Starting phenix.real_space_refine on Sun Aug 11 04:22:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9m_14574/08_2024/7z9m_14574_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9m_14574/08_2024/7z9m_14574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9m_14574/08_2024/7z9m_14574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9m_14574/08_2024/7z9m_14574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9m_14574/08_2024/7z9m_14574_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9m_14574/08_2024/7z9m_14574_trim.cif" } resolution = 3.3 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= 0.002 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 64 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 9821 2.51 5 N 2840 2.21 5 O 3181 1.98 5 H 15371 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 706": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 31337 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 8213 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 21, 'TRANS': 495} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 6405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 6405 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 15, 'TRANS': 386} Chain: "C" Number of atoms: 8213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 8213 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 21, 'TRANS': 495} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 6405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 6405 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 15, 'TRANS': 386} Chain: "E" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 450 Classifications: {'DNA': 14} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 13} Chain: "F" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 448 Classifications: {'DNA': 14} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 13} Chain: "G" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 561 Classifications: {'DNA': 18} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 17} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 568 Classifications: {'DNA': 18} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 17} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IL1': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 15.83, per 1000 atoms: 0.51 Number of scatterers: 31337 At special positions: 0 Unit cell: (128.14, 139.32, 134.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 58 16.00 P 64 15.00 Mg 2 11.99 O 3181 8.00 N 2840 7.00 C 9821 6.00 H 15371 1.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 26.33 Conformation dependent library (CDL) restraints added in 3.0 seconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 23 sheets defined 51.7% alpha, 10.8% beta 7 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 13.48 Creating SS restraints... Processing helix chain 'A' and resid 13 through 32 removed outlier: 3.846A pdb=" N VAL A 30 " --> pdb=" O MET A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 55 Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 81 through 92 removed outlier: 3.891A pdb=" N VAL A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 122 Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.891A pdb=" N LEU A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 130 through 135' Processing helix chain 'A' and resid 164 through 170 Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.591A pdb=" N GLU A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N HIS A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 236 removed outlier: 4.313A pdb=" N GLU A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 283 Processing helix chain 'A' and resid 312 through 324 removed outlier: 3.614A pdb=" N VAL A 316 " --> pdb=" O VAL A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 388 removed outlier: 3.562A pdb=" N ALA A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 402 through 413 removed outlier: 4.033A pdb=" N ASN A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 removed outlier: 3.986A pdb=" N LEU A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 460 Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.528A pdb=" N LYS A 465 " --> pdb=" O ARG A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 494 removed outlier: 3.581A pdb=" N LEU A 474 " --> pdb=" O GLU A 470 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 514 Processing helix chain 'B' and resid 425 through 436 removed outlier: 3.570A pdb=" N GLY B 429 " --> pdb=" O GLY B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 464 removed outlier: 3.746A pdb=" N LEU B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 463 " --> pdb=" O ASP B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 475 Processing helix chain 'B' and resid 500 through 518 Processing helix chain 'B' and resid 518 through 525 removed outlier: 3.707A pdb=" N VAL B 522 " --> pdb=" O MET B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 561 removed outlier: 4.130A pdb=" N ALA B 551 " --> pdb=" O LYS B 547 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET B 552 " --> pdb=" O ASP B 548 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 561 " --> pdb=" O ILE B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 597 removed outlier: 3.552A pdb=" N MET B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 601 removed outlier: 3.645A pdb=" N TYR B 601 " --> pdb=" O GLU B 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 598 through 601' Processing helix chain 'B' and resid 602 through 610 removed outlier: 3.555A pdb=" N LEU B 606 " --> pdb=" O PRO B 602 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE B 610 " --> pdb=" O LEU B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 639 removed outlier: 4.171A pdb=" N TRP B 629 " --> pdb=" O THR B 625 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 630 " --> pdb=" O VAL B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.663A pdb=" N ILE B 682 " --> pdb=" O ASP B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 697 removed outlier: 3.794A pdb=" N ARG B 688 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 696 " --> pdb=" O THR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 731 removed outlier: 3.743A pdb=" N ALA B 722 " --> pdb=" O SER B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 734 No H-bonds generated for 'chain 'B' and resid 732 through 734' Processing helix chain 'B' and resid 741 through 745 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 769 through 782 removed outlier: 3.632A pdb=" N ALA B 773 " --> pdb=" O ASP B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 795 removed outlier: 3.831A pdb=" N ARG B 788 " --> pdb=" O ALA B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 801 Processing helix chain 'C' and resid 13 through 32 Processing helix chain 'C' and resid 42 through 55 Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.624A pdb=" N MET C 92 " --> pdb=" O THR C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 122 Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.772A pdb=" N LEU C 134 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 130 through 135' Processing helix chain 'C' and resid 164 through 170 Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 204 through 212 removed outlier: 3.506A pdb=" N GLU C 210 " --> pdb=" O GLU C 206 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N HIS C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 236 removed outlier: 3.512A pdb=" N GLU C 230 " --> pdb=" O ARG C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 283 Processing helix chain 'C' and resid 312 through 324 removed outlier: 3.571A pdb=" N TYR C 321 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER C 322 " --> pdb=" O ASN C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 389 removed outlier: 3.539A pdb=" N ILE C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 399 removed outlier: 3.889A pdb=" N HIS C 399 " --> pdb=" O GLU C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 412 Processing helix chain 'C' and resid 420 through 427 removed outlier: 3.695A pdb=" N ARG C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 427 " --> pdb=" O MET C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 460 Processing helix chain 'C' and resid 462 through 466 Processing helix chain 'C' and resid 467 through 493 removed outlier: 3.738A pdb=" N LEU C 474 " --> pdb=" O GLU C 470 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 475 " --> pdb=" O HIS C 471 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP C 483 " --> pdb=" O LYS C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 514 Processing helix chain 'D' and resid 425 through 435 removed outlier: 3.728A pdb=" N GLN D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY D 435 " --> pdb=" O SER D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 464 Processing helix chain 'D' and resid 465 through 475 Processing helix chain 'D' and resid 500 through 518 Processing helix chain 'D' and resid 518 through 525 removed outlier: 3.715A pdb=" N VAL D 522 " --> pdb=" O MET D 518 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY D 525 " --> pdb=" O ILE D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 561 Processing helix chain 'D' and resid 577 through 596 Processing helix chain 'D' and resid 602 through 610 removed outlier: 3.590A pdb=" N LEU D 606 " --> pdb=" O PRO D 602 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 609 " --> pdb=" O MET D 605 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE D 610 " --> pdb=" O LEU D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 621 removed outlier: 3.954A pdb=" N SER D 621 " --> pdb=" O GLU D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 640 removed outlier: 4.277A pdb=" N ARG D 628 " --> pdb=" O GLN D 624 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 684 Processing helix chain 'D' and resid 684 through 697 removed outlier: 3.570A pdb=" N ARG D 688 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 731 Processing helix chain 'D' and resid 741 through 745 removed outlier: 3.549A pdb=" N GLU D 744 " --> pdb=" O GLY D 741 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET D 745 " --> pdb=" O LEU D 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 741 through 745' Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 769 through 782 Processing helix chain 'D' and resid 784 through 795 removed outlier: 3.819A pdb=" N ARG D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.303A pdb=" N THR A 9 " --> pdb=" O ARG B 764 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N THR B 766 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL A 11 " --> pdb=" O THR B 766 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL B 527 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE B 493 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA B 530 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU B 420 " --> pdb=" O ILE B 494 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 174 Processing sheet with id=AA5, first strand: chain 'A' and resid 327 through 333 removed outlier: 4.786A pdb=" N TYR A 241 " --> pdb=" O ASN A 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 245 through 250 removed outlier: 3.821A pdb=" N GLU A 263 " --> pdb=" O ARG A 245 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLU A 247 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL A 261 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLU A 249 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE A 259 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLU A 257 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 307 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL A 304 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU A 292 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLU A 306 " --> pdb=" O SER A 290 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AA8, first strand: chain 'A' and resid 415 through 416 removed outlier: 3.600A pdb=" N TYR A 449 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY A 442 " --> pdb=" O TYR A 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 542 through 546 removed outlier: 4.010A pdb=" N GLN B 542 " --> pdb=" O LYS B 539 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 566 through 568 removed outlier: 4.054A pdb=" N LEU B 566 " --> pdb=" O GLU B 708 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 648 Processing sheet with id=AB3, first strand: chain 'B' and resid 651 through 653 Processing sheet with id=AB4, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.755A pdb=" N THR C 9 " --> pdb=" O MET D 762 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL D 527 " --> pdb=" O VAL D 765 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE D 493 " --> pdb=" O TYR D 528 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA D 530 " --> pdb=" O ILE D 493 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU D 420 " --> pdb=" O ILE D 494 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AB6, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB7, first strand: chain 'C' and resid 171 through 174 Processing sheet with id=AB8, first strand: chain 'C' and resid 327 through 333 removed outlier: 4.082A pdb=" N TYR C 241 " --> pdb=" O ASN C 224 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 245 through 250 removed outlier: 7.123A pdb=" N ARG C 245 " --> pdb=" O HIS C 262 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N GLU C 257 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL C 307 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 336 through 337 Processing sheet with id=AC2, first strand: chain 'C' and resid 415 through 416 Processing sheet with id=AC3, first strand: chain 'D' and resid 542 through 546 removed outlier: 4.055A pdb=" N GLN D 542 " --> pdb=" O LYS D 539 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 646 through 652 Processing sheet with id=AC5, first strand: chain 'D' and resid 706 through 707 removed outlier: 3.715A pdb=" N GLN D 714 " --> pdb=" O ILE D 707 " (cutoff:3.500A) 711 hydrogen bonds defined for protein. 2034 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 12.02 Time building geometry restraints manager: 27.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15363 1.03 - 1.23: 35 1.23 - 1.42: 6727 1.42 - 1.61: 9490 1.61 - 1.81: 109 Bond restraints: 31724 Sorted by residual: bond pdb=" OH PTR C 122 " pdb=" P PTR C 122 " ideal model delta sigma weight residual 1.769 1.610 0.159 2.00e-02 2.50e+03 6.31e+01 bond pdb=" OH PTR A 122 " pdb=" P PTR A 122 " ideal model delta sigma weight residual 1.769 1.613 0.156 2.00e-02 2.50e+03 6.06e+01 bond pdb=" C ALA A 412 " pdb=" N ASN A 413 " ideal model delta sigma weight residual 1.327 1.392 -0.065 1.71e-02 3.42e+03 1.45e+01 bond pdb=" C7 IL1 A 901 " pdb=" O3 IL1 A 901 " ideal model delta sigma weight residual 1.247 1.308 -0.061 2.00e-02 2.50e+03 9.33e+00 bond pdb=" O1P PTR C 122 " pdb=" P PTR C 122 " ideal model delta sigma weight residual 1.522 1.476 0.046 2.00e-02 2.50e+03 5.29e+00 ... (remaining 31719 not shown) Histogram of bond angle deviations from ideal: 100.04 - 115.71: 41128 115.71 - 131.39: 16301 131.39 - 147.06: 38 147.06 - 162.74: 0 162.74 - 178.41: 1 Bond angle restraints: 57468 Sorted by residual: angle pdb=" OH PTR C 122 " pdb=" P PTR C 122 " pdb=" O2P PTR C 122 " ideal model delta sigma weight residual 99.92 111.24 -11.32 3.00e+00 1.11e-01 1.42e+01 angle pdb=" OH PTR A 122 " pdb=" P PTR A 122 " pdb=" O2P PTR A 122 " ideal model delta sigma weight residual 99.92 109.57 -9.65 3.00e+00 1.11e-01 1.03e+01 angle pdb=" O3' DG E 7 " pdb=" C3' DG E 7 " pdb=" C2' DG E 7 " ideal model delta sigma weight residual 111.50 116.08 -4.58 1.50e+00 4.44e-01 9.33e+00 angle pdb=" O3' DA F 7 " pdb=" C3' DA F 7 " pdb=" C2' DA F 7 " ideal model delta sigma weight residual 111.50 115.81 -4.31 1.50e+00 4.44e-01 8.27e+00 angle pdb=" C ASP B 414 " pdb=" N PRO B 415 " pdb=" CA PRO B 415 " ideal model delta sigma weight residual 121.65 119.04 2.61 1.01e+00 9.80e-01 6.67e+00 ... (remaining 57463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.29: 13816 27.29 - 54.57: 584 54.57 - 81.86: 103 81.86 - 109.15: 5 109.15 - 136.44: 2 Dihedral angle restraints: 14510 sinusoidal: 8536 harmonic: 5974 Sorted by residual: dihedral pdb=" CA ARG A 32 " pdb=" C ARG A 32 " pdb=" N ALA A 33 " pdb=" CA ALA A 33 " ideal model delta harmonic sigma weight residual -180.00 -158.15 -21.85 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ASP A 297 " pdb=" C ASP A 297 " pdb=" N LYS A 298 " pdb=" CA LYS A 298 " ideal model delta harmonic sigma weight residual 180.00 158.55 21.45 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA ARG C 32 " pdb=" C ARG C 32 " pdb=" N ALA C 33 " pdb=" CA ALA C 33 " ideal model delta harmonic sigma weight residual 180.00 -161.03 -18.97 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 14507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1699 0.036 - 0.071: 595 0.071 - 0.106: 123 0.106 - 0.142: 80 0.142 - 0.177: 6 Chirality restraints: 2503 Sorted by residual: chirality pdb=" CA ILE A 163 " pdb=" N ILE A 163 " pdb=" C ILE A 163 " pdb=" CB ILE A 163 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CA ILE C 163 " pdb=" N ILE C 163 " pdb=" C ILE C 163 " pdb=" CB ILE C 163 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" CA ILE A 155 " pdb=" N ILE A 155 " pdb=" C ILE A 155 " pdb=" CB ILE A 155 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.18e-01 ... (remaining 2500 not shown) Planarity restraints: 4515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 IL1 A 901 " -0.246 2.00e-02 2.50e+03 1.23e-01 3.41e+02 pdb=" C29 IL1 A 901 " 0.023 2.00e-02 2.50e+03 pdb=" C30 IL1 A 901 " 0.073 2.00e-02 2.50e+03 pdb=" C31 IL1 A 901 " 0.105 2.00e-02 2.50e+03 pdb=" C32 IL1 A 901 " 0.092 2.00e-02 2.50e+03 pdb=" C33 IL1 A 901 " -0.050 2.00e-02 2.50e+03 pdb=" C34 IL1 A 901 " 0.105 2.00e-02 2.50e+03 pdb=" C35 IL1 A 901 " 0.075 2.00e-02 2.50e+03 pdb=" N8 IL1 A 901 " -0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C19 IL1 A 901 " -0.123 2.00e-02 2.50e+03 1.02e-01 1.30e+02 pdb=" C23 IL1 A 901 " 0.033 2.00e-02 2.50e+03 pdb=" C24 IL1 A 901 " -0.093 2.00e-02 2.50e+03 pdb=" N6 IL1 A 901 " 0.163 2.00e-02 2.50e+03 pdb=" O6 IL1 A 901 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C IL1 A 901 " 0.016 2.00e-02 2.50e+03 5.98e-02 8.93e+01 pdb=" O IL1 A 901 " 0.076 2.00e-02 2.50e+03 pdb=" C1 IL1 A 901 " -0.011 2.00e-02 2.50e+03 pdb=" C10 IL1 A 901 " -0.048 2.00e-02 2.50e+03 pdb=" C11 IL1 A 901 " -0.027 2.00e-02 2.50e+03 pdb=" C12 IL1 A 901 " 0.011 2.00e-02 2.50e+03 pdb=" C2 IL1 A 901 " 0.009 2.00e-02 2.50e+03 pdb=" C38 IL1 A 901 " 0.004 2.00e-02 2.50e+03 pdb=" N1 IL1 A 901 " 0.099 2.00e-02 2.50e+03 pdb=" O8 IL1 A 901 " -0.128 2.00e-02 2.50e+03 ... (remaining 4512 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.30: 4955 2.30 - 2.87: 69354 2.87 - 3.45: 71379 3.45 - 4.02: 98835 4.02 - 4.60: 154410 Nonbonded interactions: 398933 Sorted by model distance: nonbonded pdb=" O GLN D 749 " pdb=" HG1 THR D 753 " model vdw 1.722 2.450 nonbonded pdb="HD21 ASN B 569 " pdb=" O LEU B 700 " model vdw 1.725 2.450 nonbonded pdb="HH22 ARG B 516 " pdb=" OD1 ASP B 774 " model vdw 1.727 2.450 nonbonded pdb=" OD1 ASP B 622 " pdb=" HG1 THR B 653 " model vdw 1.730 2.450 nonbonded pdb="MG MG D 901 " pdb=" O HOH D1003 " model vdw 1.731 2.050 ... (remaining 398928 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 8 through 524) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.130 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: 0.450 Extract box with map and model: 1.250 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 112.170 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.159 16353 Z= 0.265 Angle : 0.629 11.324 22381 Z= 0.338 Chirality : 0.041 0.177 2503 Planarity : 0.005 0.123 2710 Dihedral : 14.233 136.435 6438 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.26 % Allowed : 3.03 % Favored : 96.71 % 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: 0.56 (0.20), residues: 1824 helix: 2.34 (0.18), residues: 831 sheet: -0.21 (0.40), residues: 180 loop : -1.71 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 647 HIS 0.004 0.001 HIS B 669 PHE 0.009 0.001 PHE D 777 TYR 0.013 0.001 TYR C 266 ARG 0.003 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 225 time to evaluate : 2.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7865 (mmm) cc_final: 0.7600 (mmt) REVERT: A 491 ILE cc_start: 0.7944 (mt) cc_final: 0.7627 (mt) REVERT: B 483 TYR cc_start: 0.7855 (t80) cc_final: 0.7603 (t80) REVERT: B 548 ASP cc_start: 0.8060 (t0) cc_final: 0.7822 (m-30) REVERT: B 581 GLU cc_start: 0.8429 (tt0) cc_final: 0.8090 (tm-30) REVERT: B 642 GLN cc_start: 0.6727 (pm20) cc_final: 0.6436 (mm-40) REVERT: D 593 MET cc_start: 0.7049 (mtt) cc_final: 0.6755 (mtt) outliers start: 4 outliers final: 2 residues processed: 228 average time/residue: 0.8143 time to fit residues: 251.5931 Evaluate side-chains 112 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 82 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 631 ASN D 591 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16353 Z= 0.215 Angle : 0.529 5.092 22381 Z= 0.295 Chirality : 0.040 0.141 2503 Planarity : 0.004 0.045 2710 Dihedral : 16.385 142.220 2790 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.52 % Allowed : 6.19 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.20), residues: 1824 helix: 2.52 (0.17), residues: 842 sheet: -0.06 (0.40), residues: 176 loop : -1.83 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 647 HIS 0.005 0.001 HIS A 262 PHE 0.017 0.001 PHE B 719 TYR 0.012 0.001 TYR C 266 ARG 0.004 0.000 ARG A 302 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7881 (mmm) cc_final: 0.7575 (mmt) REVERT: A 306 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6578 (mm-30) REVERT: B 483 TYR cc_start: 0.7835 (t80) cc_final: 0.7608 (t80) REVERT: B 581 GLU cc_start: 0.8344 (tt0) cc_final: 0.8067 (tm-30) outliers start: 8 outliers final: 7 residues processed: 130 average time/residue: 0.7178 time to fit residues: 135.0006 Evaluate side-chains 112 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 726 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 chunk 150 optimal weight: 0.0670 chunk 167 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS A 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16353 Z= 0.142 Angle : 0.477 5.741 22381 Z= 0.264 Chirality : 0.039 0.136 2503 Planarity : 0.004 0.043 2710 Dihedral : 16.225 141.372 2788 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.65 % Allowed : 6.97 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.20), residues: 1824 helix: 2.72 (0.18), residues: 846 sheet: 0.03 (0.39), residues: 175 loop : -1.79 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 629 HIS 0.004 0.001 HIS A 262 PHE 0.008 0.001 PHE B 681 TYR 0.010 0.001 TYR C 266 ARG 0.002 0.000 ARG D 689 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7877 (mmm) cc_final: 0.7545 (mmt) REVERT: B 581 GLU cc_start: 0.8348 (tt0) cc_final: 0.8057 (tm-30) outliers start: 10 outliers final: 7 residues processed: 113 average time/residue: 0.6610 time to fit residues: 109.6649 Evaluate side-chains 105 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 719 PHE Chi-restraints excluded: chain D residue 726 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16353 Z= 0.262 Angle : 0.527 7.835 22381 Z= 0.291 Chirality : 0.041 0.149 2503 Planarity : 0.004 0.043 2710 Dihedral : 16.238 142.330 2788 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.77 % Allowed : 7.23 % Favored : 92.00 % 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 (0.20), residues: 1824 helix: 2.58 (0.17), residues: 843 sheet: -0.27 (0.39), residues: 179 loop : -1.90 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 647 HIS 0.004 0.001 HIS A 262 PHE 0.008 0.001 PHE C 330 TYR 0.013 0.001 TYR C 266 ARG 0.003 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 2.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7894 (mmm) cc_final: 0.7571 (mmt) REVERT: B 581 GLU cc_start: 0.8359 (tt0) cc_final: 0.8078 (tm-30) outliers start: 12 outliers final: 10 residues processed: 111 average time/residue: 0.7288 time to fit residues: 115.8321 Evaluate side-chains 100 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 595 ASN Chi-restraints excluded: chain D residue 726 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 0.0020 chunk 133 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 153 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16353 Z= 0.159 Angle : 0.474 6.107 22381 Z= 0.263 Chirality : 0.039 0.139 2503 Planarity : 0.004 0.041 2710 Dihedral : 16.173 142.593 2788 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.71 % Allowed : 7.29 % Favored : 92.00 % 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: 0.82 (0.20), residues: 1824 helix: 2.71 (0.18), residues: 847 sheet: -0.22 (0.39), residues: 179 loop : -1.83 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 629 HIS 0.003 0.001 HIS C 78 PHE 0.009 0.001 PHE B 719 TYR 0.010 0.001 TYR C 266 ARG 0.002 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 2.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7861 (mmm) cc_final: 0.7523 (mmt) REVERT: B 581 GLU cc_start: 0.8356 (tt0) cc_final: 0.8079 (tm-30) REVERT: D 601 TYR cc_start: 0.7100 (m-80) cc_final: 0.6656 (m-80) outliers start: 11 outliers final: 8 residues processed: 108 average time/residue: 0.6696 time to fit residues: 107.0934 Evaluate side-chains 98 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 2.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 595 ASN Chi-restraints excluded: chain D residue 726 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16353 Z= 0.214 Angle : 0.497 6.566 22381 Z= 0.274 Chirality : 0.040 0.146 2503 Planarity : 0.004 0.040 2710 Dihedral : 16.254 142.875 2788 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.58 % Allowed : 7.94 % Favored : 91.48 % 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: 0.73 (0.20), residues: 1824 helix: 2.64 (0.17), residues: 850 sheet: -0.25 (0.39), residues: 179 loop : -1.89 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 647 HIS 0.004 0.001 HIS A 262 PHE 0.008 0.001 PHE D 681 TYR 0.011 0.001 TYR C 266 ARG 0.005 0.000 ARG D 712 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7891 (mmm) cc_final: 0.7559 (mmt) REVERT: B 581 GLU cc_start: 0.8365 (tt0) cc_final: 0.8097 (tm-30) outliers start: 9 outliers final: 8 residues processed: 111 average time/residue: 0.6714 time to fit residues: 108.2643 Evaluate side-chains 103 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 595 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 131 optimal weight: 0.1980 chunk 101 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: