Starting phenix.real_space_refine on Thu Feb 5 21:36:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qc7_53005/02_2026/9qc7_53005.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qc7_53005/02_2026/9qc7_53005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qc7_53005/02_2026/9qc7_53005.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qc7_53005/02_2026/9qc7_53005.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qc7_53005/02_2026/9qc7_53005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qc7_53005/02_2026/9qc7_53005.map" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.025 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 60 5.16 5 C 12725 2.51 5 N 3182 2.21 5 O 3813 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 19780 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1264, 10433 Classifications: {'peptide': 1264} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 1225} Chain breaks: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 9347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 9347 Classifications: {'peptide': 1140} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 1107} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 4.27, per 1000 atoms: 0.22 Number of scatterers: 19780 At special positions: 0 Unit cell: (110.08, 119.54, 173.72, 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 60 16.00 O 3813 8.00 N 3182 7.00 C 12725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 438 " - pdb=" SG CYS A 447 " distance=2.06 Simple disulfide: pdb=" SG CYS B 583 " - pdb=" SG CYS B 754 " distance=2.08 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: 1.39 Conformation dependent library (CDL) restraints added in 958.6 milliseconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4618 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 32 sheets defined 35.3% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 25 through 29 Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.692A pdb=" N PHE A 60 " --> pdb=" O PRO A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 101 removed outlier: 3.677A pdb=" N LEU A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 116 Processing helix chain 'A' and resid 224 through 242 removed outlier: 3.844A pdb=" N TYR A 235 " --> pdb=" O HIS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 274 removed outlier: 3.688A pdb=" N LEU A 270 " --> pdb=" O GLN A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 282 through 305 Processing helix chain 'A' and resid 317 through 329 Processing helix chain 'A' and resid 342 through 356 Processing helix chain 'A' and resid 358 through 367 Processing helix chain 'A' and resid 407 through 414 removed outlier: 5.974A pdb=" N GLY A 412 " --> pdb=" O GLU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 460 through 464 removed outlier: 4.062A pdb=" N PHE A 464 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 removed outlier: 3.606A pdb=" N SER A 469 " --> pdb=" O ASP A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 495 removed outlier: 3.727A pdb=" N LEU A 492 " --> pdb=" O PRO A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 544 Processing helix chain 'A' and resid 559 through 566 Processing helix chain 'A' and resid 575 through 583 Processing helix chain 'A' and resid 590 through 606 removed outlier: 4.028A pdb=" N LYS A 596 " --> pdb=" O ALA A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 630 Processing helix chain 'A' and resid 639 through 648 removed outlier: 3.597A pdb=" N ILE A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 652 Processing helix chain 'A' and resid 675 through 709 removed outlier: 3.631A pdb=" N ASN A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 692 " --> pdb=" O THR A 688 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 695 " --> pdb=" O ASN A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 742 removed outlier: 3.522A pdb=" N ASN A 740 " --> pdb=" O LYS A 736 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR A 742 " --> pdb=" O ARG A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 748 Processing helix chain 'A' and resid 753 through 788 removed outlier: 3.508A pdb=" N ASN A 771 " --> pdb=" O GLN A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 814 removed outlier: 3.545A pdb=" N ALA A 792 " --> pdb=" O MET A 788 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 819 removed outlier: 3.634A pdb=" N ILE A 819 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 833 Processing helix chain 'A' and resid 840 through 844 removed outlier: 3.714A pdb=" N ILE A 843 " --> pdb=" O ASP A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 949 Processing helix chain 'A' and resid 1068 through 1081 removed outlier: 3.593A pdb=" N LYS A1077 " --> pdb=" O GLU A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1107 No H-bonds generated for 'chain 'A' and resid 1105 through 1107' Processing helix chain 'A' and resid 1263 through 1268 removed outlier: 3.805A pdb=" N GLU A1267 " --> pdb=" O TRP A1263 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 91 removed outlier: 3.752A pdb=" N LYS B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 105 Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 217 through 235 removed outlier: 3.771A pdb=" N GLU B 221 " --> pdb=" O ASP B 217 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 229 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR B 231 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 269 removed outlier: 3.980A pdb=" N GLY B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 285 through 306 removed outlier: 4.020A pdb=" N SER B 289 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 304 " --> pdb=" O ASN B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 326 removed outlier: 3.818A pdb=" N LYS B 321 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN B 322 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 334 removed outlier: 3.633A pdb=" N ILE B 331 " --> pdb=" O ASN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 344 removed outlier: 3.978A pdb=" N PHE B 339 " --> pdb=" O ASN B 335 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS B 341 " --> pdb=" O ASN B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 removed outlier: 4.129A pdb=" N PHE B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 384 removed outlier: 4.153A pdb=" N ASN B 383 " --> pdb=" O ASN B 379 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 379 through 384' Processing helix chain 'B' and resid 389 through 395 removed outlier: 3.917A pdb=" N ASN B 392 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN B 393 " --> pdb=" O ASP B 390 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE B 395 " --> pdb=" O ASN B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 458 through 464 removed outlier: 3.591A pdb=" N ILE B 462 " --> pdb=" O ASN B 458 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 506 Processing helix chain 'B' and resid 519 through 526 removed outlier: 3.656A pdb=" N VAL B 523 " --> pdb=" O ASP B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 545 Processing helix chain 'B' and resid 554 through 574 Processing helix chain 'B' and resid 591 through 597 removed outlier: 3.592A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 613 removed outlier: 3.822A pdb=" N GLU B 608 " --> pdb=" O SER B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 617 Processing helix chain 'B' and resid 643 through 645 No H-bonds generated for 'chain 'B' and resid 643 through 645' Processing helix chain 'B' and resid 646 through 676 removed outlier: 3.649A pdb=" N ASN B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 653 " --> pdb=" O LYS B 649 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 658 " --> pdb=" O TYR B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 710 removed outlier: 3.758A pdb=" N TYR B 680 " --> pdb=" O TYR B 676 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 683 " --> pdb=" O GLN B 679 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN B 700 " --> pdb=" O LYS B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 759 removed outlier: 3.792A pdb=" N ILE B 731 " --> pdb=" O GLU B 727 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE B 756 " --> pdb=" O ALA B 752 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP B 757 " --> pdb=" O ILE B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 786 removed outlier: 3.763A pdb=" N LYS B 763 " --> pdb=" O ASN B 759 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B 770 " --> pdb=" O SER B 766 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS B 771 " --> pdb=" O PHE B 767 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN B 773 " --> pdb=" O GLU B 769 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 775 " --> pdb=" O CYS B 771 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER B 777 " --> pdb=" O ASN B 773 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASN B 778 " --> pdb=" O SER B 774 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE B 782 " --> pdb=" O ASN B 778 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 784 " --> pdb=" O THR B 780 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 785 " --> pdb=" O ALA B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 801 removed outlier: 3.626A pdb=" N LYS B 794 " --> pdb=" O THR B 790 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU B 795 " --> pdb=" O GLU B 791 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN B 796 " --> pdb=" O ASP B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 821 removed outlier: 3.519A pdb=" N LYS B 817 " --> pdb=" O ILE B 813 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU B 819 " --> pdb=" O SER B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 831 removed outlier: 3.683A pdb=" N LEU B 826 " --> pdb=" O SER B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 894 Processing helix chain 'B' and resid 1024 through 1037 Processing helix chain 'B' and resid 1186 through 1190 Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 174 removed outlier: 3.504A pdb=" N GLU A 172 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY A 163 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU A 49 " --> pdb=" O GLY A 163 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 41 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE A 46 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LYS A 39 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ALA A 37 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 11.817A pdb=" N ARG A 50 " --> pdb=" O TYR A 35 " (cutoff:3.500A) removed outlier: 10.564A pdb=" N TYR A 35 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N MET A 22 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASN A 140 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA5, first strand: chain 'A' and resid 177 through 178 Processing sheet with id=AA6, first strand: chain 'A' and resid 221 through 222 removed outlier: 6.548A pdb=" N VAL A 201 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL A 203 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 332 through 333 Processing sheet with id=AA8, first strand: chain 'A' and resid 447 through 451 Processing sheet with id=AA9, first strand: chain 'A' and resid 472 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 555 through 557 removed outlier: 6.224A pdb=" N SER A 555 " --> pdb=" O VAL A 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 610 through 611 Processing sheet with id=AB3, first strand: chain 'A' and resid 864 through 866 removed outlier: 6.558A pdb=" N ILE A1062 " --> pdb=" O ILE A 865 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 864 through 866 removed outlier: 6.558A pdb=" N ILE A1062 " --> pdb=" O ILE A 865 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP A1056 " --> pdb=" O ARG A 934 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A1058 " --> pdb=" O TRP A 932 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE A1060 " --> pdb=" O SER A 930 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N SER A 930 " --> pdb=" O PHE A1060 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE A1062 " --> pdb=" O SER A 928 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER A 928 " --> pdb=" O ILE A1062 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 927 " --> pdb=" O ASN A1010 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA A1015 " --> pdb=" O ASN A1026 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASN A1026 " --> pdb=" O ALA A1015 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE A1017 " --> pdb=" O GLU A1024 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 870 through 871 removed outlier: 4.056A pdb=" N ARG A 870 " --> pdb=" O ILE A 877 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 877 " --> pdb=" O ARG A 870 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 885 through 888 removed outlier: 9.840A pdb=" N GLU A1040 " --> pdb=" O LYS A 958 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS A 958 " --> pdb=" O GLU A1040 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE A1042 " --> pdb=" O CYS A 956 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N CYS A 956 " --> pdb=" O ILE A1042 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LYS A1044 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE A 954 " --> pdb=" O LYS A1044 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A 951 " --> pdb=" O ILE A 967 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE A 965 " --> pdb=" O ILE A 953 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASN A 955 " --> pdb=" O TRP A 963 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N TRP A 963 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N MET A 957 " --> pdb=" O SER A 961 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER A 961 " --> pdb=" O MET A 957 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 964 " --> pdb=" O THR A 975 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 976 " --> pdb=" O LYS A 984 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1191 through 1193 removed outlier: 4.045A pdb=" N LYS A1255 " --> pdb=" O PHE A1244 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY A1237 " --> pdb=" O PHE A1226 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LEU A1224 " --> pdb=" O ILE A1239 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP A1166 " --> pdb=" O ILE A1211 " (cutoff:3.500A) removed outlier: 14.937A pdb=" N ILE A1168 " --> pdb=" O THR A1183 " (cutoff:3.500A) removed outlier: 11.256A pdb=" N THR A1183 " --> pdb=" O ILE A1168 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU A1170 " --> pdb=" O VAL A1181 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A1181 " --> pdb=" O LEU A1170 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A1172 " --> pdb=" O TRP A1179 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1195 through 1198 removed outlier: 3.517A pdb=" N PHE A1172 " --> pdb=" O TRP A1179 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A1181 " --> pdb=" O LEU A1170 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU A1170 " --> pdb=" O VAL A1181 " (cutoff:3.500A) removed outlier: 11.256A pdb=" N THR A1183 " --> pdb=" O ILE A1168 " (cutoff:3.500A) removed outlier: 14.937A pdb=" N ILE A1168 " --> pdb=" O THR A1183 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LYS A1145 " --> pdb=" O PHE A1173 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1109 through 1113 Processing sheet with id=AC1, first strand: chain 'B' and resid 18 through 22 removed outlier: 9.144A pdb=" N PHE B 30 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 10.827A pdb=" N ARG B 45 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N ALA B 32 " --> pdb=" O PRO B 43 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LYS B 34 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL B 41 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA B 36 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY B 173 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU B 44 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 170 " --> pdb=" O THR B 199 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 156 through 157 Processing sheet with id=AC3, first strand: chain 'B' and resid 214 through 215 Processing sheet with id=AC4, first strand: chain 'B' and resid 243 through 248 removed outlier: 5.564A pdb=" N LEU B 260 " --> pdb=" O PRO B 245 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG B 247 " --> pdb=" O SER B 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 372 through 373 Processing sheet with id=AC6, first strand: chain 'B' and resid 412 through 418 removed outlier: 6.878A pdb=" N LEU B 405 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG B 415 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE B 403 " --> pdb=" O ARG B 415 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASN B 417 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLU B 401 " --> pdb=" O ASN B 417 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 402 " --> pdb=" O ARG B 491 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 515 through 517 Processing sheet with id=AC8, first strand: chain 'B' and resid 576 through 581 Processing sheet with id=AC9, first strand: chain 'B' and resid 847 through 852 removed outlier: 6.470A pdb=" N ILE B1018 " --> pdb=" O ASN B 836 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N PHE B 838 " --> pdb=" O LEU B1016 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU B1016 " --> pdb=" O PHE B 838 " (cutoff:3.500A) removed outlier: 9.651A pdb=" N PHE B 840 " --> pdb=" O GLU B1014 " (cutoff:3.500A) removed outlier: 10.929A pdb=" N GLU B1014 " --> pdb=" O PHE B 840 " (cutoff:3.500A) removed outlier: 14.621A pdb=" N LEU B 842 " --> pdb=" O TYR B1012 " (cutoff:3.500A) removed outlier: 16.591A pdb=" N TYR B1012 " --> pdb=" O LEU B 842 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B1011 " --> pdb=" O LEU B 879 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLY B1015 " --> pdb=" O ASP B 875 " (cutoff:3.500A) removed outlier: 10.647A pdb=" N ASP B 875 " --> pdb=" O GLY B1015 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 867 " --> pdb=" O TYR B 878 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 847 through 852 removed outlier: 6.470A pdb=" N ILE B1018 " --> pdb=" O ASN B 836 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N PHE B 838 " --> pdb=" O LEU B1016 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU B1016 " --> pdb=" O PHE B 838 " (cutoff:3.500A) removed outlier: 9.651A pdb=" N PHE B 840 " --> pdb=" O GLU B1014 " (cutoff:3.500A) removed outlier: 10.929A pdb=" N GLU B1014 " --> pdb=" O PHE B 840 " (cutoff:3.500A) removed outlier: 14.621A pdb=" N LEU B 842 " --> pdb=" O TYR B1012 " (cutoff:3.500A) removed outlier: 16.591A pdb=" N TYR B1012 " --> pdb=" O LEU B 842 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU B1016 " --> pdb=" O CYS B 904 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N CYS B 904 " --> pdb=" O LEU B1016 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE B1018 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N SER B 902 " --> pdb=" O ILE B1018 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE B 980 " --> pdb=" O LEU B 984 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 859 through 862 removed outlier: 4.971A pdb=" N LEU B 919 " --> pdb=" O VAL B1005 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LYS B 918 " --> pdb=" O PHE B 933 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N PHE B 933 " --> pdb=" O LYS B 918 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1076 through 1080 removed outlier: 6.351A pdb=" N ASN B1065 " --> pdb=" O ASN B1059 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASN B1059 " --> pdb=" O ASN B1065 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU B1057 " --> pdb=" O LEU B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1093 through 1096 removed outlier: 16.071A pdb=" N GLY B1111 " --> pdb=" O ILE B1125 " (cutoff:3.500A) removed outlier: 11.228A pdb=" N ILE B1125 " --> pdb=" O GLY B1111 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL B1113 " --> pdb=" O VAL B1123 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS B1121 " --> pdb=" O LEU B1115 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1093 through 1096 removed outlier: 4.879A pdb=" N ASP B1149 " --> pdb=" O CYS B1155 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N CYS B1155 " --> pdb=" O ASP B1149 " (cutoff:3.500A) removed outlier: 15.024A pdb=" N LEU B1156 " --> pdb=" O LEU B1167 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N LEU B1167 " --> pdb=" O LEU B1156 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N PHE B1158 " --> pdb=" O LEU B1165 " (cutoff:3.500A) 791 hydrogen bonds defined for protein. 2181 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: 4.47 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3523 1.32 - 1.45: 5298 1.45 - 1.58: 11279 1.58 - 1.72: 0 1.72 - 1.85: 97 Bond restraints: 20197 Sorted by residual: bond pdb=" CE1 HIS B1190 " pdb=" NE2 HIS B1190 " ideal model delta sigma weight residual 1.321 1.368 -0.047 1.00e-02 1.00e+04 2.18e+01 bond pdb=" C PRO B1153 " pdb=" O PRO B1153 " ideal model delta sigma weight residual 1.238 1.181 0.056 1.24e-02 6.50e+03 2.05e+01 bond pdb=" C SER A1061 " pdb=" O SER A1061 " ideal model delta sigma weight residual 1.234 1.181 0.053 1.20e-02 6.94e+03 1.95e+01 bond pdb=" CA SER B1045 " pdb=" CB SER B1045 " ideal model delta sigma weight residual 1.532 1.459 0.073 1.79e-02 3.12e+03 1.67e+01 bond pdb=" C ASN B1059 " pdb=" O ASN B1059 " ideal model delta sigma weight residual 1.236 1.188 0.047 1.21e-02 6.83e+03 1.53e+01 ... (remaining 20192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 24645 1.93 - 3.86: 2598 3.86 - 5.79: 71 5.79 - 7.72: 7 7.72 - 9.65: 2 Bond angle restraints: 27323 Sorted by residual: angle pdb=" CA ILE A1000 " pdb=" C ILE A1000 " pdb=" O ILE A1000 " ideal model delta sigma weight residual 120.95 114.39 6.56 1.04e+00 9.25e-01 3.98e+01 angle pdb=" CA PHE A 900 " pdb=" CB PHE A 900 " pdb=" CG PHE A 900 " ideal model delta sigma weight residual 113.80 119.64 -5.84 1.00e+00 1.00e+00 3.42e+01 angle pdb=" C PHE A 900 " pdb=" CA PHE A 900 " pdb=" CB PHE A 900 " ideal model delta sigma weight residual 109.50 119.15 -9.65 1.69e+00 3.50e-01 3.26e+01 angle pdb=" N LEU A 796 " pdb=" CA LEU A 796 " pdb=" C LEU A 796 " ideal model delta sigma weight residual 111.69 105.07 6.62 1.23e+00 6.61e-01 2.90e+01 angle pdb=" CA ALA A 606 " pdb=" C ALA A 606 " pdb=" O ALA A 606 " ideal model delta sigma weight residual 121.99 116.20 5.79 1.14e+00 7.69e-01 2.58e+01 ... (remaining 27318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 11047 17.99 - 35.98: 914 35.98 - 53.97: 138 53.97 - 71.95: 33 71.95 - 89.94: 24 Dihedral angle restraints: 12156 sinusoidal: 4995 harmonic: 7161 Sorted by residual: dihedral pdb=" CA ILE B 920 " pdb=" C ILE B 920 " pdb=" N GLU B 921 " pdb=" CA GLU B 921 " ideal model delta harmonic sigma weight residual 180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA TYR A 999 " pdb=" C TYR A 999 " pdb=" N ILE A1000 " pdb=" CA ILE A1000 " ideal model delta harmonic sigma weight residual -180.00 -157.47 -22.53 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA LEU B 954 " pdb=" C LEU B 954 " pdb=" N SER B 955 " pdb=" CA SER B 955 " ideal model delta harmonic sigma weight residual -180.00 -157.71 -22.29 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 12153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1356 0.048 - 0.096: 966 0.096 - 0.144: 530 0.144 - 0.192: 118 0.192 - 0.240: 11 Chirality restraints: 2981 Sorted by residual: chirality pdb=" CA LYS A 901 " pdb=" N LYS A 901 " pdb=" C LYS A 901 " pdb=" CB LYS A 901 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ILE B 850 " pdb=" N ILE B 850 " pdb=" C ILE B 850 " pdb=" CB ILE B 850 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ILE B 985 " pdb=" N ILE B 985 " pdb=" C ILE B 985 " pdb=" CB ILE B 985 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 2978 not shown) Planarity restraints: 3521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1018 " -0.063 2.00e-02 2.50e+03 3.28e-02 2.15e+01 pdb=" CG TYR A1018 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A1018 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR A1018 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A1018 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A1018 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A1018 " -0.015 2.00e-02 2.50e+03 pdb=" OH TYR A1018 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1099 " 0.043 2.00e-02 2.50e+03 2.58e-02 1.33e+01 pdb=" CG TYR A1099 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR A1099 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR A1099 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A1099 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A1099 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR A1099 " 0.030 2.00e-02 2.50e+03 pdb=" OH TYR A1099 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 672 " -0.028 2.00e-02 2.50e+03 2.21e-02 1.22e+01 pdb=" CG TRP B 672 " -0.000 2.00e-02 2.50e+03 pdb=" CD1 TRP B 672 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B 672 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 672 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TRP B 672 " -0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP B 672 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 672 " -0.040 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 672 " 0.031 2.00e-02 2.50e+03 pdb=" CH2 TRP B 672 " 0.003 2.00e-02 2.50e+03 ... (remaining 3518 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 418 2.69 - 3.24: 19305 3.24 - 3.79: 26978 3.79 - 4.35: 40664 4.35 - 4.90: 65967 Nonbonded interactions: 153332 Sorted by model distance: nonbonded pdb=" OG1 THR A 82 " pdb=" OD1 ASP A 84 " model vdw 2.131 3.040 nonbonded pdb=" OE1 GLN A 914 " pdb=" N ASN A 915 " model vdw 2.132 3.120 nonbonded pdb=" ND2 ASN B 154 " pdb=" OD1 ASN B 168 " model vdw 2.132 3.120 nonbonded pdb=" N GLU B1047 " pdb=" OE1 GLU B1047 " model vdw 2.159 3.120 nonbonded pdb=" O TYR A 476 " pdb=" NZ LYS A 681 " model vdw 2.168 3.120 ... (remaining 153327 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 ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 18.960 Find NCS groups from input model: 0.140 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:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 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 : 0.012 0.073 20199 Z= 0.889 Angle : 1.172 9.650 27327 Z= 0.840 Chirality : 0.075 0.240 2981 Planarity : 0.006 0.035 3521 Dihedral : 13.941 89.943 7532 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.31 % Allowed : 6.33 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.62 (0.16), residues: 2384 helix: 0.61 (0.19), residues: 718 sheet: -0.53 (0.27), residues: 345 loop : -0.93 (0.16), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG B 563 TYR 0.063 0.007 TYR A1018 PHE 0.039 0.006 PHE A 357 TRP 0.040 0.008 TRP B 672 HIS 0.024 0.005 HIS B1190 Details of bonding type rmsd covalent geometry : bond 0.01231 (20197) covalent geometry : angle 1.17103 (27323) SS BOND : bond 0.04270 ( 2) SS BOND : angle 4.68066 ( 4) hydrogen bonds : bond 0.26764 ( 776) hydrogen bonds : angle 7.65660 ( 2181) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 989 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8273 (tp30) REVERT: A 1051 ARG cc_start: 0.8892 (ptm-80) cc_final: 0.8618 (tpm170) REVERT: A 1244 PHE cc_start: 0.5057 (m-10) cc_final: 0.4547 (m-10) REVERT: B 198 MET cc_start: 0.8165 (ttm) cc_final: 0.7944 (ttm) REVERT: B 1152 MET cc_start: 0.8291 (mmm) cc_final: 0.8046 (mmm) outliers start: 7 outliers final: 3 residues processed: 73 average time/residue: 0.6571 time to fit residues: 54.8338 Evaluate side-chains 65 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 989 GLU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 240 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 970 ASN A1053 GLN A1108 ASN B 182 ASN B 801 ASN B 873 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.071851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.051930 restraints weight = 59771.350| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.49 r_work: 0.2854 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20199 Z= 0.137 Angle : 0.528 7.711 27327 Z= 0.300 Chirality : 0.044 0.162 2981 Planarity : 0.003 0.029 3521 Dihedral : 4.668 44.260 2618 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.45 % Allowed : 6.83 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 0.19 (0.17), residues: 2384 helix: 1.60 (0.19), residues: 766 sheet: -0.13 (0.26), residues: 382 loop : -0.72 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1149 TYR 0.018 0.001 TYR B 211 PHE 0.015 0.001 PHE B 78 TRP 0.008 0.001 TRP A 974 HIS 0.008 0.001 HIS B1190 Details of bonding type rmsd covalent geometry : bond 0.00273 (20197) covalent geometry : angle 0.52742 (27323) SS BOND : bond 0.00253 ( 2) SS BOND : angle 2.71970 ( 4) hydrogen bonds : bond 0.08022 ( 776) hydrogen bonds : angle 5.29779 ( 2181) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.617 Fit side-chains REVERT: A 354 MET cc_start: 0.9069 (mmt) cc_final: 0.8837 (mmt) REVERT: A 989 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7728 (tp30) REVERT: A 1051 ARG cc_start: 0.8622 (ptm-80) cc_final: 0.8231 (tpm170) REVERT: A 1176 ASN cc_start: 0.9398 (m-40) cc_final: 0.9047 (p0) REVERT: A 1235 GLU cc_start: 0.8041 (mp0) cc_final: 0.7829 (mp0) REVERT: B 474 TYR cc_start: 0.8196 (t80) cc_final: 0.7690 (t80) REVERT: B 784 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.7041 (mp10) REVERT: B 788 ASN cc_start: 0.8101 (m110) cc_final: 0.6805 (t0) outliers start: 10 outliers final: 4 residues processed: 75 average time/residue: 0.5673 time to fit residues: 49.0351 Evaluate side-chains 67 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 989 GLU Chi-restraints excluded: chain A residue 1259 CYS Chi-restraints excluded: chain B residue 772 ILE Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 820 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 239 optimal weight: 0.8980 chunk 135 optimal weight: 9.9990 chunk 198 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 226 optimal weight: 7.9990 chunk 225 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 54 optimal weight: 0.0170 overall best weight: 1.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1014 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.071418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.051330 restraints weight = 60979.664| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.53 r_work: 0.2855 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20199 Z= 0.153 Angle : 0.492 7.422 27327 Z= 0.277 Chirality : 0.044 0.153 2981 Planarity : 0.003 0.032 3521 Dihedral : 4.542 40.263 2612 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.03 % Allowed : 7.90 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.17), residues: 2384 helix: 1.83 (0.19), residues: 764 sheet: -0.01 (0.25), residues: 390 loop : -0.72 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1149 TYR 0.013 0.001 TYR B 211 PHE 0.017 0.001 PHE A 900 TRP 0.012 0.001 TRP A 974 HIS 0.009 0.001 HIS B1190 Details of bonding type rmsd covalent geometry : bond 0.00349 (20197) covalent geometry : angle 0.49098 (27323) SS BOND : bond 0.00126 ( 2) SS BOND : angle 2.99809 ( 4) hydrogen bonds : bond 0.06834 ( 776) hydrogen bonds : angle 4.82474 ( 2181) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.831 Fit side-chains REVERT: A 576 MET cc_start: 0.8073 (mmm) cc_final: 0.7740 (tpp) REVERT: A 989 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: A 1051 ARG cc_start: 0.8629 (ptm-80) cc_final: 0.8188 (tpm170) REVERT: A 1176 ASN cc_start: 0.9398 (m-40) cc_final: 0.8785 (p0) REVERT: A 1235 GLU cc_start: 0.8207 (mp0) cc_final: 0.7829 (mp0) REVERT: B 110 TYR cc_start: 0.8446 (m-10) cc_final: 0.8019 (m-80) REVERT: B 474 TYR cc_start: 0.8314 (t80) cc_final: 0.7909 (t80) REVERT: B 638 MET cc_start: 0.5595 (tpt) cc_final: 0.5253 (tpt) REVERT: B 788 ASN cc_start: 0.7837 (m110) cc_final: 0.6632 (t0) REVERT: B 831 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7581 (ttmm) outliers start: 23 outliers final: 6 residues processed: 85 average time/residue: 0.6185 time to fit residues: 60.0590 Evaluate side-chains 68 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 989 GLU Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain B residue 772 ILE Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 831 LYS Chi-restraints excluded: chain B residue 1132 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 226 optimal weight: 0.0050 chunk 40 optimal weight: 0.0870 chunk 153 optimal weight: 0.8980 chunk 171 optimal weight: 0.0470 chunk 134 optimal weight: 7.9990 chunk 204 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 overall best weight: 1.2072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 970 ASN B 801 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.072664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.052693 restraints weight = 60689.692| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.52 r_work: 0.2887 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20199 Z= 0.114 Angle : 0.451 7.315 27327 Z= 0.253 Chirality : 0.043 0.147 2981 Planarity : 0.003 0.033 3521 Dihedral : 4.306 40.485 2612 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.94 % Allowed : 8.94 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 0.53 (0.17), residues: 2384 helix: 2.03 (0.19), residues: 768 sheet: 0.05 (0.25), residues: 398 loop : -0.64 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 968 TYR 0.011 0.001 TYR B 211 PHE 0.014 0.001 PHE A 900 TRP 0.012 0.001 TRP A 974 HIS 0.008 0.001 HIS B1190 Details of bonding type rmsd covalent geometry : bond 0.00250 (20197) covalent geometry : angle 0.44994 (27323) SS BOND : bond 0.00346 ( 2) SS BOND : angle 2.67565 ( 4) hydrogen bonds : bond 0.05618 ( 776) hydrogen bonds : angle 4.52826 ( 2181) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.671 Fit side-chains REVERT: A 576 MET cc_start: 0.8056 (mmm) cc_final: 0.7760 (tpp) REVERT: A 989 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7695 (tp30) REVERT: A 1051 ARG cc_start: 0.8625 (ptm-80) cc_final: 0.8149 (tpm170) REVERT: A 1176 ASN cc_start: 0.9401 (m-40) cc_final: 0.8813 (p0) REVERT: A 1235 GLU cc_start: 0.8236 (mp0) cc_final: 0.7981 (mp0) REVERT: B 110 TYR cc_start: 0.8437 (m-10) cc_final: 0.8110 (m-80) REVERT: B 195 MET cc_start: 0.7083 (mmt) cc_final: 0.6762 (mmt) REVERT: B 474 TYR cc_start: 0.8323 (t80) cc_final: 0.7978 (t80) REVERT: B 638 MET cc_start: 0.5567 (tpt) cc_final: 0.5214 (tpt) REVERT: B 788 ASN cc_start: 0.7783 (m110) cc_final: 0.6643 (t0) REVERT: B 831 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7550 (ttmm) outliers start: 21 outliers final: 7 residues processed: 87 average time/residue: 0.6425 time to fit residues: 63.7510 Evaluate side-chains 69 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 989 GLU Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 772 ILE Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 831 LYS Chi-restraints excluded: chain B residue 1165 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 162 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 133 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 223 optimal weight: 0.5980 chunk 198 optimal weight: 7.9990 chunk 239 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.072610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.052731 restraints weight = 60197.135| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.50 r_work: 0.2891 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20199 Z= 0.116 Angle : 0.450 7.291 27327 Z= 0.250 Chirality : 0.043 0.144 2981 Planarity : 0.003 0.032 3521 Dihedral : 4.191 38.474 2612 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.99 % Allowed : 9.79 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 0.61 (0.17), residues: 2384 helix: 2.10 (0.20), residues: 770 sheet: 0.13 (0.25), residues: 400 loop : -0.60 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 968 TYR 0.009 0.001 TYR B 211 PHE 0.015 0.001 PHE A 900 TRP 0.011 0.001 TRP A 974 HIS 0.008 0.001 HIS B1190 Details of bonding type rmsd covalent geometry : bond 0.00259 (20197) covalent geometry : angle 0.44902 (27323) SS BOND : bond 0.00311 ( 2) SS BOND : angle 2.39812 ( 4) hydrogen bonds : bond 0.05507 ( 776) hydrogen bonds : angle 4.42255 ( 2181) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.671 Fit side-chains REVERT: A 576 MET cc_start: 0.8054 (mmm) cc_final: 0.7734 (tpp) REVERT: A 989 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7751 (tp30) REVERT: A 1051 ARG cc_start: 0.8620 (ptm-80) cc_final: 0.8144 (tpm170) REVERT: A 1176 ASN cc_start: 0.9389 (m-40) cc_final: 0.8817 (p0) REVERT: A 1235 GLU cc_start: 0.8253 (mp0) cc_final: 0.7988 (mp0) REVERT: B 110 TYR cc_start: 0.8463 (m-10) cc_final: 0.8065 (m-80) REVERT: B 195 MET cc_start: 0.7114 (mmt) cc_final: 0.6725 (mmt) REVERT: B 474 TYR cc_start: 0.8354 (t80) cc_final: 0.8018 (t80) REVERT: B 638 MET cc_start: 0.5587 (tpt) cc_final: 0.5214 (tpt) REVERT: B 788 ASN cc_start: 0.7718 (m110) cc_final: 0.6633 (t0) REVERT: B 831 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7539 (ttmm) outliers start: 22 outliers final: 10 residues processed: 80 average time/residue: 0.5957 time to fit residues: 54.9773 Evaluate side-chains 70 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 989 GLU Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 772 ILE Chi-restraints excluded: chain B residue 774 SER Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 831 LYS Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 1165 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 16 optimal weight: 0.8980 chunk 229 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 209 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 222 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 215 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 144 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 970 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.072662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.052812 restraints weight = 60365.704| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.48 r_work: 0.2892 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20199 Z= 0.114 Angle : 0.439 7.255 27327 Z= 0.245 Chirality : 0.043 0.146 2981 Planarity : 0.003 0.033 3521 Dihedral : 4.123 38.261 2612 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.03 % Allowed : 9.79 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 0.68 (0.17), residues: 2384 helix: 2.17 (0.20), residues: 765 sheet: 0.21 (0.25), residues: 412 loop : -0.58 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 185 TYR 0.008 0.001 TYR B1012 PHE 0.015 0.001 PHE A 900 TRP 0.006 0.001 TRP A 974 HIS 0.008 0.001 HIS B1190 Details of bonding type rmsd covalent geometry : bond 0.00255 (20197) covalent geometry : angle 0.43845 (27323) SS BOND : bond 0.00285 ( 2) SS BOND : angle 2.40802 ( 4) hydrogen bonds : bond 0.05337 ( 776) hydrogen bonds : angle 4.36355 ( 2181) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.800 Fit side-chains REVERT: A 576 MET cc_start: 0.8023 (mmm) cc_final: 0.7717 (tpp) REVERT: A 989 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7740 (tp30) REVERT: A 1051 ARG cc_start: 0.8610 (ptm-80) cc_final: 0.8136 (tpm170) REVERT: A 1176 ASN cc_start: 0.9385 (m-40) cc_final: 0.8832 (p0) REVERT: A 1235 GLU cc_start: 0.8229 (mp0) cc_final: 0.7964 (mp0) REVERT: B 110 TYR cc_start: 0.8472 (m-10) cc_final: 0.8147 (m-80) REVERT: B 195 MET cc_start: 0.7113 (mmt) cc_final: 0.6773 (mmt) REVERT: B 474 TYR cc_start: 0.8357 (t80) cc_final: 0.8040 (t80) REVERT: B 638 MET cc_start: 0.5587 (tpt) cc_final: 0.5193 (tpt) REVERT: B 788 ASN cc_start: 0.7723 (m110) cc_final: 0.6688 (t0) REVERT: B 831 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7551 (ttmm) outliers start: 23 outliers final: 12 residues processed: 80 average time/residue: 0.6325 time to fit residues: 58.5203 Evaluate side-chains 73 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 989 GLU Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 772 ILE Chi-restraints excluded: chain B residue 774 SER Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 831 LYS Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1165 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 16 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 214 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 140 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.071774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.051755 restraints weight = 60901.273| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.52 r_work: 0.2839 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20199 Z= 0.158 Angle : 0.475 9.559 27327 Z= 0.262 Chirality : 0.044 0.148 2981 Planarity : 0.003 0.033 3521 Dihedral : 4.237 38.029 2612 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.81 % Allowed : 10.28 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 0.64 (0.17), residues: 2384 helix: 2.15 (0.20), residues: 762 sheet: 0.20 (0.25), residues: 412 loop : -0.62 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 185 TYR 0.010 0.001 TYR A1018 PHE 0.018 0.001 PHE A 900 TRP 0.007 0.001 TRP A 974 HIS 0.008 0.001 HIS B1190 Details of bonding type rmsd covalent geometry : bond 0.00371 (20197) covalent geometry : angle 0.47436 (27323) SS BOND : bond 0.00321 ( 2) SS BOND : angle 2.58042 ( 4) hydrogen bonds : bond 0.05939 ( 776) hydrogen bonds : angle 4.46170 ( 2181) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.774 Fit side-chains REVERT: A 576 MET cc_start: 0.8052 (mmm) cc_final: 0.7746 (tpp) REVERT: A 989 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7777 (tp30) REVERT: A 1051 ARG cc_start: 0.8671 (ptm-80) cc_final: 0.8204 (tpm170) REVERT: A 1176 ASN cc_start: 0.9418 (m-40) cc_final: 0.8893 (p0) REVERT: A 1235 GLU cc_start: 0.8222 (mp0) cc_final: 0.7958 (mp0) REVERT: B 110 TYR cc_start: 0.8527 (m-10) cc_final: 0.8104 (m-80) REVERT: B 195 MET cc_start: 0.7145 (mmt) cc_final: 0.6729 (mmt) REVERT: B 474 TYR cc_start: 0.8410 (t80) cc_final: 0.8180 (t80) REVERT: B 626 MET cc_start: 0.8069 (ttt) cc_final: 0.7846 (ttt) REVERT: B 638 MET cc_start: 0.5743 (tpt) cc_final: 0.5339 (tpt) REVERT: B 788 ASN cc_start: 0.7678 (m110) cc_final: 0.6652 (t0) REVERT: B 818 ASP cc_start: 0.7768 (p0) cc_final: 0.7438 (t0) REVERT: B 831 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7604 (ttmm) outliers start: 18 outliers final: 12 residues processed: 79 average time/residue: 0.6251 time to fit residues: 56.8028 Evaluate side-chains 75 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 989 GLU Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 772 ILE Chi-restraints excluded: chain B residue 774 SER Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 831 LYS Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 1132 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 135 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 112 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 178 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 801 ASN ** 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 = 0.3476 r_free = 0.3476 target = 0.071135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.051199 restraints weight = 60588.252| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.48 r_work: 0.2824 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20199 Z= 0.179 Angle : 0.485 7.756 27327 Z= 0.269 Chirality : 0.044 0.152 2981 Planarity : 0.003 0.036 3521 Dihedral : 4.347 37.861 2612 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.03 % Allowed : 10.51 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 0.52 (0.17), residues: 2384 helix: 2.03 (0.19), residues: 768 sheet: 0.15 (0.25), residues: 412 loop : -0.70 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 185 TYR 0.023 0.001 TYR B 211 PHE 0.019 0.001 PHE A 900 TRP 0.007 0.001 TRP B 906 HIS 0.008 0.001 HIS B1190 Details of bonding type rmsd covalent geometry : bond 0.00423 (20197) covalent geometry : angle 0.48395 (27323) SS BOND : bond 0.00315 ( 2) SS BOND : angle 2.68348 ( 4) hydrogen bonds : bond 0.06270 ( 776) hydrogen bonds : angle 4.52579 ( 2181) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.829 Fit side-chains REVERT: A 576 MET cc_start: 0.8115 (mmm) cc_final: 0.7812 (tpp) REVERT: A 1051 ARG cc_start: 0.8690 (ptm-80) cc_final: 0.8227 (tpm170) REVERT: A 1176 ASN cc_start: 0.9409 (m-40) cc_final: 0.8888 (p0) REVERT: A 1235 GLU cc_start: 0.8218 (mp0) cc_final: 0.7950 (mp0) REVERT: B 110 TYR cc_start: 0.8541 (m-10) cc_final: 0.8179 (m-80) REVERT: B 195 MET cc_start: 0.7187 (mmt) cc_final: 0.6848 (mmt) REVERT: B 474 TYR cc_start: 0.8422 (t80) cc_final: 0.8184 (t80) REVERT: B 638 MET cc_start: 0.5813 (tpt) cc_final: 0.5382 (tpt) REVERT: B 788 ASN cc_start: 0.7612 (m110) cc_final: 0.6593 (t0) REVERT: B 818 ASP cc_start: 0.7749 (p0) cc_final: 0.7478 (t0) REVERT: B 831 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7593 (ttmm) outliers start: 23 outliers final: 13 residues processed: 80 average time/residue: 0.6299 time to fit residues: 58.3531 Evaluate side-chains 74 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 772 ILE Chi-restraints excluded: chain B residue 774 SER Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 831 LYS Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 1132 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 59 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 185 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 801 ASN ** 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 = 0.3465 r_free = 0.3465 target = 0.070528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.050499 restraints weight = 60383.755| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.48 r_work: 0.2840 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 20199 Z= 0.234 Angle : 0.536 11.757 27327 Z= 0.294 Chirality : 0.045 0.157 2981 Planarity : 0.003 0.046 3521 Dihedral : 4.479 22.110 2609 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.48 % Favored : 96.48 % Rotamer: Outliers : 0.94 % Allowed : 10.60 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.17), residues: 2384 helix: 1.86 (0.19), residues: 766 sheet: 0.06 (0.25), residues: 410 loop : -0.78 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 185 TYR 0.016 0.001 TYR B 211 PHE 0.021 0.002 PHE A 900 TRP 0.008 0.001 TRP B 906 HIS 0.009 0.001 HIS B1190 Details of bonding type rmsd covalent geometry : bond 0.00559 (20197) covalent geometry : angle 0.53486 (27323) SS BOND : bond 0.00321 ( 2) SS BOND : angle 2.96143 ( 4) hydrogen bonds : bond 0.06974 ( 776) hydrogen bonds : angle 4.67826 ( 2181) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.863 Fit side-chains REVERT: A 576 MET cc_start: 0.8148 (mmm) cc_final: 0.7847 (tpp) REVERT: A 989 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7828 (tp30) REVERT: A 1051 ARG cc_start: 0.8726 (ptm-80) cc_final: 0.8300 (tpm170) REVERT: A 1176 ASN cc_start: 0.9391 (m-40) cc_final: 0.8863 (p0) REVERT: A 1235 GLU cc_start: 0.8201 (mp0) cc_final: 0.7932 (mp0) REVERT: B 110 TYR cc_start: 0.8594 (m-10) cc_final: 0.8154 (m-80) REVERT: B 626 MET cc_start: 0.8154 (ttt) cc_final: 0.7918 (ttt) REVERT: B 638 MET cc_start: 0.5911 (tpt) cc_final: 0.5486 (tpt) REVERT: B 788 ASN cc_start: 0.7642 (m110) cc_final: 0.6608 (t0) REVERT: B 792 ASP cc_start: 0.8911 (t0) cc_final: 0.8628 (p0) REVERT: B 818 ASP cc_start: 0.7755 (p0) cc_final: 0.7480 (t0) REVERT: B 831 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7642 (ttmm) outliers start: 21 outliers final: 14 residues processed: 78 average time/residue: 0.6480 time to fit residues: 58.3400 Evaluate side-chains 76 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 989 GLU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 772 ILE Chi-restraints excluded: chain B residue 774 SER Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 831 LYS Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 1132 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 138 optimal weight: 20.0000 chunk 37 optimal weight: 0.0040 chunk 60 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 184 optimal weight: 0.2980 chunk 208 optimal weight: 2.9990 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 477 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.071944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.052066 restraints weight = 60523.170| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.49 r_work: 0.2861 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20199 Z= 0.118 Angle : 0.453 7.617 27327 Z= 0.252 Chirality : 0.043 0.151 2981 Planarity : 0.003 0.037 3521 Dihedral : 4.205 22.333 2609 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.63 % Allowed : 11.00 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 0.51 (0.17), residues: 2384 helix: 2.05 (0.20), residues: 770 sheet: 0.15 (0.25), residues: 414 loop : -0.74 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1042 TYR 0.019 0.001 TYR B 211 PHE 0.014 0.001 PHE A 900 TRP 0.010 0.001 TRP A 974 HIS 0.008 0.001 HIS B1190 Details of bonding type rmsd covalent geometry : bond 0.00261 (20197) covalent geometry : angle 0.45174 (27323) SS BOND : bond 0.00251 ( 2) SS BOND : angle 2.55600 ( 4) hydrogen bonds : bond 0.05648 ( 776) hydrogen bonds : angle 4.41998 ( 2181) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.837 Fit side-chains REVERT: A 576 MET cc_start: 0.8096 (mmm) cc_final: 0.7802 (tpp) REVERT: A 989 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7794 (tp30) REVERT: A 1051 ARG cc_start: 0.8706 (ptm-80) cc_final: 0.8211 (tpm170) REVERT: A 1176 ASN cc_start: 0.9379 (m-40) cc_final: 0.8864 (p0) REVERT: A 1235 GLU cc_start: 0.8228 (mp0) cc_final: 0.7957 (mp0) REVERT: B 110 TYR cc_start: 0.8574 (m-10) cc_final: 0.8199 (m-80) REVERT: B 195 MET cc_start: 0.7130 (mmt) cc_final: 0.6783 (mmt) REVERT: B 638 MET cc_start: 0.5774 (tpt) cc_final: 0.5283 (tpt) REVERT: B 788 ASN cc_start: 0.7618 (m110) cc_final: 0.6556 (t0) REVERT: B 792 ASP cc_start: 0.8899 (t0) cc_final: 0.8644 (p0) REVERT: B 818 ASP cc_start: 0.7712 (p0) cc_final: 0.7443 (OUTLIER) REVERT: B 831 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7493 (ttmm) outliers start: 14 outliers final: 12 residues processed: 76 average time/residue: 0.6356 time to fit residues: 55.6514 Evaluate side-chains 73 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 989 GLU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 772 ILE Chi-restraints excluded: chain B residue 774 SER Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 831 LYS Chi-restraints excluded: chain B residue 954 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 9 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.071489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.051544 restraints weight = 60778.654| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.49 r_work: 0.2855 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20199 Z= 0.150 Angle : 0.478 10.471 27327 Z= 0.264 Chirality : 0.043 0.150 2981 Planarity : 0.003 0.034 3521 Dihedral : 4.204 22.133 2609 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.81 % Allowed : 10.91 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 0.51 (0.17), residues: 2384 helix: 2.05 (0.19), residues: 770 sheet: 0.15 (0.25), residues: 414 loop : -0.73 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 185 TYR 0.021 0.001 TYR B 211 PHE 0.017 0.001 PHE A 900 TRP 0.008 0.001 TRP A 974 HIS 0.008 0.001 HIS B1190 Details of bonding type rmsd covalent geometry : bond 0.00349 (20197) covalent geometry : angle 0.47730 (27323) SS BOND : bond 0.00297 ( 2) SS BOND : angle 2.64783 ( 4) hydrogen bonds : bond 0.05901 ( 776) hydrogen bonds : angle 4.43701 ( 2181) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4991.86 seconds wall clock time: 86 minutes 12.30 seconds (5172.30 seconds total)