Starting phenix.real_space_refine on Sat Mar 16 04:36:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sjr_25164/03_2024/7sjr_25164_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sjr_25164/03_2024/7sjr_25164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sjr_25164/03_2024/7sjr_25164.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sjr_25164/03_2024/7sjr_25164.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sjr_25164/03_2024/7sjr_25164_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sjr_25164/03_2024/7sjr_25164_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 38 5.49 5 Mg 1 5.21 5 S 44 5.16 5 C 8437 2.51 5 N 2518 2.21 5 O 2654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 234": "OE1" <-> "OE2" Residue "B GLU 468": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13696 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 6056 Classifications: {'peptide': 802} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 50, 'TRANS': 751} Chain breaks: 11 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 6885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 911, 6885 Classifications: {'peptide': 911} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 50, 'TRANS': 860} Chain breaks: 21 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 715 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain breaks: 1 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' MG': 1, 'ANP': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12877 SG CYS A1030 45.987 45.214 59.684 1.00 21.76 S ATOM 12920 SG CYS A1036 48.104 39.890 57.626 1.00 19.87 S ATOM 12858 SG CYS A1027 45.045 43.486 55.074 1.00 25.39 S ATOM 11241 SG CYS A 807 41.638 40.092 59.852 1.00 18.07 S Time building chain proxies: 8.05, per 1000 atoms: 0.59 Number of scatterers: 13696 At special positions: 0 Unit cell: (145.768, 104.272, 112.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 44 16.00 P 38 15.00 Mg 1 11.99 O 2654 8.00 N 2518 7.00 C 8437 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 - 3.50 Amino acid : False - 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: 5.85 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1102 " pdb="FE4 SF4 A1102 " - pdb=" SG CYS A 807 " pdb="FE3 SF4 A1102 " - pdb=" SG CYS A1027 " pdb="FE1 SF4 A1102 " - pdb=" SG CYS A1030 " pdb="FE2 SF4 A1102 " - pdb=" SG CYS A1036 " Number of angles added : 12 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3180 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 69 helices and 9 sheets defined 46.6% alpha, 4.1% beta 5 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 5.63 Creating SS restraints... Processing helix chain 'B' and resid 15 through 21 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 55 through 66 Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 81 through 100 removed outlier: 3.897A pdb=" N GLY B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 133 removed outlier: 6.940A pdb=" N LEU B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU B 133 " --> pdb=" O GLU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 157 removed outlier: 3.963A pdb=" N TRP B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN B 150 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP B 154 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS B 157 " --> pdb=" O TYR B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.661A pdb=" N ALA B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.577A pdb=" N LEU B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 248 Proline residue: B 237 - end of helix Processing helix chain 'B' and resid 254 through 267 Processing helix chain 'B' and resid 269 through 278 Processing helix chain 'B' and resid 292 through 299 removed outlier: 3.852A pdb=" N ILE B 296 " --> pdb=" O HIS B 292 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 299 " --> pdb=" O ARG B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 336 No H-bonds generated for 'chain 'B' and resid 333 through 336' Processing helix chain 'B' and resid 360 through 363 No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 403 through 424 removed outlier: 3.618A pdb=" N ALA B 421 " --> pdb=" O ALA B 417 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 449 removed outlier: 3.597A pdb=" N GLU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 485 through 492 removed outlier: 3.983A pdb=" N ARG B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 513 Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'B' and resid 540 through 543 No H-bonds generated for 'chain 'B' and resid 540 through 543' Processing helix chain 'B' and resid 555 through 574 removed outlier: 4.249A pdb=" N GLU B 559 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N HIS B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 589 removed outlier: 3.800A pdb=" N ALA B 584 " --> pdb=" O PRO B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 598 removed outlier: 4.122A pdb=" N ARG B 597 " --> pdb=" O ASP B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 622 Processing helix chain 'B' and resid 633 through 642 Processing helix chain 'B' and resid 729 through 760 removed outlier: 3.844A pdb=" N SER B 736 " --> pdb=" O SER B 732 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 745 " --> pdb=" O SER B 741 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG B 746 " --> pdb=" O LEU B 742 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG B 752 " --> pdb=" O ASP B 748 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU B 753 " --> pdb=" O GLU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 794 Processing helix chain 'B' and resid 839 through 852 Processing helix chain 'B' and resid 864 through 876 Processing helix chain 'A' and resid 35 through 45 removed outlier: 3.618A pdb=" N LEU A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.685A pdb=" N ALA A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 106 Processing helix chain 'A' and resid 119 through 135 removed outlier: 3.976A pdb=" N GLU A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 4.077A pdb=" N THR A 153 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 171 Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 188 through 202 Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.917A pdb=" N GLU A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 262 through 271 Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'A' and resid 357 through 373 removed outlier: 3.916A pdb=" N GLY A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 removed outlier: 4.009A pdb=" N ARG A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 434 removed outlier: 3.509A pdb=" N LEU A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 455 through 468 removed outlier: 4.149A pdb=" N GLN A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 486 Processing helix chain 'A' and resid 496 through 513 removed outlier: 4.637A pdb=" N LEU A 503 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 530 Processing helix chain 'A' and resid 533 through 539 Processing helix chain 'A' and resid 548 through 570 Processing helix chain 'A' and resid 578 through 581 No H-bonds generated for 'chain 'A' and resid 578 through 581' Processing helix chain 'A' and resid 641 through 648 removed outlier: 3.703A pdb=" N ASP A 646 " --> pdb=" O GLN A 642 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 647 " --> pdb=" O HIS A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 679 removed outlier: 4.102A pdb=" N ARG A 670 " --> pdb=" O ALA A 667 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ARG A 671 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET A 677 " --> pdb=" O MET A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 710 removed outlier: 4.126A pdb=" N GLU A 706 " --> pdb=" O PRO A 702 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TRP A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 739 removed outlier: 4.040A pdb=" N GLY A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A 737 " --> pdb=" O GLY A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 762 Processing helix chain 'A' and resid 775 through 777 No H-bonds generated for 'chain 'A' and resid 775 through 777' Processing helix chain 'A' and resid 798 through 804 removed outlier: 3.619A pdb=" N GLN A 802 " --> pdb=" O PRO A 798 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 815 Processing helix chain 'A' and resid 824 through 837 removed outlier: 3.750A pdb=" N GLY A 829 " --> pdb=" O ARG A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 856 removed outlier: 3.577A pdb=" N VAL A 847 " --> pdb=" O GLU A 843 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASN A 848 " --> pdb=" O SER A 844 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 849 " --> pdb=" O GLN A 845 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A 853 " --> pdb=" O GLU A 849 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP A 855 " --> pdb=" O GLU A 851 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASP A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 888 removed outlier: 3.664A pdb=" N ASP A 866 " --> pdb=" O LYS A 862 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN A 867 " --> pdb=" O TRP A 863 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ARG A 888 " --> pdb=" O GLU A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 961 Processing helix chain 'A' and resid 997 through 1013 removed outlier: 4.354A pdb=" N GLU A1002 " --> pdb=" O ASP A 998 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 42 through 46 removed outlier: 7.587A pdb=" N ILE B 45 " --> pdb=" O PRO B 349 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU B 351 " --> pdb=" O ILE B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 281 through 284 removed outlier: 6.709A pdb=" N THR B 115 " --> pdb=" O GLY B 76 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR B 78 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N SER B 117 " --> pdb=" O THR B 78 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 395 through 398 Processing sheet with id= D, first strand: chain 'A' and resid 306 through 309 removed outlier: 9.207A pdb=" N ILE A 307 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ARG A 26 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N LEU A 309 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU A 28 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N THR A 278 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU A 27 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ILE A 280 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLY A 29 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 254 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA A 281 " --> pdb=" O VAL A 254 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 57 through 59 removed outlier: 7.084A pdb=" N LEU A 90 " --> pdb=" O LEU A 58 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 348 through 354 removed outlier: 3.509A pdb=" N THR A 350 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 688 " --> pdb=" O ARG A 352 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 383 through 386 removed outlier: 7.136A pdb=" N ALA A 604 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL A 386 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU A 606 " --> pdb=" O VAL A 386 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 898 through 900 Processing sheet with id= I, first strand: chain 'A' and resid 921 through 923 removed outlier: 3.999A pdb=" N ARG A 921 " --> pdb=" O VAL A 933 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1383 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 3.56 Time building geometry restraints manager: 6.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 5700 1.42 - 1.64: 8222 1.64 - 1.85: 67 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 14001 Sorted by residual: bond pdb=" O3A ANP A1103 " pdb=" PB ANP A1103 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.29e+01 bond pdb=" N3B ANP A1103 " pdb=" PG ANP A1103 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" O5' ANP A1103 " pdb=" PA ANP A1103 " ideal model delta sigma weight residual 1.655 1.578 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" O3G ANP A1103 " pdb=" PG ANP A1103 " ideal model delta sigma weight residual 1.528 1.578 -0.050 2.00e-02 2.50e+03 6.25e+00 bond pdb=" O2B ANP A1103 " pdb=" PB ANP A1103 " ideal model delta sigma weight residual 1.508 1.555 -0.047 2.00e-02 2.50e+03 5.46e+00 ... (remaining 13996 not shown) Histogram of bond angle deviations from ideal: 73.59 - 85.69: 12 85.69 - 97.80: 0 97.80 - 109.90: 2543 109.90 - 122.00: 13830 122.00 - 134.10: 2830 Bond angle restraints: 19215 Sorted by residual: angle pdb=" PB ANP A1103 " pdb=" N3B ANP A1103 " pdb=" PG ANP A1103 " ideal model delta sigma weight residual 126.95 106.41 20.54 3.00e+00 1.11e-01 4.69e+01 angle pdb=" C VAL B 643 " pdb=" N GLU B 644 " pdb=" CA GLU B 644 " ideal model delta sigma weight residual 123.93 131.87 -7.94 1.54e+00 4.22e-01 2.66e+01 angle pdb=" O1B ANP A1103 " pdb=" PB ANP A1103 " pdb=" O2B ANP A1103 " ideal model delta sigma weight residual 120.08 108.69 11.39 3.00e+00 1.11e-01 1.44e+01 angle pdb=" C GLU B 807 " pdb=" N HIS B 808 " pdb=" CA HIS B 808 " ideal model delta sigma weight residual 121.54 128.54 -7.00 1.91e+00 2.74e-01 1.34e+01 angle pdb=" N GLY B 804 " pdb=" CA GLY B 804 " pdb=" C GLY B 804 " ideal model delta sigma weight residual 111.12 117.51 -6.39 1.89e+00 2.80e-01 1.14e+01 ... (remaining 19210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 8082 35.86 - 71.71: 255 71.71 - 107.57: 18 107.57 - 143.43: 1 143.43 - 179.28: 7 Dihedral angle restraints: 8363 sinusoidal: 3484 harmonic: 4879 Sorted by residual: dihedral pdb=" CA SER B 783 " pdb=" C SER B 783 " pdb=" N GLU B 784 " pdb=" CA GLU B 784 " ideal model delta harmonic sigma weight residual 180.00 155.09 24.91 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA GLN A 472 " pdb=" C GLN A 472 " pdb=" N PRO A 473 " pdb=" CA PRO A 473 " ideal model delta harmonic sigma weight residual 180.00 155.23 24.77 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" O1A ANP A1103 " pdb=" O3A ANP A1103 " pdb=" PA ANP A1103 " pdb=" PB ANP A1103 " ideal model delta sinusoidal sigma weight residual 83.11 -90.53 173.64 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 8360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1869 0.056 - 0.113: 343 0.113 - 0.169: 44 0.169 - 0.225: 2 0.225 - 0.281: 1 Chirality restraints: 2259 Sorted by residual: chirality pdb=" C3' ANP A1103 " pdb=" C2' ANP A1103 " pdb=" C4' ANP A1103 " pdb=" O3' ANP A1103 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CB ILE B 395 " pdb=" CA ILE B 395 " pdb=" CG1 ILE B 395 " pdb=" CG2 ILE B 395 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" CB ILE A 450 " pdb=" CA ILE A 450 " pdb=" CG1 ILE A 450 " pdb=" CG2 ILE A 450 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.38e-01 ... (remaining 2256 not shown) Planarity restraints: 2377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 497 " 0.018 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP B 497 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP B 497 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B 497 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 497 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 497 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 497 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 497 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 497 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 497 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 781 " 0.043 5.00e-02 4.00e+02 6.60e-02 6.96e+00 pdb=" N PRO B 782 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 782 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 782 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 357 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.09e+00 pdb=" C TRP B 357 " -0.043 2.00e-02 2.50e+03 pdb=" O TRP B 357 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG B 358 " 0.014 2.00e-02 2.50e+03 ... (remaining 2374 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 104 2.50 - 3.10: 10288 3.10 - 3.70: 20622 3.70 - 4.30: 27467 4.30 - 4.90: 45229 Nonbonded interactions: 103710 Sorted by model distance: nonbonded pdb=" NE2 HIS A 833 " pdb="MG MG A1101 " model vdw 1.895 2.250 nonbonded pdb=" OD2 ASP A 920 " pdb="MG MG A1101 " model vdw 2.051 2.170 nonbonded pdb=" O VAL A 624 " pdb=" OG SER A 701 " model vdw 2.200 2.440 nonbonded pdb=" OG1 THR A 348 " pdb=" OG1 THR A 712 " model vdw 2.211 2.440 nonbonded pdb=" OG1 THR B 689 " pdb=" OE1 GLN B 690 " model vdw 2.225 2.440 ... (remaining 103705 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.040 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: 4.450 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 44.110 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.005 0.145 14001 Z= 0.358 Angle : 0.787 20.544 19215 Z= 0.419 Chirality : 0.045 0.281 2259 Planarity : 0.005 0.066 2377 Dihedral : 17.634 179.282 5183 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 0.08 % Allowed : 0.53 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.21), residues: 1645 helix: 0.21 (0.18), residues: 828 sheet: -2.08 (0.47), residues: 126 loop : -2.49 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 497 HIS 0.007 0.001 HIS B 665 PHE 0.021 0.002 PHE B 685 TYR 0.016 0.002 TYR A 200 ARG 0.014 0.001 ARG B 572 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 1.585 Fit side-chains REVERT: B 258 MET cc_start: 0.8579 (tpt) cc_final: 0.7956 (tpt) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.2527 time to fit residues: 51.0743 Evaluate side-chains 95 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 chunk 158 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS ** A 775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14001 Z= 0.217 Angle : 0.640 9.752 19215 Z= 0.325 Chirality : 0.041 0.162 2259 Planarity : 0.005 0.046 2377 Dihedral : 17.236 178.422 2257 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 1.36 % Allowed : 9.55 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.21), residues: 1645 helix: 0.66 (0.18), residues: 845 sheet: -1.90 (0.49), residues: 124 loop : -2.30 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 497 HIS 0.006 0.001 HIS B 665 PHE 0.015 0.002 PHE A 879 TYR 0.018 0.001 TYR A 522 ARG 0.004 0.000 ARG B 572 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 1.519 Fit side-chains outliers start: 18 outliers final: 14 residues processed: 134 average time/residue: 0.2290 time to fit residues: 47.1350 Evaluate side-chains 109 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 699 SER Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 808 HIS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 357 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 126 optimal weight: 10.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN B 220 GLN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 ASN A 775 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14001 Z= 0.264 Angle : 0.623 10.934 19215 Z= 0.313 Chirality : 0.041 0.197 2259 Planarity : 0.004 0.044 2377 Dihedral : 17.143 179.796 2257 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.88 % Allowed : 13.79 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.21), residues: 1645 helix: 0.81 (0.18), residues: 851 sheet: -1.93 (0.48), residues: 124 loop : -2.23 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 497 HIS 0.005 0.001 HIS B 625 PHE 0.014 0.001 PHE B 685 TYR 0.010 0.001 TYR A 200 ARG 0.007 0.000 ARG A 736 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 104 time to evaluate : 1.581 Fit side-chains REVERT: B 78 THR cc_start: 0.9372 (m) cc_final: 0.9099 (p) REVERT: B 581 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7618 (tm-30) outliers start: 38 outliers final: 21 residues processed: 134 average time/residue: 0.2162 time to fit residues: 45.3015 Evaluate side-chains 116 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 808 HIS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 998 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 140 optimal weight: 0.0980 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14001 Z= 0.342 Angle : 0.656 11.538 19215 Z= 0.330 Chirality : 0.042 0.167 2259 Planarity : 0.005 0.043 2377 Dihedral : 17.183 178.871 2257 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 3.64 % Allowed : 16.74 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.21), residues: 1645 helix: 0.82 (0.18), residues: 852 sheet: -2.05 (0.47), residues: 125 loop : -2.26 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 497 HIS 0.007 0.001 HIS B 665 PHE 0.017 0.002 PHE B 302 TYR 0.014 0.001 TYR A 200 ARG 0.004 0.000 ARG A 736 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 106 time to evaluate : 1.446 Fit side-chains REVERT: B 78 THR cc_start: 0.9419 (m) cc_final: 0.9168 (p) REVERT: B 301 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8539 (mp) REVERT: B 581 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7645 (tm-30) outliers start: 48 outliers final: 29 residues processed: 145 average time/residue: 0.2356 time to fit residues: 52.6264 Evaluate side-chains 125 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 95 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 143 optimal weight: 0.4980 chunk 116 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 150 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS A 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14001 Z= 0.158 Angle : 0.573 10.846 19215 Z= 0.286 Chirality : 0.038 0.137 2259 Planarity : 0.004 0.045 2377 Dihedral : 16.824 174.409 2257 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.73 % Allowed : 18.64 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.22), residues: 1645 helix: 1.15 (0.19), residues: 843 sheet: -1.93 (0.49), residues: 120 loop : -2.10 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 497 HIS 0.005 0.001 HIS A 872 PHE 0.010 0.001 PHE A 879 TYR 0.008 0.001 TYR A 200 ARG 0.006 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 125 time to evaluate : 1.486 Fit side-chains REVERT: B 78 THR cc_start: 0.9390 (m) cc_final: 0.9109 (p) REVERT: B 581 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7465 (tm-30) REVERT: A 183 ARG cc_start: 0.7586 (mpp80) cc_final: 0.7180 (mtp85) REVERT: A 483 ASP cc_start: 0.8182 (m-30) cc_final: 0.7925 (m-30) outliers start: 36 outliers final: 26 residues processed: 155 average time/residue: 0.2239 time to fit residues: 53.0149 Evaluate side-chains 133 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 98 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 162 optimal weight: 0.0670 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14001 Z= 0.181 Angle : 0.570 11.660 19215 Z= 0.283 Chirality : 0.039 0.206 2259 Planarity : 0.004 0.042 2377 Dihedral : 16.767 175.227 2257 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.88 % Allowed : 19.39 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.22), residues: 1645 helix: 1.24 (0.19), residues: 848 sheet: -1.87 (0.49), residues: 120 loop : -2.03 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 497 HIS 0.011 0.001 HIS B 625 PHE 0.010 0.001 PHE B 685 TYR 0.008 0.001 TYR A 200 ARG 0.007 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 114 time to evaluate : 1.589 Fit side-chains REVERT: B 581 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7496 (tm-30) REVERT: A 183 ARG cc_start: 0.7562 (mpp80) cc_final: 0.7138 (mtp85) outliers start: 38 outliers final: 31 residues processed: 145 average time/residue: 0.2600 time to fit residues: 56.0273 Evaluate side-chains 137 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 106 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 3.9990 chunk 95 optimal weight: 0.0770 chunk 122 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 overall best weight: 1.3940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14001 Z= 0.200 Angle : 0.572 11.511 19215 Z= 0.285 Chirality : 0.039 0.178 2259 Planarity : 0.004 0.040 2377 Dihedral : 16.747 175.711 2257 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.11 % Allowed : 19.62 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.22), residues: 1645 helix: 1.32 (0.19), residues: 854 sheet: -1.85 (0.49), residues: 120 loop : -2.02 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 497 HIS 0.004 0.001 HIS B 625 PHE 0.012 0.001 PHE B 685 TYR 0.021 0.001 TYR A 200 ARG 0.009 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 108 time to evaluate : 1.492 Fit side-chains REVERT: B 581 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7499 (tm-30) REVERT: A 183 ARG cc_start: 0.7510 (mpp80) cc_final: 0.7063 (mtp85) REVERT: A 204 MET cc_start: 0.7165 (tpp) cc_final: 0.6713 (tpp) REVERT: A 525 TRP cc_start: 0.7772 (t60) cc_final: 0.7139 (t60) outliers start: 41 outliers final: 31 residues processed: 143 average time/residue: 0.3061 time to fit residues: 67.7820 Evaluate side-chains 138 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 107 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 160 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14001 Z= 0.336 Angle : 0.650 11.727 19215 Z= 0.324 Chirality : 0.042 0.174 2259 Planarity : 0.005 0.040 2377 Dihedral : 16.920 177.259 2257 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 3.56 % Allowed : 20.15 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.22), residues: 1645 helix: 1.20 (0.18), residues: 857 sheet: -1.87 (0.50), residues: 118 loop : -2.12 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 497 HIS 0.005 0.001 HIS B 665 PHE 0.018 0.002 PHE B 302 TYR 0.019 0.002 TYR A 200 ARG 0.007 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 104 time to evaluate : 1.527 Fit side-chains REVERT: B 78 THR cc_start: 0.9445 (m) cc_final: 0.9176 (p) REVERT: B 581 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7562 (tm-30) REVERT: B 767 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8836 (pp) REVERT: A 183 ARG cc_start: 0.7515 (mpp80) cc_final: 0.7081 (mtp85) outliers start: 47 outliers final: 36 residues processed: 143 average time/residue: 0.2347 time to fit residues: 51.2797 Evaluate side-chains 140 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 103 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 141 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14001 Z= 0.204 Angle : 0.592 11.359 19215 Z= 0.293 Chirality : 0.039 0.167 2259 Planarity : 0.004 0.042 2377 Dihedral : 16.822 176.164 2257 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.11 % Allowed : 20.76 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.22), residues: 1645 helix: 1.33 (0.19), residues: 857 sheet: -1.81 (0.50), residues: 120 loop : -2.07 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 497 HIS 0.004 0.001 HIS A 872 PHE 0.012 0.001 PHE B 685 TYR 0.021 0.001 TYR A 200 ARG 0.007 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 108 time to evaluate : 1.519 Fit side-chains REVERT: B 78 THR cc_start: 0.9413 (m) cc_final: 0.9162 (p) REVERT: B 225 MET cc_start: 0.7871 (tmm) cc_final: 0.7654 (ttp) REVERT: B 581 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7465 (tm-30) REVERT: B 767 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8866 (pp) REVERT: A 183 ARG cc_start: 0.7496 (mpp80) cc_final: 0.7087 (mtp85) REVERT: A 483 ASP cc_start: 0.7991 (m-30) cc_final: 0.7759 (m-30) outliers start: 41 outliers final: 36 residues processed: 140 average time/residue: 0.2417 time to fit residues: 51.4399 Evaluate side-chains 141 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 104 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 173 optimal weight: 7.9990 chunk 159 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 147 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14001 Z= 0.330 Angle : 0.653 11.680 19215 Z= 0.324 Chirality : 0.042 0.167 2259 Planarity : 0.005 0.041 2377 Dihedral : 16.943 177.403 2257 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 3.18 % Allowed : 20.68 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.22), residues: 1645 helix: 1.23 (0.18), residues: 856 sheet: -1.82 (0.50), residues: 119 loop : -2.11 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 497 HIS 0.004 0.001 HIS B 770 PHE 0.017 0.002 PHE B 302 TYR 0.023 0.002 TYR A 200 ARG 0.009 0.000 ARG B 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 103 time to evaluate : 1.679 Fit side-chains REVERT: B 78 THR cc_start: 0.9446 (m) cc_final: 0.9182 (p) REVERT: B 581 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7546 (tm-30) REVERT: B 767 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8847 (pp) REVERT: A 183 ARG cc_start: 0.7611 (mpp80) cc_final: 0.7170 (mtp85) outliers start: 42 outliers final: 38 residues processed: 137 average time/residue: 0.2312 time to fit residues: 48.9699 Evaluate side-chains 140 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 101 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 138 optimal weight: 0.0020 chunk 57 optimal weight: 2.9990 chunk 141 optimal weight: 0.0980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.125567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.099923 restraints weight = 25056.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.098913 restraints weight = 22444.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.099691 restraints weight = 25740.616| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14001 Z= 0.159 Angle : 0.575 11.371 19215 Z= 0.283 Chirality : 0.038 0.168 2259 Planarity : 0.004 0.043 2377 Dihedral : 16.735 175.548 2257 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.73 % Allowed : 21.44 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.22), residues: 1645 helix: 1.43 (0.19), residues: 856 sheet: -1.81 (0.49), residues: 125 loop : -1.98 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 525 HIS 0.004 0.001 HIS A 872 PHE 0.010 0.001 PHE A 879 TYR 0.028 0.001 TYR A 200 ARG 0.006 0.000 ARG B 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2268.21 seconds wall clock time: 41 minutes 49.98 seconds (2509.98 seconds total)