Starting phenix.real_space_refine on Thu Feb 5 10:22:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lq2_63291/02_2026/9lq2_63291.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lq2_63291/02_2026/9lq2_63291.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lq2_63291/02_2026/9lq2_63291.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lq2_63291/02_2026/9lq2_63291.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lq2_63291/02_2026/9lq2_63291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lq2_63291/02_2026/9lq2_63291.map" } resolution = 3.58 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= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 106 5.16 5 C 10509 2.51 5 N 2834 2.21 5 O 2952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16401 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 941, 7507 Classifications: {'peptide': 941} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 908} Chain breaks: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5425 Classifications: {'peptide': 686} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 658} Chain breaks: 3 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "D" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 818 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 6, 'TRANS': 89} Chain: "E" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 886 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 96} Chain: "F" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 895 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "G" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 870 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 96} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 3.37, per 1000 atoms: 0.21 Number of scatterers: 16401 At special positions: 0 Unit cell: (115.5, 123.2, 160.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 106 16.00 O 2952 8.00 N 2834 7.00 C 10509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 703.0 milliseconds 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3892 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 13 sheets defined 48.2% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 removed outlier: 4.051A pdb=" N GLU A 7 " --> pdb=" O SER A 3 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 32 Processing helix chain 'A' and resid 35 through 40 removed outlier: 3.613A pdb=" N GLN A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 35 through 40' Processing helix chain 'A' and resid 42 through 49 removed outlier: 3.655A pdb=" N VAL A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 80 through 92 Processing helix chain 'A' and resid 146 through 156 removed outlier: 3.776A pdb=" N ARG A 153 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.753A pdb=" N LEU A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.511A pdb=" N SER A 216 " --> pdb=" O CYS A 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 216' Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 231 through 236 removed outlier: 4.066A pdb=" N ASP A 236 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 243 Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 278 through 288 Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 305 through 313 removed outlier: 4.537A pdb=" N LEU A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 338 Processing helix chain 'A' and resid 339 through 352 Processing helix chain 'A' and resid 353 through 359 removed outlier: 3.535A pdb=" N LEU A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 379 removed outlier: 3.556A pdb=" N CYS A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 388 Processing helix chain 'A' and resid 389 through 400 removed outlier: 3.513A pdb=" N LEU A 393 " --> pdb=" O THR A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 426 Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 443 through 451 removed outlier: 4.341A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 482 Processing helix chain 'A' and resid 487 through 491 removed outlier: 3.502A pdb=" N ASP A 491 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 504 Processing helix chain 'A' and resid 505 through 512 Processing helix chain 'A' and resid 515 through 525 Processing helix chain 'A' and resid 527 through 539 removed outlier: 3.990A pdb=" N ALA A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 553 removed outlier: 3.805A pdb=" N LEU A 551 " --> pdb=" O LYS A 547 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 557 Processing helix chain 'A' and resid 564 through 579 Processing helix chain 'A' and resid 580 through 589 removed outlier: 3.512A pdb=" N ALA A 584 " --> pdb=" O GLU A 580 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 586 " --> pdb=" O GLU A 582 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 612 removed outlier: 3.561A pdb=" N VAL A 604 " --> pdb=" O ASN A 600 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS A 612 " --> pdb=" O SER A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 668 removed outlier: 3.563A pdb=" N SER A 660 " --> pdb=" O GLN A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 674 removed outlier: 4.536A pdb=" N SER A 672 " --> pdb=" O CYS A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 700 Processing helix chain 'A' and resid 717 through 727 removed outlier: 4.552A pdb=" N ARG A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 758 removed outlier: 4.390A pdb=" N LEU A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 786 removed outlier: 3.724A pdb=" N LYS A 786 " --> pdb=" O PHE A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 814 Processing helix chain 'A' and resid 834 through 845 Processing helix chain 'A' and resid 859 through 871 Processing helix chain 'A' and resid 888 through 900 Processing helix chain 'A' and resid 918 through 928 Processing helix chain 'A' and resid 944 through 946 No H-bonds generated for 'chain 'A' and resid 944 through 946' Processing helix chain 'A' and resid 947 through 958 removed outlier: 3.782A pdb=" N LEU A 951 " --> pdb=" O TYR A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 984 Processing helix chain 'A' and resid 1001 through 1015 Processing helix chain 'B' and resid 122 through 135 removed outlier: 3.794A pdb=" N LYS B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL B 133 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP B 134 " --> pdb=" O GLN B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 154 removed outlier: 4.065A pdb=" N VAL B 150 " --> pdb=" O PHE B 146 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN B 154 " --> pdb=" O VAL B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 removed outlier: 3.889A pdb=" N ILE B 158 " --> pdb=" O GLN B 155 " (cutoff:3.500A) Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 184 through 198 removed outlier: 3.528A pdb=" N CYS B 198 " --> pdb=" O ASP B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 216 removed outlier: 3.652A pdb=" N SER B 216 " --> pdb=" O CYS B 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 212 through 216' Processing helix chain 'B' and resid 222 through 228 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 237 through 244 Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 254 through 258 removed outlier: 3.727A pdb=" N LEU B 258 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 267 removed outlier: 3.959A pdb=" N GLN B 267 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 288 Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 307 through 313 removed outlier: 3.706A pdb=" N LEU B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 338 Processing helix chain 'B' and resid 339 through 353 removed outlier: 3.996A pdb=" N ASN B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 359 removed outlier: 3.702A pdb=" N LEU B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 380 Processing helix chain 'B' and resid 385 through 388 Processing helix chain 'B' and resid 389 through 400 removed outlier: 3.745A pdb=" N SER B 400 " --> pdb=" O ARG B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 426 Processing helix chain 'B' and resid 431 through 438 removed outlier: 3.709A pdb=" N LEU B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 451 Processing helix chain 'B' and resid 468 through 482 removed outlier: 3.753A pdb=" N GLN B 472 " --> pdb=" O HIS B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 505 Processing helix chain 'B' and resid 505 through 512 Processing helix chain 'B' and resid 515 through 525 removed outlier: 3.742A pdb=" N GLY B 519 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS B 520 " --> pdb=" O ILE B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 539 Processing helix chain 'B' and resid 545 through 553 removed outlier: 3.730A pdb=" N CYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 558 removed outlier: 3.655A pdb=" N HIS B 558 " --> pdb=" O ALA B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 579 removed outlier: 3.657A pdb=" N ASP B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 588 removed outlier: 3.674A pdb=" N ALA B 584 " --> pdb=" O GLU B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 612 removed outlier: 3.609A pdb=" N VAL B 604 " --> pdb=" O ASN B 600 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS B 612 " --> pdb=" O SER B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 668 Processing helix chain 'B' and resid 668 through 674 removed outlier: 4.497A pdb=" N SER B 672 " --> pdb=" O CYS B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 700 Processing helix chain 'B' and resid 717 through 727 removed outlier: 4.247A pdb=" N ARG B 721 " --> pdb=" O ASP B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 758 Processing helix chain 'B' and resid 774 through 786 Processing helix chain 'B' and resid 802 through 815 Processing helix chain 'D' and resid 63 through 68 Processing helix chain 'E' and resid 63 through 68 Processing helix chain 'F' and resid 63 through 68 Processing helix chain 'G' and resid 63 through 68 Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 211 removed outlier: 6.566A pdb=" N THR A 173 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL A 319 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL A 175 " --> pdb=" O VAL A 319 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 221 through 222 Processing sheet with id=AA3, first strand: chain 'A' and resid 430 through 431 Processing sheet with id=AA4, first strand: chain 'A' and resid 620 through 622 removed outlier: 3.761A pdb=" N LYS A 683 " --> pdb=" O LEU A 622 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL A 714 " --> pdb=" O GLN A 684 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N PHE A 686 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN A 713 " --> pdb=" O ALA A 739 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 742 through 743 removed outlier: 7.184A pdb=" N ILE A 742 " --> pdb=" O CYS A 772 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 909 through 911 removed outlier: 3.593A pdb=" N TRP A 939 " --> pdb=" O LEU A 910 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY A 967 " --> pdb=" O LEU A 938 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU A 993 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 207 through 211 removed outlier: 6.690A pdb=" N THR B 173 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL B 319 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL B 175 " --> pdb=" O VAL B 319 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 593 through 598 removed outlier: 3.681A pdb=" N ILE B 594 " --> pdb=" O LYS B 619 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 621 " --> pdb=" O ILE B 594 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL B 624 " --> pdb=" O LYS B 683 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER B 685 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 710 " --> pdb=" O LEU B 680 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL B 714 " --> pdb=" O GLN B 684 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N PHE B 686 " --> pdb=" O VAL B 714 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B 709 " --> pdb=" O THR B 737 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N ALA B 739 " --> pdb=" O VAL B 709 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE B 711 " --> pdb=" O ALA B 739 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 742 through 743 removed outlier: 7.337A pdb=" N ILE B 742 " --> pdb=" O CYS B 772 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 822 through 824 removed outlier: 6.316A pdb=" N LEU B 823 " --> pdb=" O CYS B 852 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 33 through 43 removed outlier: 6.962A pdb=" N VAL D 25 " --> pdb=" O TRP D 21 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TRP D 92 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU D 111 " --> pdb=" O TRP D 92 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU D 94 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU D 109 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR D 96 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU D 104 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU D 47 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN D 46 " --> pdb=" O LYS D 42 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR D 38 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ARG D 52 " --> pdb=" O PRO D 36 " (cutoff:3.500A) removed outlier: 12.132A pdb=" N LEU D 35 " --> pdb=" O ASP E 43 " (cutoff:3.500A) removed outlier: 9.143A pdb=" N ASP E 43 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU D 37 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LEU E 37 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 10.441A pdb=" N ASP D 43 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 11.810A pdb=" N LEU E 35 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU E 50 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ILE E 39 " --> pdb=" O ARG E 48 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG E 48 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE E 41 " --> pdb=" O GLN E 46 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLN E 46 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU E 47 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG E 53 " --> pdb=" O GLU E 104 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLU E 104 " --> pdb=" O ARG E 53 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL E 103 " --> pdb=" O LYS E 99 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS E 99 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASP E 105 " --> pdb=" O HIS E 97 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N HIS E 97 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU E 107 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE E 91 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG E 83 " --> pdb=" O TYR E 79 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU E 18 " --> pdb=" O TRP E 76 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL E 25 " --> pdb=" O TRP E 21 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 19 through 22 removed outlier: 5.913A pdb=" N ALA F 20 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU F 27 " --> pdb=" O ALA F 20 " (cutoff:3.500A) removed outlier: 12.567A pdb=" N LEU F 35 " --> pdb=" O ASP G 43 " (cutoff:3.500A) removed outlier: 10.059A pdb=" N ASP G 43 " --> pdb=" O LEU F 35 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU F 37 " --> pdb=" O ILE G 41 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LEU G 37 " --> pdb=" O ILE F 41 " (cutoff:3.500A) removed outlier: 10.237A pdb=" N ASP F 43 " --> pdb=" O LEU G 35 " (cutoff:3.500A) removed outlier: 11.248A pdb=" N LEU G 35 " --> pdb=" O ASP F 43 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 33 through 43 current: chain 'F' and resid 103 through 110 removed outlier: 3.864A pdb=" N TYR F 96 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU F 109 " --> pdb=" O LEU F 94 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU F 94 " --> pdb=" O GLU F 109 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 19 through 22 removed outlier: 5.913A pdb=" N ALA F 20 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU F 27 " --> pdb=" O ALA F 20 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 33 through 43 current: chain 'G' and resid 103 through 110 removed outlier: 4.387A pdb=" N TYR G 96 " --> pdb=" O LEU G 107 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU G 109 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU G 94 " --> pdb=" O GLU G 109 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL G 25 " --> pdb=" O TRP G 21 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 33 through 43 current: chain 'F' and resid 103 through 110 removed outlier: 3.864A pdb=" N TYR F 96 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU F 109 " --> pdb=" O LEU F 94 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU F 94 " --> pdb=" O GLU F 109 " (cutoff:3.500A) 708 hydrogen bonds defined for protein. 2049 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5346 1.34 - 1.46: 3327 1.46 - 1.58: 7933 1.58 - 1.69: 0 1.69 - 1.81: 152 Bond restraints: 16758 Sorted by residual: bond pdb=" N ARG B 164 " pdb=" CA ARG B 164 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.30e-02 5.92e+03 5.65e+00 bond pdb=" C ASP F 13 " pdb=" N HIS F 14 " ideal model delta sigma weight residual 1.329 1.350 -0.021 1.35e-02 5.49e+03 2.53e+00 bond pdb=" C SER B 361 " pdb=" N ALA B 362 " ideal model delta sigma weight residual 1.335 1.299 0.036 3.59e-02 7.76e+02 1.01e+00 bond pdb=" CA CYS B 198 " pdb=" C CYS B 198 " ideal model delta sigma weight residual 1.532 1.523 0.010 9.60e-03 1.09e+04 1.01e+00 bond pdb=" CB GLU A 327 " pdb=" CG GLU A 327 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.84e-01 ... (remaining 16753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 21371 1.03 - 2.05: 1035 2.05 - 3.08: 184 3.08 - 4.10: 91 4.10 - 5.13: 7 Bond angle restraints: 22688 Sorted by residual: angle pdb=" N ASP F 81 " pdb=" CA ASP F 81 " pdb=" CB ASP F 81 " ideal model delta sigma weight residual 114.17 110.26 3.91 1.14e+00 7.69e-01 1.18e+01 angle pdb=" C ILE B 238 " pdb=" CA ILE B 238 " pdb=" CB ILE B 238 " ideal model delta sigma weight residual 114.35 111.17 3.18 1.06e+00 8.90e-01 8.99e+00 angle pdb=" N ASN A 145 " pdb=" CA ASN A 145 " pdb=" CB ASN A 145 " ideal model delta sigma weight residual 114.17 110.88 3.29 1.14e+00 7.69e-01 8.32e+00 angle pdb=" N THR B 165 " pdb=" CA THR B 165 " pdb=" C THR B 165 " ideal model delta sigma weight residual 109.64 113.25 -3.61 1.27e+00 6.20e-01 8.09e+00 angle pdb=" C ASP B 237 " pdb=" N ILE B 238 " pdb=" CA ILE B 238 " ideal model delta sigma weight residual 120.24 121.94 -1.70 6.30e-01 2.52e+00 7.24e+00 ... (remaining 22683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 8912 17.84 - 35.67: 981 35.67 - 53.51: 207 53.51 - 71.35: 34 71.35 - 89.18: 16 Dihedral angle restraints: 10150 sinusoidal: 4189 harmonic: 5961 Sorted by residual: dihedral pdb=" CB GLU F 109 " pdb=" CG GLU F 109 " pdb=" CD GLU F 109 " pdb=" OE1 GLU F 109 " ideal model delta sinusoidal sigma weight residual 0.00 89.18 -89.18 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CG ARG B 351 " pdb=" CD ARG B 351 " pdb=" NE ARG B 351 " pdb=" CZ ARG B 351 " ideal model delta sinusoidal sigma weight residual 180.00 135.56 44.44 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CA ASP A 339 " pdb=" CB ASP A 339 " pdb=" CG ASP A 339 " pdb=" OD1 ASP A 339 " ideal model delta sinusoidal sigma weight residual -30.00 -84.83 54.83 1 2.00e+01 2.50e-03 1.02e+01 ... (remaining 10147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1890 0.036 - 0.072: 506 0.072 - 0.108: 114 0.108 - 0.144: 47 0.144 - 0.181: 1 Chirality restraints: 2558 Sorted by residual: chirality pdb=" CA ILE A 158 " pdb=" N ILE A 158 " pdb=" C ILE A 158 " pdb=" CB ILE A 158 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CA ILE A 711 " pdb=" N ILE A 711 " pdb=" C ILE A 711 " pdb=" CB ILE A 711 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE B 711 " pdb=" N ILE B 711 " pdb=" C ILE B 711 " pdb=" CB ILE B 711 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 2555 not shown) Planarity restraints: 2872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 164 " 0.390 9.50e-02 1.11e+02 1.75e-01 1.87e+01 pdb=" NE ARG B 164 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG B 164 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 164 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 164 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 35 " 0.053 5.00e-02 4.00e+02 8.04e-02 1.03e+01 pdb=" N PRO D 36 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO D 36 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 36 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 803 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.94e+00 pdb=" C ASP A 803 " 0.038 2.00e-02 2.50e+03 pdb=" O ASP A 803 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU A 804 " -0.013 2.00e-02 2.50e+03 ... (remaining 2869 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 103 2.56 - 3.14: 12919 3.14 - 3.73: 23271 3.73 - 4.31: 30866 4.31 - 4.90: 53101 Nonbonded interactions: 120260 Sorted by model distance: nonbonded pdb=" OD1 ASP B 253 " pdb=" OG1 THR B 300 " model vdw 1.974 3.040 nonbonded pdb=" O ASP E 88 " pdb=" OG SER E 89 " model vdw 2.064 3.040 nonbonded pdb=" O LYS G 30 " pdb=" NZ LYS G 30 " model vdw 2.112 3.120 nonbonded pdb=" N GLU G 9 " pdb=" OE1 GLU G 9 " model vdw 2.131 3.120 nonbonded pdb=" O ASP F 81 " pdb=" OD1 ASP F 81 " model vdw 2.150 3.040 ... (remaining 120255 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 'D' and (resid 16 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 or (resid 81 and (name N or name CA or nam \ e C or name O or name CB )) or resid 82 or (resid 83 and (name N or name CA or n \ ame C or name O or name CB )) or resid 84 through 111)) selection = (chain 'E' and (resid 16 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 or (resid 81 and (name N or name CA or nam \ e C or name O or name CB )) or resid 82 or (resid 83 and (name N or name CA or n \ ame C or name O or name CB )) or resid 84 through 111)) selection = (chain 'F' and (resid 16 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 or (resid 81 and (name N or name CA or nam \ e C or name O or name CB )) or resid 82 or (resid 83 and (name N or name CA or n \ ame C or name O or name CB )) or resid 84 through 111)) selection = (chain 'G' and resid 16 through 111) } 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 group one per residue 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: 1.170 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 14.830 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 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 0.043 16758 Z= 0.168 Angle : 0.552 5.125 22688 Z= 0.302 Chirality : 0.037 0.181 2558 Planarity : 0.005 0.175 2872 Dihedral : 15.432 89.183 6258 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 15.06 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.76 (0.19), residues: 2013 helix: 1.86 (0.19), residues: 822 sheet: -0.77 (0.25), residues: 403 loop : -0.12 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 917 TYR 0.013 0.001 TYR B 765 PHE 0.013 0.001 PHE B 223 TRP 0.012 0.001 TRP D 76 HIS 0.008 0.001 HIS G 97 Details of bonding type rmsd covalent geometry : bond 0.00375 (16758) covalent geometry : angle 0.55182 (22688) hydrogen bonds : bond 0.19450 ( 695) hydrogen bonds : angle 6.85721 ( 2049) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.1185 time to fit residues: 43.5844 Evaluate side-chains 166 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 0.0370 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.0270 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 overall best weight: 2.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN A 472 GLN A 656 GLN ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN F 97 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.095000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.066783 restraints weight = 58638.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.069053 restraints weight = 31583.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.070499 restraints weight = 22262.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.071363 restraints weight = 18113.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.071925 restraints weight = 16054.931| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16758 Z= 0.174 Angle : 0.646 10.650 22688 Z= 0.329 Chirality : 0.042 0.181 2558 Planarity : 0.004 0.057 2872 Dihedral : 4.061 18.103 2193 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.33 % Allowed : 16.12 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 1.00 (0.19), residues: 2013 helix: 2.00 (0.18), residues: 840 sheet: -0.63 (0.25), residues: 395 loop : -0.01 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 93 TYR 0.024 0.002 TYR G 84 PHE 0.019 0.001 PHE A 223 TRP 0.019 0.001 TRP A 195 HIS 0.008 0.001 HIS G 97 Details of bonding type rmsd covalent geometry : bond 0.00395 (16758) covalent geometry : angle 0.64644 (22688) hydrogen bonds : bond 0.05037 ( 695) hydrogen bonds : angle 5.30468 ( 2049) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.6884 (mtt) cc_final: 0.5964 (tmm) REVERT: A 327 GLU cc_start: 0.9306 (mp0) cc_final: 0.9033 (pm20) REVERT: A 807 MET cc_start: 0.8708 (mpp) cc_final: 0.8415 (mpp) REVERT: A 989 SER cc_start: 0.8682 (OUTLIER) cc_final: 0.8116 (p) REVERT: B 137 THR cc_start: 0.4248 (OUTLIER) cc_final: 0.4001 (m) REVERT: B 251 VAL cc_start: 0.7981 (t) cc_final: 0.7724 (m) REVERT: B 482 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8757 (mm) REVERT: B 542 MET cc_start: 0.8539 (mmm) cc_final: 0.8118 (mmp) REVERT: D 16 ASP cc_start: 0.6529 (t0) cc_final: 0.6152 (t0) REVERT: D 32 HIS cc_start: 0.6828 (m-70) cc_final: 0.6472 (m-70) REVERT: D 91 PHE cc_start: 0.8571 (m-10) cc_final: 0.8330 (m-10) REVERT: E 47 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6703 (tt) REVERT: E 84 TYR cc_start: 0.7820 (m-80) cc_final: 0.7595 (m-80) REVERT: G 54 GLU cc_start: 0.8307 (mm-30) cc_final: 0.6644 (tm-30) REVERT: G 60 ARG cc_start: 0.8422 (ttp80) cc_final: 0.8155 (ttp80) outliers start: 42 outliers final: 15 residues processed: 221 average time/residue: 0.1212 time to fit residues: 39.7816 Evaluate side-chains 185 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain G residue 63 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 184 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 chunk 128 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN D 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.096403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.067894 restraints weight = 60244.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.070232 restraints weight = 32059.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.071699 restraints weight = 22515.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.072559 restraints weight = 18361.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.073142 restraints weight = 16297.718| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16758 Z= 0.154 Angle : 0.607 10.235 22688 Z= 0.306 Chirality : 0.040 0.219 2558 Planarity : 0.004 0.041 2872 Dihedral : 4.075 20.553 2193 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.22 % Allowed : 17.18 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 1.04 (0.19), residues: 2013 helix: 2.04 (0.18), residues: 847 sheet: -0.55 (0.25), residues: 405 loop : -0.05 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 164 TYR 0.019 0.002 TYR D 79 PHE 0.021 0.001 PHE A 223 TRP 0.015 0.001 TRP D 76 HIS 0.004 0.001 HIS G 97 Details of bonding type rmsd covalent geometry : bond 0.00351 (16758) covalent geometry : angle 0.60727 (22688) hydrogen bonds : bond 0.04471 ( 695) hydrogen bonds : angle 4.98140 ( 2049) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8392 (tptp) cc_final: 0.8145 (tptp) REVERT: A 77 GLU cc_start: 0.8507 (mp0) cc_final: 0.8107 (mm-30) REVERT: A 92 MET cc_start: 0.8279 (tmm) cc_final: 0.7846 (tmm) REVERT: A 192 MET cc_start: 0.6908 (mtt) cc_final: 0.6007 (tmm) REVERT: A 327 GLU cc_start: 0.9249 (mp0) cc_final: 0.8994 (pm20) REVERT: A 909 ASP cc_start: 0.7239 (OUTLIER) cc_final: 0.6991 (p0) REVERT: A 915 ILE cc_start: 0.8865 (pt) cc_final: 0.8584 (pt) REVERT: A 956 LEU cc_start: 0.9068 (tt) cc_final: 0.8724 (pp) REVERT: A 989 SER cc_start: 0.8704 (OUTLIER) cc_final: 0.8070 (p) REVERT: B 482 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8646 (mm) REVERT: B 751 MET cc_start: 0.8732 (mmm) cc_final: 0.8334 (mmm) REVERT: D 76 TRP cc_start: 0.8225 (OUTLIER) cc_final: 0.8024 (m100) REVERT: D 91 PHE cc_start: 0.8544 (m-10) cc_final: 0.8314 (m-10) REVERT: E 21 TRP cc_start: 0.8000 (t-100) cc_final: 0.7408 (t-100) REVERT: E 46 GLN cc_start: 0.7205 (mt0) cc_final: 0.6978 (mp10) REVERT: E 47 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6722 (tt) REVERT: F 62 MET cc_start: 0.8182 (mtm) cc_final: 0.7710 (ptp) REVERT: G 14 HIS cc_start: 0.7896 (OUTLIER) cc_final: 0.7408 (p-80) REVERT: G 22 GLU cc_start: 0.6387 (mp0) cc_final: 0.5971 (mp0) REVERT: G 106 MET cc_start: 0.5937 (tpp) cc_final: 0.5732 (tpp) outliers start: 40 outliers final: 21 residues processed: 210 average time/residue: 0.1255 time to fit residues: 40.2349 Evaluate side-chains 193 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 76 TRP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 90 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 99 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 161 optimal weight: 8.9990 chunk 39 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 164 optimal weight: 4.9990 chunk 117 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.097643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.069390 restraints weight = 59954.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.071811 restraints weight = 31351.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.073345 restraints weight = 21794.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.074265 restraints weight = 17628.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.074657 restraints weight = 15617.954| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16758 Z= 0.107 Angle : 0.560 8.609 22688 Z= 0.283 Chirality : 0.039 0.199 2558 Planarity : 0.004 0.043 2872 Dihedral : 3.942 24.409 2193 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.17 % Allowed : 17.23 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 1.21 (0.20), residues: 2013 helix: 2.21 (0.18), residues: 844 sheet: -0.46 (0.25), residues: 422 loop : 0.04 (0.24), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 17 TYR 0.021 0.001 TYR D 79 PHE 0.024 0.001 PHE A 223 TRP 0.014 0.001 TRP D 19 HIS 0.003 0.001 HIS G 97 Details of bonding type rmsd covalent geometry : bond 0.00225 (16758) covalent geometry : angle 0.55985 (22688) hydrogen bonds : bond 0.03582 ( 695) hydrogen bonds : angle 4.59870 ( 2049) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8437 (tptp) cc_final: 0.8178 (tptp) REVERT: A 69 ASN cc_start: 0.7435 (m-40) cc_final: 0.7075 (t0) REVERT: A 77 GLU cc_start: 0.8483 (mp0) cc_final: 0.8093 (mm-30) REVERT: A 192 MET cc_start: 0.6852 (mtt) cc_final: 0.6000 (tmm) REVERT: A 327 GLU cc_start: 0.9279 (mp0) cc_final: 0.9013 (pm20) REVERT: A 807 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8558 (mmt) REVERT: A 822 MET cc_start: 0.8761 (mpp) cc_final: 0.8354 (mpp) REVERT: A 956 LEU cc_start: 0.9115 (tt) cc_final: 0.8627 (pp) REVERT: B 751 MET cc_start: 0.8899 (mmm) cc_final: 0.8480 (mmm) REVERT: D 19 TRP cc_start: 0.8513 (OUTLIER) cc_final: 0.8208 (m-90) REVERT: D 44 ARG cc_start: 0.8114 (mmp80) cc_final: 0.7756 (mmp80) REVERT: D 91 PHE cc_start: 0.8512 (m-10) cc_final: 0.8168 (m-10) REVERT: E 21 TRP cc_start: 0.8224 (t-100) cc_final: 0.7365 (t-100) REVERT: E 22 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8242 (mm-30) REVERT: E 23 LYS cc_start: 0.9080 (mmtp) cc_final: 0.8795 (mmmt) REVERT: E 46 GLN cc_start: 0.7217 (mt0) cc_final: 0.6914 (mp10) REVERT: E 47 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6769 (tt) REVERT: E 84 TYR cc_start: 0.7869 (m-80) cc_final: 0.7612 (m-80) REVERT: G 14 HIS cc_start: 0.7899 (OUTLIER) cc_final: 0.7421 (p-80) REVERT: G 54 GLU cc_start: 0.8234 (mm-30) cc_final: 0.6489 (tm-30) REVERT: G 62 MET cc_start: 0.8658 (mtp) cc_final: 0.7947 (mtp) outliers start: 39 outliers final: 18 residues processed: 208 average time/residue: 0.1310 time to fit residues: 41.1565 Evaluate side-chains 189 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain D residue 19 TRP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 49 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 118 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 197 optimal weight: 0.6980 chunk 154 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN G 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.100615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.071555 restraints weight = 58103.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.074005 restraints weight = 31176.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.075548 restraints weight = 21993.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.076431 restraints weight = 17910.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.077037 restraints weight = 15918.421| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16758 Z= 0.114 Angle : 0.571 11.344 22688 Z= 0.283 Chirality : 0.039 0.181 2558 Planarity : 0.004 0.042 2872 Dihedral : 3.906 27.170 2193 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.45 % Allowed : 17.34 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 1.21 (0.20), residues: 2013 helix: 2.22 (0.18), residues: 853 sheet: -0.45 (0.25), residues: 421 loop : -0.02 (0.24), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 44 TYR 0.022 0.001 TYR D 79 PHE 0.023 0.001 PHE A 223 TRP 0.022 0.001 TRP D 76 HIS 0.003 0.001 HIS G 97 Details of bonding type rmsd covalent geometry : bond 0.00259 (16758) covalent geometry : angle 0.57124 (22688) hydrogen bonds : bond 0.03485 ( 695) hydrogen bonds : angle 4.48987 ( 2049) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8986 (mm) REVERT: A 53 LYS cc_start: 0.8533 (tptp) cc_final: 0.8196 (tptp) REVERT: A 69 ASN cc_start: 0.7472 (m-40) cc_final: 0.7043 (t0) REVERT: A 77 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8097 (mm-30) REVERT: A 192 MET cc_start: 0.6815 (mtt) cc_final: 0.5999 (tmm) REVERT: A 327 GLU cc_start: 0.9278 (mp0) cc_final: 0.9019 (pm20) REVERT: A 807 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8554 (mmt) REVERT: A 822 MET cc_start: 0.8666 (mpp) cc_final: 0.8140 (mpp) REVERT: A 956 LEU cc_start: 0.9092 (tt) cc_final: 0.8861 (pp) REVERT: A 989 SER cc_start: 0.8703 (OUTLIER) cc_final: 0.8018 (p) REVERT: B 452 ASP cc_start: 0.7927 (t0) cc_final: 0.7705 (t0) REVERT: B 751 MET cc_start: 0.8913 (mmm) cc_final: 0.8476 (mmm) REVERT: B 851 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7469 (tt) REVERT: D 19 TRP cc_start: 0.8516 (OUTLIER) cc_final: 0.8236 (m-90) REVERT: D 44 ARG cc_start: 0.8067 (mmp80) cc_final: 0.7808 (mmp80) REVERT: E 21 TRP cc_start: 0.8239 (t-100) cc_final: 0.7499 (t-100) REVERT: E 23 LYS cc_start: 0.9088 (mmtp) cc_final: 0.8764 (mmmt) REVERT: E 46 GLN cc_start: 0.7131 (mt0) cc_final: 0.6796 (mp10) REVERT: E 47 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.7023 (tt) REVERT: E 84 TYR cc_start: 0.7881 (m-80) cc_final: 0.7616 (m-80) REVERT: G 14 HIS cc_start: 0.7863 (OUTLIER) cc_final: 0.7413 (p-80) REVERT: G 62 MET cc_start: 0.8760 (mtp) cc_final: 0.8220 (mtp) outliers start: 44 outliers final: 23 residues processed: 206 average time/residue: 0.1265 time to fit residues: 39.6613 Evaluate side-chains 197 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain D residue 19 TRP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 32 HIS Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 49 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 132 optimal weight: 0.0370 chunk 103 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 197 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 overall best weight: 1.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 HIS D 31 GLN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.096804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.068472 restraints weight = 59309.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.070804 restraints weight = 31182.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.072292 restraints weight = 21800.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.073208 restraints weight = 17729.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.073764 restraints weight = 15683.661| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16758 Z= 0.128 Angle : 0.576 13.391 22688 Z= 0.285 Chirality : 0.039 0.170 2558 Planarity : 0.004 0.041 2872 Dihedral : 3.908 24.760 2193 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.72 % Allowed : 17.62 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 1.24 (0.20), residues: 2013 helix: 2.28 (0.18), residues: 853 sheet: -0.36 (0.25), residues: 412 loop : -0.10 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 60 TYR 0.019 0.001 TYR D 79 PHE 0.026 0.001 PHE A 223 TRP 0.011 0.001 TRP D 76 HIS 0.017 0.001 HIS G 32 Details of bonding type rmsd covalent geometry : bond 0.00290 (16758) covalent geometry : angle 0.57577 (22688) hydrogen bonds : bond 0.03554 ( 695) hydrogen bonds : angle 4.43285 ( 2049) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 171 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8914 (mm) REVERT: A 53 LYS cc_start: 0.8478 (tptp) cc_final: 0.8254 (tptp) REVERT: A 77 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8122 (mm-30) REVERT: A 192 MET cc_start: 0.6959 (mtt) cc_final: 0.6150 (tmm) REVERT: A 327 GLU cc_start: 0.9283 (mp0) cc_final: 0.9016 (pm20) REVERT: A 350 MET cc_start: 0.8229 (ttt) cc_final: 0.7703 (tmm) REVERT: A 807 MET cc_start: 0.8840 (mpp) cc_final: 0.8575 (mmt) REVERT: A 822 MET cc_start: 0.8712 (mpp) cc_final: 0.8104 (mpp) REVERT: A 956 LEU cc_start: 0.9156 (tt) cc_final: 0.8764 (pp) REVERT: A 989 SER cc_start: 0.8676 (OUTLIER) cc_final: 0.8020 (p) REVERT: B 452 ASP cc_start: 0.7993 (t0) cc_final: 0.7772 (t0) REVERT: B 751 MET cc_start: 0.8947 (mmm) cc_final: 0.8502 (mmm) REVERT: D 19 TRP cc_start: 0.8537 (OUTLIER) cc_final: 0.8185 (m-90) REVERT: D 44 ARG cc_start: 0.8159 (mmp80) cc_final: 0.7868 (mmp80) REVERT: E 21 TRP cc_start: 0.8207 (t-100) cc_final: 0.7151 (t-100) REVERT: E 22 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7839 (mm-30) REVERT: E 23 LYS cc_start: 0.9047 (mmtp) cc_final: 0.8740 (mmmt) REVERT: E 46 GLN cc_start: 0.7164 (mt0) cc_final: 0.6820 (mp10) REVERT: E 47 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.7020 (tt) REVERT: E 56 VAL cc_start: 0.8260 (t) cc_final: 0.8042 (t) REVERT: E 84 TYR cc_start: 0.7911 (m-80) cc_final: 0.7627 (m-80) REVERT: E 106 MET cc_start: 0.8508 (mmm) cc_final: 0.8305 (mmm) REVERT: G 14 HIS cc_start: 0.7883 (OUTLIER) cc_final: 0.7438 (p-80) REVERT: G 62 MET cc_start: 0.8777 (mtp) cc_final: 0.8082 (mtp) outliers start: 49 outliers final: 32 residues processed: 204 average time/residue: 0.1299 time to fit residues: 40.0948 Evaluate side-chains 201 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 480 TYR Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain D residue 19 TRP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 90 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 69 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 195 optimal weight: 30.0000 chunk 187 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 HIS B 407 GLN B 613 HIS ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.096569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.067371 restraints weight = 61203.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.069588 restraints weight = 33841.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.070993 restraints weight = 24447.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.071846 restraints weight = 20289.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.072303 restraints weight = 18215.403| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 16758 Z= 0.278 Angle : 0.727 12.433 22688 Z= 0.360 Chirality : 0.043 0.162 2558 Planarity : 0.005 0.061 2872 Dihedral : 4.396 27.609 2193 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.06 % Allowed : 18.18 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.86 (0.19), residues: 2013 helix: 2.02 (0.18), residues: 846 sheet: -0.53 (0.26), residues: 404 loop : -0.37 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 93 TYR 0.018 0.002 TYR F 79 PHE 0.019 0.002 PHE F 24 TRP 0.013 0.002 TRP F 19 HIS 0.011 0.002 HIS A 468 Details of bonding type rmsd covalent geometry : bond 0.00639 (16758) covalent geometry : angle 0.72712 (22688) hydrogen bonds : bond 0.05042 ( 695) hydrogen bonds : angle 4.97471 ( 2049) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 166 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8894 (mm) REVERT: A 77 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8177 (mm-30) REVERT: A 192 MET cc_start: 0.7058 (mtt) cc_final: 0.6190 (tmm) REVERT: A 327 GLU cc_start: 0.9342 (mp0) cc_final: 0.9091 (pm20) REVERT: A 350 MET cc_start: 0.8373 (ttt) cc_final: 0.7653 (tmm) REVERT: A 807 MET cc_start: 0.8854 (mpp) cc_final: 0.8299 (mpp) REVERT: A 822 MET cc_start: 0.8817 (mpp) cc_final: 0.8171 (mpp) REVERT: A 956 LEU cc_start: 0.9297 (tt) cc_final: 0.9074 (pp) REVERT: A 989 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8264 (p) REVERT: B 751 MET cc_start: 0.8938 (mmm) cc_final: 0.8539 (mmm) REVERT: B 851 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7767 (tt) REVERT: D 19 TRP cc_start: 0.8539 (OUTLIER) cc_final: 0.8160 (m-90) REVERT: D 44 ARG cc_start: 0.8179 (mmp80) cc_final: 0.7956 (mmp80) REVERT: E 23 LYS cc_start: 0.9076 (mmtp) cc_final: 0.8751 (mmmt) REVERT: E 46 GLN cc_start: 0.7228 (mt0) cc_final: 0.6909 (mp10) REVERT: E 47 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7028 (tt) REVERT: E 56 VAL cc_start: 0.8253 (t) cc_final: 0.8047 (t) REVERT: E 84 TYR cc_start: 0.8014 (m-80) cc_final: 0.7778 (m-80) REVERT: F 113 ASP cc_start: 0.8647 (t0) cc_final: 0.8284 (t0) REVERT: G 14 HIS cc_start: 0.7913 (OUTLIER) cc_final: 0.7468 (p-80) REVERT: G 62 MET cc_start: 0.8767 (mtp) cc_final: 0.8036 (mtp) outliers start: 55 outliers final: 37 residues processed: 204 average time/residue: 0.1249 time to fit residues: 38.7716 Evaluate side-chains 201 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain D residue 19 TRP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 32 HIS Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 74 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 133 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 196 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN G 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.097220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.068750 restraints weight = 60246.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.071699 restraints weight = 34290.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.072026 restraints weight = 20836.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.072377 restraints weight = 20022.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.072436 restraints weight = 18022.098| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16758 Z= 0.149 Angle : 0.621 10.424 22688 Z= 0.308 Chirality : 0.040 0.169 2558 Planarity : 0.004 0.044 2872 Dihedral : 4.231 27.533 2193 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.50 % Allowed : 19.46 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 1.11 (0.20), residues: 2013 helix: 2.29 (0.18), residues: 841 sheet: -0.53 (0.26), residues: 410 loop : -0.22 (0.24), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 44 TYR 0.014 0.001 TYR D 79 PHE 0.020 0.001 PHE A 223 TRP 0.011 0.001 TRP G 76 HIS 0.005 0.001 HIS G 32 Details of bonding type rmsd covalent geometry : bond 0.00340 (16758) covalent geometry : angle 0.62108 (22688) hydrogen bonds : bond 0.03973 ( 695) hydrogen bonds : angle 4.60342 ( 2049) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8204 (mm-30) REVERT: A 192 MET cc_start: 0.7186 (mtt) cc_final: 0.6328 (tmm) REVERT: A 327 GLU cc_start: 0.9391 (mp0) cc_final: 0.9103 (pm20) REVERT: A 350 MET cc_start: 0.8253 (ttt) cc_final: 0.7620 (tmm) REVERT: A 807 MET cc_start: 0.8830 (mpp) cc_final: 0.8203 (mpp) REVERT: A 822 MET cc_start: 0.8814 (mpp) cc_final: 0.8394 (mpp) REVERT: A 956 LEU cc_start: 0.9232 (tt) cc_final: 0.8863 (pp) REVERT: A 989 SER cc_start: 0.8786 (OUTLIER) cc_final: 0.8117 (p) REVERT: B 751 MET cc_start: 0.8953 (mmm) cc_final: 0.8536 (mmm) REVERT: D 19 TRP cc_start: 0.8572 (OUTLIER) cc_final: 0.8244 (m-90) REVERT: D 44 ARG cc_start: 0.8103 (mmp80) cc_final: 0.7838 (mmp80) REVERT: E 21 TRP cc_start: 0.8161 (t-100) cc_final: 0.7045 (t-100) REVERT: E 22 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8122 (mm-30) REVERT: E 23 LYS cc_start: 0.9089 (mmtp) cc_final: 0.8769 (mmmt) REVERT: E 46 GLN cc_start: 0.7215 (mt0) cc_final: 0.6888 (mp10) REVERT: E 47 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6974 (tp) REVERT: E 84 TYR cc_start: 0.7930 (m-80) cc_final: 0.7714 (m-80) REVERT: F 54 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7702 (tm-30) REVERT: G 14 HIS cc_start: 0.7957 (OUTLIER) cc_final: 0.7482 (p-80) REVERT: G 62 MET cc_start: 0.8621 (mtp) cc_final: 0.7968 (mtp) outliers start: 45 outliers final: 33 residues processed: 188 average time/residue: 0.1359 time to fit residues: 38.8545 Evaluate side-chains 198 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 480 TYR Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain D residue 19 TRP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 32 HIS Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 74 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 7 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 156 optimal weight: 0.3980 chunk 152 optimal weight: 0.0570 chunk 184 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 overall best weight: 2.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.093432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.065710 restraints weight = 59211.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.067985 restraints weight = 31193.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.069407 restraints weight = 21895.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.070250 restraints weight = 17873.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.070675 restraints weight = 15916.988| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16758 Z= 0.163 Angle : 0.640 13.614 22688 Z= 0.313 Chirality : 0.040 0.171 2558 Planarity : 0.004 0.043 2872 Dihedral : 4.199 26.373 2193 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.22 % Allowed : 19.68 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 1.12 (0.20), residues: 2013 helix: 2.31 (0.18), residues: 840 sheet: -0.53 (0.26), residues: 405 loop : -0.23 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 93 TYR 0.015 0.001 TYR D 79 PHE 0.052 0.001 PHE G 24 TRP 0.011 0.001 TRP E 76 HIS 0.012 0.001 HIS G 32 Details of bonding type rmsd covalent geometry : bond 0.00374 (16758) covalent geometry : angle 0.63980 (22688) hydrogen bonds : bond 0.03932 ( 695) hydrogen bonds : angle 4.58045 ( 2049) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8807 (mm) REVERT: A 77 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8219 (mm-30) REVERT: A 192 MET cc_start: 0.7211 (mtt) cc_final: 0.6367 (tmm) REVERT: A 327 GLU cc_start: 0.9327 (mp0) cc_final: 0.9057 (pm20) REVERT: A 350 MET cc_start: 0.8293 (ttt) cc_final: 0.7652 (tmm) REVERT: A 807 MET cc_start: 0.8819 (mpp) cc_final: 0.8194 (mpp) REVERT: A 822 MET cc_start: 0.8817 (mpp) cc_final: 0.8392 (mpp) REVERT: A 956 LEU cc_start: 0.9233 (tt) cc_final: 0.9006 (pp) REVERT: A 989 SER cc_start: 0.8802 (OUTLIER) cc_final: 0.8153 (p) REVERT: B 751 MET cc_start: 0.8988 (mmm) cc_final: 0.8568 (mmm) REVERT: D 19 TRP cc_start: 0.8586 (OUTLIER) cc_final: 0.8281 (m-90) REVERT: D 32 HIS cc_start: 0.7379 (m-70) cc_final: 0.7169 (m170) REVERT: E 21 TRP cc_start: 0.8195 (t-100) cc_final: 0.7030 (t-100) REVERT: E 22 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8125 (mm-30) REVERT: E 23 LYS cc_start: 0.9079 (mmtp) cc_final: 0.8764 (mmmt) REVERT: E 46 GLN cc_start: 0.7173 (mt0) cc_final: 0.6828 (mp10) REVERT: E 47 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.7019 (tp) REVERT: E 84 TYR cc_start: 0.7953 (m-80) cc_final: 0.7720 (m-80) REVERT: F 54 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7675 (tm-30) REVERT: F 113 ASP cc_start: 0.8629 (t0) cc_final: 0.8276 (t0) REVERT: G 14 HIS cc_start: 0.7931 (OUTLIER) cc_final: 0.7461 (p-80) REVERT: G 62 MET cc_start: 0.8623 (mtp) cc_final: 0.7917 (mtp) outliers start: 40 outliers final: 34 residues processed: 188 average time/residue: 0.1349 time to fit residues: 38.2887 Evaluate side-chains 200 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 480 TYR Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain D residue 19 TRP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 74 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 182 optimal weight: 0.0670 chunk 163 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 151 optimal weight: 0.4980 chunk 138 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 162 optimal weight: 7.9990 chunk 104 optimal weight: 0.0980 chunk 24 optimal weight: 0.0670 chunk 181 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 HIS ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.100213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.071303 restraints weight = 58052.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.073760 restraints weight = 30999.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.075312 restraints weight = 21756.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.076270 restraints weight = 17647.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.076836 restraints weight = 15643.268| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16758 Z= 0.102 Angle : 0.608 11.322 22688 Z= 0.296 Chirality : 0.039 0.176 2558 Planarity : 0.004 0.042 2872 Dihedral : 3.942 26.138 2193 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.33 % Allowed : 20.96 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 1.29 (0.20), residues: 2013 helix: 2.42 (0.18), residues: 844 sheet: -0.36 (0.26), residues: 395 loop : -0.17 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 44 TYR 0.017 0.001 TYR D 79 PHE 0.041 0.001 PHE G 24 TRP 0.016 0.001 TRP A 972 HIS 0.005 0.001 HIS G 97 Details of bonding type rmsd covalent geometry : bond 0.00217 (16758) covalent geometry : angle 0.60826 (22688) hydrogen bonds : bond 0.02944 ( 695) hydrogen bonds : angle 4.20908 ( 2049) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASN cc_start: 0.7430 (m-40) cc_final: 0.7108 (t0) REVERT: A 77 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8132 (mm-30) REVERT: A 192 MET cc_start: 0.7072 (mtt) cc_final: 0.6259 (tmm) REVERT: A 327 GLU cc_start: 0.9324 (mp0) cc_final: 0.9025 (pm20) REVERT: A 358 GLN cc_start: 0.9176 (tp40) cc_final: 0.8705 (tm-30) REVERT: A 685 SER cc_start: 0.9375 (OUTLIER) cc_final: 0.9102 (t) REVERT: A 807 MET cc_start: 0.8855 (mpp) cc_final: 0.8487 (mmt) REVERT: A 822 MET cc_start: 0.8796 (mpp) cc_final: 0.8313 (mpp) REVERT: A 956 LEU cc_start: 0.9165 (tt) cc_final: 0.8761 (pp) REVERT: B 751 MET cc_start: 0.8986 (mmm) cc_final: 0.8549 (mmm) REVERT: D 17 ARG cc_start: 0.7602 (mtm-85) cc_final: 0.7348 (mtm-85) REVERT: D 19 TRP cc_start: 0.8646 (OUTLIER) cc_final: 0.8330 (m-90) REVERT: D 44 ARG cc_start: 0.8135 (mmp80) cc_final: 0.7632 (mmp80) REVERT: E 21 TRP cc_start: 0.8140 (t-100) cc_final: 0.6986 (t-100) REVERT: E 22 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8120 (mm-30) REVERT: E 23 LYS cc_start: 0.9062 (mmtp) cc_final: 0.8703 (mmmt) REVERT: E 84 TYR cc_start: 0.7914 (m-80) cc_final: 0.7705 (m-80) REVERT: E 106 MET cc_start: 0.8329 (mmm) cc_final: 0.7752 (mmm) REVERT: F 54 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7696 (tm-30) REVERT: G 14 HIS cc_start: 0.7852 (OUTLIER) cc_final: 0.7376 (p-80) REVERT: G 62 MET cc_start: 0.8550 (mtp) cc_final: 0.7936 (mtp) outliers start: 24 outliers final: 18 residues processed: 191 average time/residue: 0.1303 time to fit residues: 37.7609 Evaluate side-chains 184 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 822 MET Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain D residue 19 TRP Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 58 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 159 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 ASN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN G 32 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.099994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.070927 restraints weight = 58624.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.073412 restraints weight = 31222.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.074949 restraints weight = 21897.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.075906 restraints weight = 17850.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.076390 restraints weight = 15840.919| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16758 Z= 0.105 Angle : 0.615 12.069 22688 Z= 0.297 Chirality : 0.039 0.172 2558 Planarity : 0.004 0.047 2872 Dihedral : 3.895 25.550 2193 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.45 % Allowed : 21.23 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 1.32 (0.20), residues: 2013 helix: 2.38 (0.18), residues: 849 sheet: -0.34 (0.26), residues: 414 loop : -0.09 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 44 TYR 0.017 0.001 TYR D 79 PHE 0.049 0.001 PHE B 146 TRP 0.031 0.001 TRP D 21 HIS 0.006 0.001 HIS D 32 Details of bonding type rmsd covalent geometry : bond 0.00235 (16758) covalent geometry : angle 0.61483 (22688) hydrogen bonds : bond 0.02991 ( 695) hydrogen bonds : angle 4.13906 ( 2049) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2962.65 seconds wall clock time: 51 minutes 49.05 seconds (3109.05 seconds total)