6266 (mp0) REVERT: A 407 MET cc_start: 0.8588 (ttt) cc_final: 0.8376 (ttt) REVERT: A 453 GLN cc_start: 0.7408 (mt0) cc_final: 0.6970 (mt0) REVERT: A 523 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6533 (mp) REVERT: A 529 GLU cc_start: 0.7355 (mp0) cc_final: 0.7018 (tt0) REVERT: A 588 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.7931 (m-30) REVERT: A 597 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.7195 (t70) REVERT: A 636 LYS cc_start: 0.8106 (tppp) cc_final: 0.7804 (tptp) REVERT: A 675 ARG cc_start: 0.7499 (mmp-170) cc_final: 0.6849 (mtm-85) REVERT: A 730 HIS cc_start: 0.7299 (t70) cc_final: 0.6126 (m-70) REVERT: A 734 GLN cc_start: 0.7453 (mm110) cc_final: 0.7008 (pt0) REVERT: A 798 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6093 (tp30) REVERT: A 805 GLU cc_start: 0.7165 (mp0) cc_final: 0.6544 (tm-30) REVERT: A 814 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.6785 (tptt) REVERT: A 904 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: A 937 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.6863 (t70) REVERT: A 976 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.7839 (ptt) REVERT: A 984 ARG cc_start: 0.6678 (mtt-85) cc_final: 0.5818 (mtp180) REVERT: A 1007 ILE cc_start: 0.6152 (OUTLIER) cc_final: 0.5683 (mt) REVERT: A 1026 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6659 (mm-30) REVERT: A 1053 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7478 (mp) REVERT: B 24 LYS cc_start: 0.7352 (mtpp) cc_final: 0.6651 (pttp) REVERT: B 33 LYS cc_start: 0.6724 (pttt) cc_final: 0.6321 (ptpp) REVERT: B 45 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7040 (mm110) REVERT: B 170 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6676 (mm-30) REVERT: B 187 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.6967 (mmt) REVERT: B 191 GLN cc_start: 0.7905 (pt0) cc_final: 0.7659 (pt0) REVERT: B 204 LYS cc_start: 0.7891 (mtmt) cc_final: 0.7432 (tppt) REVERT: B 219 ASP cc_start: 0.7431 (m-30) cc_final: 0.7167 (m-30) REVERT: B 355 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7422 (tt0) REVERT: B 368 LYS cc_start: 0.6784 (OUTLIER) cc_final: 0.6556 (mmtt) REVERT: B 425 PHE cc_start: 0.7328 (m-80) cc_final: 0.7069 (m-80) REVERT: B 542 LYS cc_start: 0.7009 (mtmp) cc_final: 0.6479 (mmtt) REVERT: B 543 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6528 (tm-30) REVERT: B 628 GLU cc_start: 0.7194 (tt0) cc_final: 0.6878 (tp30) REVERT: B 643 GLU cc_start: 0.6686 (pt0) cc_final: 0.6278 (mp0) REVERT: B 726 LYS cc_start: 0.7253 (ptmm) cc_final: 0.7022 (ptmm) REVERT: B 739 ASN cc_start: 0.7772 (m-40) cc_final: 0.7190 (t0) REVERT: B 760 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.7276 (tm-30) REVERT: B 814 LYS cc_start: 0.7013 (OUTLIER) cc_final: 0.6308 (tttp) REVERT: B 844 LYS cc_start: 0.7825 (mtmt) cc_final: 0.7411 (mtmt) REVERT: B 939 MET cc_start: 0.6385 (ptp) cc_final: 0.5964 (ptp) REVERT: B 1010 GLN cc_start: 0.6050 (tt0) cc_final: 0.5387 (mm110) REVERT: B 1023 MET cc_start: 0.6155 (pp-130) cc_final: 0.5927 (pp-130) REVERT: B 1051 GLU cc_start: 0.6386 (mt-10) cc_final: 0.5907 (mp0) outliers start: 62 outliers final: 30 residues processed: 265 average time/residue: 0.6264 time to fit residues: 182.7888 Evaluate side-chains 275 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 226 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 GLN Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain B residue 956 ARG Chi-restraints excluded: chain B residue 993 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 101 optimal weight: 0.4980 chunk 117 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 0.0020 chunk 64 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 HIS A 741 ASN A 775 GLN A 811 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.189815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.161639 restraints weight = 16814.311| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.46 r_work: 0.3704 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17012 Z= 0.122 Angle : 0.538 9.228 23068 Z= 0.266 Chirality : 0.040 0.180 2467 Planarity : 0.004 0.056 2987 Dihedral : 7.287 84.429 2372 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.06 % Allowed : 24.32 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.19), residues: 2042 helix: 1.27 (0.17), residues: 915 sheet: -1.05 (0.30), residues: 280 loop : -0.31 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 423 TYR 0.016 0.001 TYR A 736 PHE 0.015 0.001 PHE B 160 TRP 0.014 0.001 TRP A 98 HIS 0.003 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (17010) covalent geometry : angle 0.53765 / 0.27 (23068) hydrogen bonds : bond 0.03579 / 2.35 ( 769) hydrogen bonds : angle 4.49119 / 3.24 ( 2217) Misc. bond : bond 0.02048 / 0.98 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 229 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7420 (ttpt) cc_final: 0.7081 (ttpp) REVERT: A 99 ARG cc_start: 0.6635 (tpp-160) cc_final: 0.6406 (tpp80) REVERT: A 161 ASN cc_start: 0.8099 (OUTLIER) cc_final: 0.7722 (m-40) REVERT: A 170 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7206 (tt0) REVERT: A 184 ASP cc_start: 0.7758 (t70) cc_final: 0.7443 (m-30) REVERT: A 198 LYS cc_start: 0.7617 (pttm) cc_final: 0.7049 (pptt) REVERT: A 251 LYS cc_start: 0.6248 (OUTLIER) cc_final: 0.5949 (mtmt) REVERT: A 270 GLU cc_start: 0.6135 (pt0) cc_final: 0.5499 (mm-30) REVERT: A 299 GLN cc_start: 0.6534 (mt0) cc_final: 0.5758 (tm130) REVERT: A 307 THR cc_start: 0.7767 (p) cc_final: 0.7290 (t) REVERT: A 309 LYS cc_start: 0.6778 (mtmt) cc_final: 0.6520 (mtpp) REVERT: A 318 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6989 (tpt170) REVERT: A 369 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6250 (mp0) REVERT: A 453 GLN cc_start: 0.7327 (mt0) cc_final: 0.6881 (mt0) REVERT: A 523 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6682 (mp) REVERT: A 529 GLU cc_start: 0.7393 (mp0) cc_final: 0.7025 (tt0) REVERT: A 588 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.7886 (m-30) REVERT: A 597 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.7082 (t70) REVERT: A 636 LYS cc_start: 0.8129 (tppp) cc_final: 0.7845 (tptp) REVERT: A 675 ARG cc_start: 0.7463 (mmp-170) cc_final: 0.6828 (mtm-85) REVERT: A 730 HIS cc_start: 0.7331 (t70) cc_final: 0.6212 (m-70) REVERT: A 734 GLN cc_start: 0.7431 (mm110) cc_final: 0.6996 (pt0) REVERT: A 740 GLU cc_start: 0.5963 (tm-30) cc_final: 0.5753 (tm-30) REVERT: A 798 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6070 (tp30) REVERT: A 805 GLU cc_start: 0.7167 (mp0) cc_final: 0.6500 (tm-30) REVERT: A 810 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7505 (mt-10) REVERT: A 814 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.6758 (tptt) REVERT: A 904 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: A 937 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.6893 (t70) REVERT: A 976 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.7957 (ptt) REVERT: A 984 ARG cc_start: 0.6726 (mtt-85) cc_final: 0.5919 (mtp180) REVERT: A 1007 ILE cc_start: 0.5998 (OUTLIER) cc_final: 0.5510 (mt) REVERT: A 1026 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6583 (mm-30) REVERT: A 1053 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7479 (mp) REVERT: B 24 LYS cc_start: 0.7338 (mtpp) cc_final: 0.6660 (pttp) REVERT: B 33 LYS cc_start: 0.6713 (pttt) cc_final: 0.6285 (ptpp) REVERT: B 45 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7012 (mm110) REVERT: B 78 GLU cc_start: 0.7939 (tt0) cc_final: 0.7650 (tm-30) REVERT: B 170 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6661 (mm-30) REVERT: B 187 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.6905 (mmt) REVERT: B 204 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7398 (tppt) REVERT: B 219 ASP cc_start: 0.7393 (m-30) cc_final: 0.7119 (m-30) REVERT: B 221 ILE cc_start: 0.8267 (mm) cc_final: 0.7873 (mp) REVERT: B 355 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7449 (tt0) REVERT: B 368 LYS cc_start: 0.6826 (OUTLIER) cc_final: 0.6602 (mmtt) REVERT: B 425 PHE cc_start: 0.7249 (m-80) cc_final: 0.6950 (m-80) REVERT: B 542 LYS cc_start: 0.7027 (mtmp) cc_final: 0.6505 (mmtt) REVERT: B 543 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6528 (tm-30) REVERT: B 628 GLU cc_start: 0.7175 (tt0) cc_final: 0.6874 (tp30) REVERT: B 643 GLU cc_start: 0.6735 (pt0) cc_final: 0.6326 (mp0) REVERT: B 704 ILE cc_start: 0.7404 (pt) cc_final: 0.7089 (mp) REVERT: B 726 LYS cc_start: 0.7235 (ptmm) cc_final: 0.7009 (ptmm) REVERT: B 739 ASN cc_start: 0.7759 (m-40) cc_final: 0.7171 (t0) REVERT: B 760 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: B 814 LYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6293 (tttp) REVERT: B 815 LYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6583 (mptt) REVERT: B 844 LYS cc_start: 0.7822 (mtmt) cc_final: 0.7412 (mtmt) REVERT: B 895 ASP cc_start: 0.8240 (p0) cc_final: 0.8022 (p0) REVERT: B 939 MET cc_start: 0.6373 (ptp) cc_final: 0.5959 (ptp) REVERT: B 1010 GLN cc_start: 0.6031 (tt0) cc_final: 0.5372 (mm110) REVERT: B 1051 GLU cc_start: 0.6361 (mt-10) cc_final: 0.5923 (mp0) outliers start: 54 outliers final: 25 residues processed: 261 average time/residue: 0.6519 time to fit residues: 187.1160 Evaluate side-chains 272 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 225 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 760 GLN Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 815 LYS Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain B residue 956 ARG Chi-restraints excluded: chain B residue 993 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 198 optimal weight: 0.4980 chunk 106 optimal weight: 6.9990 chunk 195 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 HIS A 811 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.186039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.157755 restraints weight = 16740.060| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.44 r_work: 0.3660 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17012 Z= 0.180 Angle : 0.605 9.918 23068 Z= 0.297 Chirality : 0.042 0.208 2467 Planarity : 0.005 0.055 2987 Dihedral : 7.501 83.828 2372 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.12 % Allowed : 24.38 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.19), residues: 2042 helix: 1.03 (0.17), residues: 921 sheet: -1.07 (0.30), residues: 280 loop : -0.35 (0.23), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 423 TYR 0.018 0.002 TYR A 736 PHE 0.020 0.002 PHE B 160 TRP 0.018 0.002 TRP B 371 HIS 0.006 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (17010) covalent geometry : angle 0.60501 / 0.30 (23068) hydrogen bonds : bond 0.04067 / 2.68 ( 769) hydrogen bonds : angle 4.68181 / 3.39 ( 2217) Misc. bond : bond 0.03286 / 1.58 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5223.29 seconds wall clock time: 89 minutes 42.07 seconds (5382.07 seconds total)