Starting phenix.real_space_refine on Sun Aug 4 21:47:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ask_43817/08_2024/9ask_43817.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ask_43817/08_2024/9ask_43817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ask_43817/08_2024/9ask_43817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ask_43817/08_2024/9ask_43817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ask_43817/08_2024/9ask_43817.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ask_43817/08_2024/9ask_43817.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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 74 5.16 5 C 7414 2.51 5 N 1978 2.21 5 O 2098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 94": "OE1" <-> "OE2" Residue "A TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A GLU 685": "OE1" <-> "OE2" Residue "A GLU 736": "OE1" <-> "OE2" Residue "A PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 314": "OE1" <-> "OE2" Residue "B GLU 645": "OE1" <-> "OE2" Residue "B GLU 685": "OE1" <-> "OE2" Residue "B PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 11564 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5782 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 21, 'TRANS': 719} Chain breaks: 8 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 5782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5782 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 21, 'TRANS': 719} Chain breaks: 8 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 7.12, per 1000 atoms: 0.62 Number of scatterers: 11564 At special positions: 0 Unit cell: (153.64, 102.12, 84.64, 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 74 16.00 O 2098 8.00 N 1978 7.00 C 7414 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.85 Conformation dependent library (CDL) restraints added in 1.8 seconds 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 10 sheets defined 56.4% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 93 through 102 Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.740A pdb=" N GLY A 120 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 136 removed outlier: 4.062A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 162 Processing helix chain 'A' and resid 191 through 204 removed outlier: 3.870A pdb=" N GLY A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.910A pdb=" N GLY A 222 " --> pdb=" O HIS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 245 removed outlier: 3.697A pdb=" N LEU A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.968A pdb=" N LEU A 329 " --> pdb=" O HIS A 325 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N CYS A 330 " --> pdb=" O VAL A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 365 removed outlier: 4.039A pdb=" N GLU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.724A pdb=" N LYS A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 423 through 435 removed outlier: 3.512A pdb=" N ILE A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 449 removed outlier: 3.504A pdb=" N LEU A 446 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 448 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 removed outlier: 3.720A pdb=" N GLN A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 510 removed outlier: 4.129A pdb=" N LYS A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU A 507 " --> pdb=" O LYS A 503 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 540 removed outlier: 4.307A pdb=" N ARG A 533 " --> pdb=" O GLY A 529 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 536 " --> pdb=" O ILE A 532 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 555 removed outlier: 3.559A pdb=" N ALA A 554 " --> pdb=" O MET A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 563 removed outlier: 3.635A pdb=" N MET A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 592 removed outlier: 3.609A pdb=" N VAL A 586 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TRP A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 622 removed outlier: 3.540A pdb=" N LEU A 619 " --> pdb=" O GLY A 615 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 636 removed outlier: 3.671A pdb=" N LEU A 629 " --> pdb=" O PRO A 625 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 647 through 653 Processing helix chain 'A' and resid 665 through 676 Processing helix chain 'A' and resid 679 through 687 removed outlier: 4.055A pdb=" N VAL A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU A 685 " --> pdb=" O LYS A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 730 removed outlier: 3.675A pdb=" N ARG A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 Processing helix chain 'A' and resid 744 through 769 removed outlier: 3.995A pdb=" N SER A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 764 " --> pdb=" O GLY A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 779 Processing helix chain 'A' and resid 780 through 788 removed outlier: 3.506A pdb=" N LEU A 785 " --> pdb=" O PHE A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 807 through 813 Processing helix chain 'A' and resid 817 through 822 removed outlier: 3.531A pdb=" N ALA A 822 " --> pdb=" O VAL A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 835 removed outlier: 4.141A pdb=" N VAL A 831 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 832 " --> pdb=" O GLU A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 890 removed outlier: 3.730A pdb=" N LEU A 887 " --> pdb=" O ALA A 883 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN A 888 " --> pdb=" O ARG A 884 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A 890 " --> pdb=" O ILE A 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 94 through 101 Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 136 removed outlier: 4.488A pdb=" N VAL B 124 " --> pdb=" O GLY B 120 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 162 Processing helix chain 'B' and resid 191 through 204 removed outlier: 3.827A pdb=" N GLY B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 204 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 removed outlier: 3.931A pdb=" N GLY B 222 " --> pdb=" O HIS B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 245 removed outlier: 3.676A pdb=" N LEU B 230 " --> pdb=" O ARG B 226 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 245 " --> pdb=" O THR B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 325 through 335 removed outlier: 3.674A pdb=" N LEU B 329 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N CYS B 330 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS B 335 " --> pdb=" O TYR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 367 removed outlier: 3.739A pdb=" N ASN B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS B 365 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 402 through 407 removed outlier: 3.645A pdb=" N LYS B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 423 through 435 removed outlier: 3.551A pdb=" N ILE B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 449 removed outlier: 3.575A pdb=" N LEU B 446 " --> pdb=" O THR B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 478 removed outlier: 3.568A pdb=" N GLN B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 510 removed outlier: 4.103A pdb=" N LYS B 503 " --> pdb=" O SER B 499 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA B 506 " --> pdb=" O SER B 502 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU B 507 " --> pdb=" O LYS B 503 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 540 removed outlier: 4.364A pdb=" N ARG B 533 " --> pdb=" O GLY B 529 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 555 removed outlier: 3.541A pdb=" N ALA B 555 " --> pdb=" O HIS B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 563 removed outlier: 3.654A pdb=" N MET B 563 " --> pdb=" O LEU B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 592 removed outlier: 3.881A pdb=" N VAL B 586 " --> pdb=" O ILE B 582 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET B 587 " --> pdb=" O GLU B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 622 removed outlier: 3.524A pdb=" N LEU B 619 " --> pdb=" O GLY B 615 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 635 removed outlier: 3.655A pdb=" N LEU B 629 " --> pdb=" O PRO B 625 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 653 Processing helix chain 'B' and resid 665 through 676 Processing helix chain 'B' and resid 679 through 687 removed outlier: 4.047A pdb=" N VAL B 683 " --> pdb=" O SER B 679 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 684 " --> pdb=" O MET B 680 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU B 685 " --> pdb=" O LYS B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 729 removed outlier: 3.642A pdb=" N ARG B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 744 through 769 removed outlier: 3.981A pdb=" N SER B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 757 " --> pdb=" O GLN B 753 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 758 " --> pdb=" O SER B 754 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL B 764 " --> pdb=" O GLY B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 779 Processing helix chain 'B' and resid 780 through 788 removed outlier: 3.554A pdb=" N LEU B 785 " --> pdb=" O PHE B 781 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 787 " --> pdb=" O LYS B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 799 Processing helix chain 'B' and resid 807 through 813 Processing helix chain 'B' and resid 817 through 822 removed outlier: 3.514A pdb=" N ALA B 822 " --> pdb=" O VAL B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 835 removed outlier: 4.146A pdb=" N VAL B 831 " --> pdb=" O VAL B 827 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE B 832 " --> pdb=" O GLU B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 890 removed outlier: 3.733A pdb=" N LEU B 887 " --> pdb=" O ALA B 883 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN B 888 " --> pdb=" O ARG B 884 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP B 890 " --> pdb=" O ILE B 886 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 169 removed outlier: 7.501A pdb=" N ALA A 140 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N CYS A 189 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N PHE A 142 " --> pdb=" O CYS A 189 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LYS A 139 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET A 212 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET A 264 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL A 112 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR A 283 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 309 through 312 removed outlier: 4.047A pdb=" N ARG A 311 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU A 293 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU A 494 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER A 295 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 457 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE A 495 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE A 459 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU A 341 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 464 Processing sheet with id=AA4, first strand: chain 'A' and resid 595 through 598 removed outlier: 3.607A pdb=" N HIS A 610 " --> pdb=" O GLN A 596 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 598 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 608 " --> pdb=" O THR A 598 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 862 through 863 Processing sheet with id=AA6, first strand: chain 'B' and resid 168 through 169 removed outlier: 7.539A pdb=" N ALA B 140 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N CYS B 189 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N PHE B 142 " --> pdb=" O CYS B 189 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL B 112 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR B 283 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 309 through 312 removed outlier: 4.041A pdb=" N ARG B 311 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 457 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU B 341 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 463 through 464 removed outlier: 3.512A pdb=" N ARG B 467 " --> pdb=" O PHE B 464 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 595 through 598 removed outlier: 3.573A pdb=" N HIS B 610 " --> pdb=" O GLN B 596 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 598 " --> pdb=" O VAL B 608 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B 608 " --> pdb=" O THR B 598 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 862 through 863 499 hydrogen bonds defined for protein. 1422 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.94 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3758 1.34 - 1.46: 2552 1.46 - 1.58: 5336 1.58 - 1.70: 0 1.70 - 1.82: 118 Bond restraints: 11764 Sorted by residual: bond pdb=" CA ILE B 166 " pdb=" CB ILE B 166 " ideal model delta sigma weight residual 1.527 1.544 -0.017 1.31e-02 5.83e+03 1.71e+00 bond pdb=" CB ASN A 270 " pdb=" CG ASN A 270 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.58e+00 bond pdb=" CB ASN B 270 " pdb=" CG ASN B 270 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.52e+00 bond pdb=" CB ARG A 242 " pdb=" CG ARG A 242 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.38e+00 bond pdb=" SD MET A 477 " pdb=" CE MET A 477 " ideal model delta sigma weight residual 1.791 1.767 0.024 2.50e-02 1.60e+03 9.44e-01 ... (remaining 11759 not shown) Histogram of bond angle deviations from ideal: 98.90 - 105.92: 169 105.92 - 112.94: 6536 112.94 - 119.96: 3971 119.96 - 126.98: 5116 126.98 - 134.00: 120 Bond angle restraints: 15912 Sorted by residual: angle pdb=" CB MET B 477 " pdb=" CG MET B 477 " pdb=" SD MET B 477 " ideal model delta sigma weight residual 112.70 102.81 9.89 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CB ARG A 242 " pdb=" CG ARG A 242 " pdb=" CD ARG A 242 " ideal model delta sigma weight residual 111.30 117.79 -6.49 2.30e+00 1.89e-01 7.96e+00 angle pdb=" CB MET A 477 " pdb=" CG MET A 477 " pdb=" SD MET A 477 " ideal model delta sigma weight residual 112.70 104.28 8.42 3.00e+00 1.11e-01 7.88e+00 angle pdb=" CA LEU A 233 " pdb=" CB LEU A 233 " pdb=" CG LEU A 233 " ideal model delta sigma weight residual 116.30 125.95 -9.65 3.50e+00 8.16e-02 7.60e+00 angle pdb=" N VAL B 486 " pdb=" CA VAL B 486 " pdb=" C VAL B 486 " ideal model delta sigma weight residual 111.62 109.54 2.08 7.90e-01 1.60e+00 6.95e+00 ... (remaining 15907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.15: 5909 18.15 - 36.30: 895 36.30 - 54.44: 210 54.44 - 72.59: 43 72.59 - 90.74: 19 Dihedral angle restraints: 7076 sinusoidal: 2790 harmonic: 4286 Sorted by residual: dihedral pdb=" CA ASP B 630 " pdb=" CB ASP B 630 " pdb=" CG ASP B 630 " pdb=" OD1 ASP B 630 " ideal model delta sinusoidal sigma weight residual -30.00 -88.49 58.49 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP A 630 " pdb=" CB ASP A 630 " pdb=" CG ASP A 630 " pdb=" OD1 ASP A 630 " ideal model delta sinusoidal sigma weight residual -30.00 -88.25 58.25 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA LEU A 282 " pdb=" C LEU A 282 " pdb=" N TYR A 283 " pdb=" CA TYR A 283 " ideal model delta harmonic sigma weight residual 180.00 163.17 16.83 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 7073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1109 0.029 - 0.058: 512 0.058 - 0.086: 162 0.086 - 0.115: 74 0.115 - 0.144: 19 Chirality restraints: 1876 Sorted by residual: chirality pdb=" CA ASN A 270 " pdb=" N ASN A 270 " pdb=" C ASN A 270 " pdb=" CB ASN A 270 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA VAL B 732 " pdb=" N VAL B 732 " pdb=" C VAL B 732 " pdb=" CB VAL B 732 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA ASN B 270 " pdb=" N ASN B 270 " pdb=" C ASN B 270 " pdb=" CB ASN B 270 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 1873 not shown) Planarity restraints: 1990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 513 " 0.042 5.00e-02 4.00e+02 6.26e-02 6.28e+00 pdb=" N PRO A 514 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 514 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 514 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 513 " -0.041 5.00e-02 4.00e+02 6.12e-02 6.00e+00 pdb=" N PRO B 514 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 514 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 514 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 204 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" C GLU B 204 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU B 204 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN B 205 " -0.012 2.00e-02 2.50e+03 ... (remaining 1987 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3139 2.80 - 3.32: 11186 3.32 - 3.85: 19097 3.85 - 4.37: 21988 4.37 - 4.90: 36960 Nonbonded interactions: 92370 Sorted by model distance: nonbonded pdb=" NZ LYS B 236 " pdb=" OE1 GLU B 537 " model vdw 2.275 3.120 nonbonded pdb=" O ASP A 549 " pdb=" OG1 THR A 552 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR B 421 " pdb=" NH1 ARG B 745 " model vdw 2.282 3.120 nonbonded pdb=" OE2 GLU B 424 " pdb=" NH1 ARG B 745 " model vdw 2.292 3.120 nonbonded pdb=" OD2 ASP A 647 " pdb=" NH1 ARG A 784 " model vdw 2.296 3.120 ... (remaining 92365 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.550 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11764 Z= 0.186 Angle : 0.604 9.891 15912 Z= 0.297 Chirality : 0.040 0.144 1876 Planarity : 0.004 0.063 1990 Dihedral : 18.522 90.740 4292 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.40 % Allowed : 36.10 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.22), residues: 1446 helix: -0.43 (0.20), residues: 696 sheet: -0.02 (0.49), residues: 114 loop : -0.97 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 95 HIS 0.005 0.001 HIS B 417 PHE 0.025 0.001 PHE B 146 TYR 0.029 0.002 TYR A 283 ARG 0.006 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 238 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 508 LEU cc_start: 0.8185 (mm) cc_final: 0.7873 (mm) REVERT: B 438 ARG cc_start: 0.6362 (ttm-80) cc_final: 0.6037 (ttm-80) REVERT: B 493 ILE cc_start: 0.8725 (mt) cc_final: 0.8505 (mt) outliers start: 5 outliers final: 2 residues processed: 242 average time/residue: 0.2346 time to fit residues: 80.7300 Evaluate side-chains 190 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 188 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 862 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.1980 chunk 112 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 70 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 134 optimal weight: 0.0670 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN B 195 ASN B 219 HIS B 498 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11764 Z= 0.195 Angle : 0.624 8.555 15912 Z= 0.311 Chirality : 0.041 0.142 1876 Planarity : 0.004 0.044 1990 Dihedral : 4.334 35.426 1583 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 5.27 % Allowed : 32.83 % Favored : 61.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.21), residues: 1446 helix: -0.27 (0.18), residues: 790 sheet: -0.01 (0.46), residues: 120 loop : -1.58 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 673 HIS 0.006 0.001 HIS B 417 PHE 0.019 0.001 PHE A 464 TYR 0.025 0.002 TYR A 283 ARG 0.009 0.001 ARG A 696 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 199 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.6752 (tm-30) cc_final: 0.6088 (tt0) REVERT: A 226 ARG cc_start: 0.7532 (ptp90) cc_final: 0.7229 (ptp90) REVERT: A 264 MET cc_start: 0.6176 (mpp) cc_final: 0.5917 (mpp) REVERT: A 483 ARG cc_start: 0.6809 (mpt-90) cc_final: 0.6571 (mtm-85) REVERT: A 531 MET cc_start: 0.6195 (tpp) cc_final: 0.5931 (ttt) REVERT: A 835 ASN cc_start: 0.7753 (m110) cc_final: 0.7465 (t0) REVERT: B 835 ASN cc_start: 0.7801 (m110) cc_final: 0.7516 (t0) outliers start: 66 outliers final: 39 residues processed: 241 average time/residue: 0.2335 time to fit residues: 80.1376 Evaluate side-chains 217 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 178 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 833 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 9.9990 chunk 41 optimal weight: 0.0170 chunk 111 optimal weight: 0.0040 chunk 91 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 chunk 133 optimal weight: 0.1980 chunk 45 optimal weight: 0.3980 chunk 108 optimal weight: 0.8980 overall best weight: 0.2830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 GLN A 596 GLN A 649 HIS ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 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 0.026 11764 Z= 0.167 Angle : 0.576 7.595 15912 Z= 0.284 Chirality : 0.040 0.160 1876 Planarity : 0.004 0.042 1990 Dihedral : 4.103 19.446 1580 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.71 % Allowed : 32.75 % Favored : 62.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.21), residues: 1446 helix: -0.05 (0.18), residues: 808 sheet: 0.14 (0.43), residues: 130 loop : -1.68 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 74 HIS 0.005 0.001 HIS B 649 PHE 0.014 0.001 PHE B 343 TYR 0.022 0.001 TYR A 283 ARG 0.004 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 192 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.6715 (tm-30) cc_final: 0.6202 (tt0) REVERT: A 226 ARG cc_start: 0.7502 (ptp90) cc_final: 0.7125 (ptp90) REVERT: A 242 ARG cc_start: 0.7301 (ttp80) cc_final: 0.7060 (tmm160) REVERT: A 307 MET cc_start: 0.4295 (mmp) cc_final: 0.3977 (mmp) REVERT: A 531 MET cc_start: 0.6127 (tpp) cc_final: 0.5869 (ttt) REVERT: A 835 ASN cc_start: 0.7757 (m110) cc_final: 0.7501 (t0) REVERT: B 309 LEU cc_start: 0.8402 (tt) cc_final: 0.8157 (tp) REVERT: B 493 ILE cc_start: 0.8649 (mt) cc_final: 0.8419 (mt) REVERT: B 668 ARG cc_start: 0.7350 (ttp-110) cc_final: 0.6901 (ttt-90) REVERT: B 835 ASN cc_start: 0.7819 (m110) cc_final: 0.7524 (t0) outliers start: 59 outliers final: 39 residues processed: 232 average time/residue: 0.2345 time to fit residues: 78.5329 Evaluate side-chains 220 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 181 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 303 TYR Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 833 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 69 optimal weight: 0.0060 chunk 14 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 143 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN B 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11764 Z= 0.212 Angle : 0.584 9.566 15912 Z= 0.286 Chirality : 0.041 0.138 1876 Planarity : 0.004 0.036 1990 Dihedral : 4.153 18.362 1580 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 6.15 % Allowed : 32.99 % Favored : 60.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.21), residues: 1446 helix: 0.02 (0.18), residues: 812 sheet: -0.57 (0.39), residues: 152 loop : -1.67 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 588 HIS 0.006 0.001 HIS A 416 PHE 0.020 0.001 PHE B 146 TYR 0.024 0.002 TYR A 283 ARG 0.006 0.000 ARG A 696 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 184 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.6821 (tm-30) cc_final: 0.6272 (tt0) REVERT: A 226 ARG cc_start: 0.7531 (ptp90) cc_final: 0.7210 (ptp90) REVERT: A 308 LYS cc_start: 0.7300 (ttmm) cc_final: 0.7040 (tttm) REVERT: A 493 ILE cc_start: 0.8647 (mt) cc_final: 0.8408 (mt) REVERT: A 835 ASN cc_start: 0.7813 (m110) cc_final: 0.7476 (t0) REVERT: B 680 MET cc_start: 0.6483 (tpp) cc_final: 0.6273 (tpp) REVERT: B 835 ASN cc_start: 0.7839 (m110) cc_final: 0.7490 (t0) outliers start: 77 outliers final: 55 residues processed: 236 average time/residue: 0.2127 time to fit residues: 73.9467 Evaluate side-chains 227 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 172 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 303 TYR Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 833 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.0060 chunk 81 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 106 optimal weight: 0.0980 chunk 59 optimal weight: 0.6980 chunk 122 optimal weight: 0.0970 chunk 98 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11764 Z= 0.162 Angle : 0.571 10.324 15912 Z= 0.274 Chirality : 0.040 0.132 1876 Planarity : 0.003 0.034 1990 Dihedral : 4.061 19.963 1580 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 5.67 % Allowed : 33.79 % Favored : 60.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.21), residues: 1446 helix: 0.15 (0.18), residues: 818 sheet: -0.44 (0.41), residues: 136 loop : -1.65 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 588 HIS 0.005 0.001 HIS A 417 PHE 0.019 0.001 PHE A 146 TYR 0.020 0.001 TYR A 283 ARG 0.003 0.000 ARG B 396 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 189 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.6774 (tm-30) cc_final: 0.6224 (tt0) REVERT: A 226 ARG cc_start: 0.7510 (ptp90) cc_final: 0.7184 (ptp90) REVERT: A 308 LYS cc_start: 0.7326 (ttmm) cc_final: 0.7053 (tttm) REVERT: A 493 ILE cc_start: 0.8635 (mt) cc_final: 0.8401 (mt) REVERT: A 685 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: A 835 ASN cc_start: 0.7784 (m110) cc_final: 0.7471 (t0) REVERT: B 685 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: B 835 ASN cc_start: 0.7845 (m110) cc_final: 0.7514 (t0) outliers start: 71 outliers final: 46 residues processed: 234 average time/residue: 0.2239 time to fit residues: 76.1162 Evaluate side-chains 225 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 177 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 303 TYR Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 833 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.0570 chunk 128 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 83 optimal weight: 0.0980 chunk 35 optimal weight: 0.0370 chunk 143 optimal weight: 0.0170 chunk 118 optimal weight: 0.0980 chunk 66 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 overall best weight: 0.0614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN B 257 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11764 Z= 0.139 Angle : 0.571 9.062 15912 Z= 0.277 Chirality : 0.039 0.135 1876 Planarity : 0.003 0.038 1990 Dihedral : 3.948 18.868 1580 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.73 % Favored : 96.13 % Rotamer: Outliers : 4.95 % Allowed : 33.71 % Favored : 61.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.21), residues: 1446 helix: 0.26 (0.18), residues: 820 sheet: -0.16 (0.41), residues: 136 loop : -1.66 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 673 HIS 0.005 0.001 HIS A 417 PHE 0.019 0.001 PHE A 464 TYR 0.015 0.001 TYR A 283 ARG 0.006 0.000 ARG A 483 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 193 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.4323 (ppp) cc_final: 0.4123 (ppp) REVERT: A 135 GLU cc_start: 0.6784 (tm-30) cc_final: 0.6176 (tt0) REVERT: A 142 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.7426 (t80) REVERT: A 226 ARG cc_start: 0.7409 (ptp90) cc_final: 0.7114 (ptp90) REVERT: A 308 LYS cc_start: 0.7347 (ttmm) cc_final: 0.7078 (tttm) REVERT: A 388 LEU cc_start: 0.6101 (mt) cc_final: 0.5832 (mt) REVERT: A 685 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: A 717 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.6842 (mmtt) REVERT: A 835 ASN cc_start: 0.7760 (m110) cc_final: 0.7457 (t0) REVERT: B 411 TRP cc_start: 0.3765 (OUTLIER) cc_final: 0.2997 (m-10) REVERT: B 681 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7497 (mtmm) REVERT: B 835 ASN cc_start: 0.7879 (m110) cc_final: 0.7539 (t0) outliers start: 62 outliers final: 39 residues processed: 233 average time/residue: 0.2319 time to fit residues: 76.9926 Evaluate side-chains 230 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 186 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 717 LYS Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 411 TRP Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 681 LYS Chi-restraints excluded: chain B residue 717 LYS Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 833 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.0570 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 88 optimal weight: 0.3980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11764 Z= 0.189 Angle : 0.578 8.704 15912 Z= 0.278 Chirality : 0.040 0.146 1876 Planarity : 0.003 0.039 1990 Dihedral : 3.984 18.287 1580 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.01 % Favored : 95.85 % Rotamer: Outliers : 4.47 % Allowed : 33.79 % Favored : 61.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1446 helix: 0.23 (0.18), residues: 820 sheet: -0.42 (0.38), residues: 152 loop : -1.67 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 95 HIS 0.005 0.001 HIS A 417 PHE 0.017 0.001 PHE A 161 TYR 0.023 0.001 TYR A 283 ARG 0.004 0.000 ARG B 668 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 184 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.6813 (tm-30) cc_final: 0.6267 (tt0) REVERT: A 142 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.7447 (t80) REVERT: A 226 ARG cc_start: 0.7488 (ptp90) cc_final: 0.7179 (ptp90) REVERT: A 308 LYS cc_start: 0.7387 (ttmm) cc_final: 0.7109 (tttm) REVERT: A 388 LEU cc_start: 0.6169 (mt) cc_final: 0.5925 (mt) REVERT: A 411 TRP cc_start: 0.4002 (OUTLIER) cc_final: 0.3300 (m-10) REVERT: A 685 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: A 835 ASN cc_start: 0.7751 (m110) cc_final: 0.7445 (t0) REVERT: B 386 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6882 (tp30) REVERT: B 835 ASN cc_start: 0.7855 (m110) cc_final: 0.7516 (t0) outliers start: 56 outliers final: 46 residues processed: 221 average time/residue: 0.2346 time to fit residues: 74.5850 Evaluate side-chains 227 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 177 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 303 TYR Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 833 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 129 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11764 Z= 0.218 Angle : 0.611 12.321 15912 Z= 0.293 Chirality : 0.041 0.153 1876 Planarity : 0.004 0.036 1990 Dihedral : 4.111 17.827 1580 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.77 % Favored : 95.09 % Rotamer: Outliers : 5.11 % Allowed : 33.87 % Favored : 61.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.21), residues: 1446 helix: 0.16 (0.18), residues: 820 sheet: -0.17 (0.43), residues: 122 loop : -1.66 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 588 HIS 0.006 0.001 HIS A 417 PHE 0.016 0.001 PHE B 146 TYR 0.024 0.002 TYR A 283 ARG 0.004 0.000 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 184 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.6888 (tm-30) cc_final: 0.6300 (tt0) REVERT: A 142 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7280 (t80) REVERT: A 226 ARG cc_start: 0.7514 (ptp90) cc_final: 0.7215 (ptp90) REVERT: A 308 LYS cc_start: 0.7425 (ttmm) cc_final: 0.7123 (tttm) REVERT: A 388 LEU cc_start: 0.6200 (mt) cc_final: 0.5923 (mt) REVERT: A 411 TRP cc_start: 0.3975 (OUTLIER) cc_final: 0.3331 (m-10) REVERT: A 668 ARG cc_start: 0.7576 (ttp-110) cc_final: 0.7141 (ttp80) REVERT: A 685 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: A 835 ASN cc_start: 0.7836 (m110) cc_final: 0.7491 (t0) REVERT: B 386 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7007 (tp30) REVERT: B 835 ASN cc_start: 0.7868 (m110) cc_final: 0.7505 (t0) outliers start: 64 outliers final: 54 residues processed: 224 average time/residue: 0.2231 time to fit residues: 73.5326 Evaluate side-chains 234 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 176 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 833 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 132 optimal weight: 0.3980 chunk 80 optimal weight: 0.9990 chunk 57 optimal weight: 0.0570 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 120 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11764 Z= 0.181 Angle : 0.599 10.145 15912 Z= 0.286 Chirality : 0.040 0.131 1876 Planarity : 0.003 0.035 1990 Dihedral : 4.062 19.339 1580 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.15 % Favored : 95.71 % Rotamer: Outliers : 5.35 % Allowed : 33.47 % Favored : 61.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.21), residues: 1446 helix: 0.21 (0.18), residues: 818 sheet: 0.05 (0.44), residues: 116 loop : -1.73 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 95 HIS 0.005 0.001 HIS A 416 PHE 0.015 0.001 PHE B 146 TYR 0.020 0.002 TYR B 667 ARG 0.006 0.000 ARG B 798 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 177 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.6940 (tm-30) cc_final: 0.6351 (tt0) REVERT: A 142 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7335 (t80) REVERT: A 226 ARG cc_start: 0.7469 (ptp90) cc_final: 0.7161 (ptp90) REVERT: A 308 LYS cc_start: 0.7416 (ttmm) cc_final: 0.7120 (tttm) REVERT: A 388 LEU cc_start: 0.6169 (mt) cc_final: 0.5927 (mt) REVERT: A 411 TRP cc_start: 0.3965 (OUTLIER) cc_final: 0.3295 (m-10) REVERT: A 685 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: A 835 ASN cc_start: 0.7836 (m110) cc_final: 0.7484 (t0) REVERT: B 386 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6952 (tp30) REVERT: B 411 TRP cc_start: 0.3870 (OUTLIER) cc_final: 0.3080 (m-10) REVERT: B 835 ASN cc_start: 0.7876 (m110) cc_final: 0.7495 (t0) outliers start: 67 outliers final: 58 residues processed: 220 average time/residue: 0.2160 time to fit residues: 70.5598 Evaluate side-chains 236 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 173 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 411 TRP Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 717 LYS Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 833 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 97 optimal weight: 0.0170 chunk 147 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 93 optimal weight: 0.3980 chunk 125 optimal weight: 0.1980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11764 Z= 0.177 Angle : 0.603 10.126 15912 Z= 0.286 Chirality : 0.040 0.142 1876 Planarity : 0.003 0.035 1990 Dihedral : 4.020 18.082 1580 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.50 % Favored : 95.37 % Rotamer: Outliers : 4.79 % Allowed : 34.35 % Favored : 60.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.21), residues: 1446 helix: 0.24 (0.18), residues: 818 sheet: 0.01 (0.41), residues: 130 loop : -1.74 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 95 HIS 0.006 0.001 HIS A 417 PHE 0.015 0.001 PHE B 146 TYR 0.020 0.001 TYR A 283 ARG 0.005 0.000 ARG B 798 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 182 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6342 (tt0) REVERT: A 142 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7382 (t80) REVERT: A 226 ARG cc_start: 0.7457 (ptp90) cc_final: 0.7126 (ptp90) REVERT: A 308 LYS cc_start: 0.7445 (ttmm) cc_final: 0.7134 (tttm) REVERT: A 411 TRP cc_start: 0.3919 (OUTLIER) cc_final: 0.3151 (m-10) REVERT: A 463 ILE cc_start: 0.7078 (mm) cc_final: 0.6876 (mm) REVERT: A 685 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6907 (mp0) REVERT: B 386 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6952 (tp30) REVERT: B 411 TRP cc_start: 0.3818 (OUTLIER) cc_final: 0.3039 (m-10) outliers start: 60 outliers final: 53 residues processed: 219 average time/residue: 0.2176 time to fit residues: 70.7931 Evaluate side-chains 235 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 177 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 411 TRP Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 833 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.0570 chunk 108 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 120 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 ASN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.208666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.176246 restraints weight = 16432.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.181430 restraints weight = 9448.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.184919 restraints weight = 6459.752| |-----------------------------------------------------------------------------| r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11764 Z= 0.195 Angle : 0.614 10.201 15912 Z= 0.292 Chirality : 0.041 0.176 1876 Planarity : 0.004 0.036 1990 Dihedral : 4.060 18.920 1580 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.50 % Favored : 95.37 % Rotamer: Outliers : 5.43 % Allowed : 34.03 % Favored : 60.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.22), residues: 1446 helix: 0.28 (0.18), residues: 806 sheet: -0.01 (0.41), residues: 130 loop : -1.60 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 95 HIS 0.006 0.001 HIS A 417 PHE 0.016 0.001 PHE B 146 TYR 0.019 0.002 TYR A 283 ARG 0.005 0.000 ARG A 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2592.85 seconds wall clock time: 47 minutes 9.50 seconds (2829.50 seconds total)