Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 20 08:18:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr6_27672/10_2023/8dr6_27672_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr6_27672/10_2023/8dr6_27672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr6_27672/10_2023/8dr6_27672.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr6_27672/10_2023/8dr6_27672.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr6_27672/10_2023/8dr6_27672_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr6_27672/10_2023/8dr6_27672_trim_updated.pdb" } resolution = 2.39 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= -0.001 sd= 0.043 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 77 5.49 5 Mg 4 5.21 5 S 101 5.16 5 C 13683 2.51 5 N 3753 2.21 5 O 4380 1.98 5 H 21632 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 295": "OD1" <-> "OD2" Residue "A ASP 397": "OD1" <-> "OD2" Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 472": "OD1" <-> "OD2" Residue "A ASP 584": "OD1" <-> "OD2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A GLU 616": "OE1" <-> "OE2" Residue "A TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 697": "OD1" <-> "OD2" Residue "A ASP 733": "OD1" <-> "OD2" Residue "A ASP 753": "OD1" <-> "OD2" Residue "A TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 13": "OE1" <-> "OE2" Residue "B ASP 22": "OD1" <-> "OD2" Residue "B ASP 39": "OD1" <-> "OD2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B ASP 73": "OD1" <-> "OD2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C GLU 194": "OE1" <-> "OE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C GLU 332": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D ASP 148": "OD1" <-> "OD2" Residue "D ASP 178": "OD1" <-> "OD2" Residue "D ASP 199": "OD1" <-> "OD2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "D ASP 214": "OD1" <-> "OD2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "D ASP 279": "OD1" <-> "OD2" Residue "D ASP 281": "OD1" <-> "OD2" Residue "D PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 6": "OD1" <-> "OD2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E ASP 35": "OD1" <-> "OD2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "E ASP 105": "OD1" <-> "OD2" Residue "E GLU 115": "OE1" <-> "OE2" Residue "E ASP 172": "OD1" <-> "OD2" Residue "E ASP 195": "OD1" <-> "OD2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E GLU 302": "OE1" <-> "OE2" Residue "E GLU 323": "OE1" <-> "OE2" Residue "F GLU 7": "OE1" <-> "OE2" Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 42": "OD1" <-> "OD2" Residue "F GLU 51": "OE1" <-> "OE2" Residue "F PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 59": "OE1" <-> "OE2" Residue "F ASP 63": "OD1" <-> "OD2" Residue "F ASP 71": "OD1" <-> "OD2" Residue "F ASP 93": "OD1" <-> "OD2" Residue "F GLU 113": "OE1" <-> "OE2" Residue "F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 150": "OD1" <-> "OD2" Residue "F ASP 172": "OD1" <-> "OD2" Residue "F ASP 204": "OD1" <-> "OD2" Residue "F ASP 214": "OD1" <-> "OD2" Residue "F GLU 232": "OE1" <-> "OE2" Residue "F PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 3": "OE1" <-> "OE2" Residue "G GLU 7": "OE1" <-> "OE2" Residue "G GLU 8": "OE1" <-> "OE2" Residue "G PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G ASP 93": "OD1" <-> "OD2" Residue "G GLU 104": "OE1" <-> "OE2" Residue "G ASP 105": "OD1" <-> "OD2" Residue "G TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 232": "OE1" <-> "OE2" Residue "G PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 8": "OE1" <-> "OE2" Residue "H ASP 21": "OD1" <-> "OD2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H ASP 33": "OD1" <-> "OD2" Residue "H ASP 42": "OD1" <-> "OD2" Residue "H GLU 55": "OE1" <-> "OE2" Residue "H GLU 59": "OE1" <-> "OE2" Residue "H ASP 97": "OD1" <-> "OD2" Residue "H ASP 105": "OD1" <-> "OD2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H ASP 120": "OD1" <-> "OD2" Residue "H GLU 143": "OE1" <-> "OE2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "H ASP 172": "OD1" <-> "OD2" Residue "H ASP 174": "OD1" <-> "OD2" Residue "H GLU 189": "OE1" <-> "OE2" Residue "H GLU 198": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 43630 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 7845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 7845 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 19, 'TRANS': 473} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 5084 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain: "C" Number of atoms: 5263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5263 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "D" Number of atoms: 5457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 5457 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 330} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5698 Classifications: {'peptide': 354} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 339} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 4055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 4055 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 4047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 4047 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain: "H" Number of atoms: 4023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 4023 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "I" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 1012 Classifications: {'DNA': 32} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 31} Chain: "J" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 553 Classifications: {'DNA': 18} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 17} Chain: "K" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 426 Classifications: {'DNA': 13} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 19.06, per 1000 atoms: 0.44 Number of scatterers: 43630 At special positions: 0 Unit cell: (132.986, 119.77, 144.55, 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 101 16.00 P 77 15.00 Mg 4 11.99 O 4380 8.00 N 3753 7.00 C 13683 6.00 H 21632 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=0, symmetry=0 Time building additional restraints: 37.19 Conformation dependent library (CDL) restraints added in 3.4 seconds 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 18 sheets defined 46.6% alpha, 15.3% beta 20 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 20.83 Creating SS restraints... Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 298 through 301 No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 314 through 325 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 359 through 369 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 392 through 397 removed outlier: 4.489A pdb=" N ASP A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 437 through 446 Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 480 through 494 removed outlier: 4.289A pdb=" N SER A 485 " --> pdb=" O ASN A 481 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ARG A 486 " --> pdb=" O SER A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 509 removed outlier: 4.244A pdb=" N ASP A 504 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 526 removed outlier: 3.686A pdb=" N THR A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 542 Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 566 through 571 Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'A' and resid 588 through 595 Processing helix chain 'A' and resid 610 through 631 Processing helix chain 'A' and resid 638 through 648 Proline residue: A 642 - end of helix removed outlier: 3.796A pdb=" N SER A 648 " --> pdb=" O ALA A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 656 removed outlier: 3.504A pdb=" N VAL A 656 " --> pdb=" O PRO A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 689 Processing helix chain 'A' and resid 698 through 703 Processing helix chain 'A' and resid 705 through 713 removed outlier: 3.727A pdb=" N LYS A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 735 removed outlier: 4.358A pdb=" N GLN A 720 " --> pdb=" O PHE A 717 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLY A 721 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA A 722 " --> pdb=" O LYS A 719 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 724 " --> pdb=" O GLY A 721 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A 725 " --> pdb=" O ALA A 722 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER A 726 " --> pdb=" O ASP A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 747 Processing helix chain 'A' and resid 751 through 753 No H-bonds generated for 'chain 'A' and resid 751 through 753' Processing helix chain 'A' and resid 756 through 760 Processing helix chain 'A' and resid 764 through 775 Processing helix chain 'B' and resid 11 through 14 No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 55 through 74 removed outlier: 7.917A pdb=" N ARG B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N SER B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ALA B 72 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ASP B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 98 removed outlier: 3.761A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 121 through 133 removed outlier: 3.569A pdb=" N ARG B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.519A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 182 Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 202 through 215 Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 245 through 255 Processing helix chain 'B' and resid 263 through 276 removed outlier: 3.521A pdb=" N ASN B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 300 Processing helix chain 'B' and resid 306 through 319 Processing helix chain 'C' and resid 10 through 12 No H-bonds generated for 'chain 'C' and resid 10 through 12' Processing helix chain 'C' and resid 15 through 18 No H-bonds generated for 'chain 'C' and resid 15 through 18' Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 31 through 42 Processing helix chain 'C' and resid 59 through 71 Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 90 through 102 removed outlier: 4.044A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 124 through 136 removed outlier: 4.530A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 155 through 160 removed outlier: 3.543A pdb=" N ARG C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 185 Processing helix chain 'C' and resid 191 through 199 Processing helix chain 'C' and resid 205 through 218 Processing helix chain 'C' and resid 229 through 236 Processing helix chain 'C' and resid 241 through 253 Processing helix chain 'C' and resid 256 through 270 removed outlier: 4.243A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 removed outlier: 4.018A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 312 removed outlier: 3.590A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 334 removed outlier: 4.107A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLU C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 24 removed outlier: 3.623A pdb=" N GLN D 24 " --> pdb=" O GLN D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 30 No H-bonds generated for 'chain 'D' and resid 27 through 30' Processing helix chain 'D' and resid 36 through 38 No H-bonds generated for 'chain 'D' and resid 36 through 38' Processing helix chain 'D' and resid 43 through 55 removed outlier: 4.435A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 91 Proline residue: D 85 - end of helix removed outlier: 5.053A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.822A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 147 through 159 removed outlier: 3.815A pdb=" N ARG D 154 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 198 through 207 Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 228 through 245 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 265 through 277 Processing helix chain 'D' and resid 280 through 293 removed outlier: 3.788A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER D 293 " --> pdb=" O THR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 309 Processing helix chain 'D' and resid 316 through 335 removed outlier: 3.507A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 352 Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 20 through 30 Processing helix chain 'E' and resid 33 through 35 No H-bonds generated for 'chain 'E' and resid 33 through 35' Processing helix chain 'E' and resid 49 through 61 Processing helix chain 'E' and resid 63 through 66 Processing helix chain 'E' and resid 98 through 110 removed outlier: 6.870A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG E 106 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 117 Processing helix chain 'E' and resid 143 through 145 No H-bonds generated for 'chain 'E' and resid 143 through 145' Processing helix chain 'E' and resid 148 through 160 removed outlier: 4.562A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 184 Processing helix chain 'E' and resid 195 through 209 Processing helix chain 'E' and resid 217 through 226 Processing helix chain 'E' and resid 230 through 242 Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 276 through 292 removed outlier: 3.515A pdb=" N ALA E 284 " --> pdb=" O ILE E 280 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N HIS E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 307 Processing helix chain 'E' and resid 315 through 333 Processing helix chain 'E' and resid 338 through 353 Processing helix chain 'F' and resid 10 through 19 removed outlier: 3.895A pdb=" N PHE F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 56 No H-bonds generated for 'chain 'F' and resid 54 through 56' Processing helix chain 'F' and resid 72 through 79 Processing helix chain 'F' and resid 141 through 152 Processing helix chain 'F' and resid 191 through 193 No H-bonds generated for 'chain 'F' and resid 191 through 193' Processing helix chain 'F' and resid 209 through 220 removed outlier: 3.943A pdb=" N LYS F 217 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY F 218 " --> pdb=" O ASP F 214 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N SER F 219 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER F 220 " --> pdb=" O ILE F 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 18 Processing helix chain 'G' and resid 54 through 56 No H-bonds generated for 'chain 'G' and resid 54 through 56' Processing helix chain 'G' and resid 72 through 81 removed outlier: 3.984A pdb=" N CYS G 81 " --> pdb=" O LYS G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'G' and resid 191 through 193 No H-bonds generated for 'chain 'G' and resid 191 through 193' Processing helix chain 'G' and resid 209 through 220 removed outlier: 3.709A pdb=" N LYS G 217 " --> pdb=" O LEU G 213 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLY G 218 " --> pdb=" O ASP G 214 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N SER G 219 " --> pdb=" O ILE G 215 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N SER G 220 " --> pdb=" O ILE G 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 19 removed outlier: 3.872A pdb=" N PHE H 19 " --> pdb=" O ILE H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 79 Processing helix chain 'H' and resid 141 through 151 Processing helix chain 'H' and resid 209 through 220 removed outlier: 3.788A pdb=" N LYS H 217 " --> pdb=" O LEU H 213 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLY H 218 " --> pdb=" O ASP H 214 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER H 219 " --> pdb=" O ILE H 215 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N SER H 220 " --> pdb=" O ILE H 216 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 471 through 475 removed outlier: 6.502A pdb=" N LEU A 451 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU A 351 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU A 453 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLY A 353 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N CYS A 455 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE A 452 " --> pdb=" O PHE A 419 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE A 421 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE A 454 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N MET A 423 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASP A 373 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE A 422 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A 375 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 599 through 601 Processing sheet with id= C, first strand: chain 'B' and resid 159 through 162 removed outlier: 6.354A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 162 through 166 removed outlier: 6.473A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 185 through 189 removed outlier: 6.394A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 186 through 190 removed outlier: 6.283A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 69 through 76 Processing sheet with id= H, first strand: chain 'F' and resid 59 through 62 removed outlier: 3.817A pdb=" N GLU F 59 " --> pdb=" O LYS F 5 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.616A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLN F 38 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 203 through 208 removed outlier: 6.065A pdb=" N SER F 157 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASP F 172 " --> pdb=" O SER F 157 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 59 through 62 removed outlier: 3.720A pdb=" N GLU G 59 " --> pdb=" O LYS G 5 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 66 through 71 removed outlier: 6.669A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 203 through 208 removed outlier: 5.553A pdb=" N SER G 157 " --> pdb=" O ASP G 172 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASP G 172 " --> pdb=" O SER G 157 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 2 through 6 Processing sheet with id= O, first strand: chain 'H' and resid 25 through 30 Processing sheet with id= P, first strand: chain 'H' and resid 34 through 40 removed outlier: 4.462A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 98 through 105 Processing sheet with id= R, first strand: chain 'H' and resid 203 through 208 removed outlier: 6.163A pdb=" N SER H 157 " --> pdb=" O ASP H 172 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASP H 172 " --> pdb=" O SER H 157 " (cutoff:3.500A) 961 hydrogen bonds defined for protein. 2682 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 17.54 Time building geometry restraints manager: 37.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 21593 1.06 - 1.28: 3624 1.28 - 1.50: 9407 1.50 - 1.73: 9319 1.73 - 1.95: 159 Bond restraints: 44102 Sorted by residual: bond pdb=" N SER H 0 " pdb=" CA SER H 0 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N ALA G -1 " pdb=" CA ALA G -1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N ALA F -1 " pdb=" CA ALA F -1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.77e+00 bond pdb=" CA ASP H 204 " pdb=" CB ASP H 204 " ideal model delta sigma weight residual 1.523 1.544 -0.021 1.35e-02 5.49e+03 2.42e+00 bond pdb=" N ALA F -1 " pdb=" H ALA F -1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.23e+00 ... (remaining 44097 not shown) Histogram of bond angle deviations from ideal: 99.01 - 106.43: 885 106.43 - 113.85: 54173 113.85 - 121.28: 16492 121.28 - 128.70: 8338 128.70 - 136.12: 126 Bond angle restraints: 80014 Sorted by residual: angle pdb=" N VAL F 45 " pdb=" CA VAL F 45 " pdb=" C VAL F 45 " ideal model delta sigma weight residual 112.96 109.70 3.26 1.00e+00 1.00e+00 1.06e+01 angle pdb=" CB MET H 188 " pdb=" CG MET H 188 " pdb=" SD MET H 188 " ideal model delta sigma weight residual 112.70 121.77 -9.07 3.00e+00 1.11e-01 9.14e+00 angle pdb=" N VAL B 303 " pdb=" CA VAL B 303 " pdb=" C VAL B 303 " ideal model delta sigma weight residual 106.21 109.33 -3.12 1.07e+00 8.73e-01 8.51e+00 angle pdb=" CG MET H 188 " pdb=" SD MET H 188 " pdb=" CE MET H 188 " ideal model delta sigma weight residual 100.90 106.28 -5.38 2.20e+00 2.07e-01 5.98e+00 angle pdb=" C ILE F 215 " pdb=" CA ILE F 215 " pdb=" CB ILE F 215 " ideal model delta sigma weight residual 112.22 108.85 3.37 1.38e+00 5.25e-01 5.95e+00 ... (remaining 80009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 16786 35.45 - 70.90: 592 70.90 - 106.36: 37 106.36 - 141.81: 1 141.81 - 177.26: 1 Dihedral angle restraints: 17417 sinusoidal: 8782 harmonic: 8635 Sorted by residual: dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 178.58 121.42 1 2.00e+01 2.50e-03 3.65e+01 dihedral pdb=" C4' DT K -1 " pdb=" C3' DT K -1 " pdb=" O3' DT K -1 " pdb=" P DA K 0 " ideal model delta sinusoidal sigma weight residual 220.00 42.74 177.26 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" O1A AGS C 402 " pdb=" O3A AGS C 402 " pdb=" PA AGS C 402 " pdb=" PB AGS C 402 " ideal model delta sinusoidal sigma weight residual -67.73 32.24 -99.97 1 3.00e+01 1.11e-03 1.25e+01 ... (remaining 17414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2403 0.030 - 0.060: 757 0.060 - 0.090: 249 0.090 - 0.120: 133 0.120 - 0.150: 27 Chirality restraints: 3569 Sorted by residual: chirality pdb=" CA ILE G 167 " pdb=" N ILE G 167 " pdb=" C ILE G 167 " pdb=" CB ILE G 167 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA ILE A 762 " pdb=" N ILE A 762 " pdb=" C ILE A 762 " pdb=" CB ILE A 762 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE F 111 " pdb=" N ILE F 111 " pdb=" C ILE F 111 " pdb=" CB ILE F 111 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 3566 not shown) Planarity restraints: 6236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 183 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.47e+00 pdb=" N PRO H 184 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO H 184 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 184 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 439 " 0.008 2.00e-02 2.50e+03 1.44e-02 3.10e+00 pdb=" CD GLN A 439 " -0.031 2.00e-02 2.50e+03 pdb=" OE1 GLN A 439 " 0.014 2.00e-02 2.50e+03 pdb=" NE2 GLN A 439 " 0.004 2.00e-02 2.50e+03 pdb="HE21 GLN A 439 " 0.005 2.00e-02 2.50e+03 pdb="HE22 GLN A 439 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 458 " -0.138 9.50e-02 1.11e+02 4.61e-02 2.63e+00 pdb=" NE ARG A 458 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 458 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 458 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 458 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 458 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 458 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 458 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 458 " 0.000 2.00e-02 2.50e+03 ... (remaining 6233 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.12: 835 2.12 - 2.74: 77013 2.74 - 3.36: 125943 3.36 - 3.98: 165331 3.98 - 4.60: 254964 Nonbonded interactions: 624086 Sorted by model distance: nonbonded pdb=" OE1 GLU A 740 " pdb=" H GLU A 740 " model vdw 1.495 1.850 nonbonded pdb=" OE1 GLU G 7 " pdb=" H GLU G 7 " model vdw 1.544 1.850 nonbonded pdb="HE22 GLN H 24 " pdb=" OG1 THR H 73 " model vdw 1.589 1.850 nonbonded pdb=" O GLY C 53 " pdb="HD22 ASN C 148 " model vdw 1.593 1.850 nonbonded pdb=" OE1 GLU H 55 " pdb=" H GLU H 55 " model vdw 1.603 1.850 ... (remaining 624081 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'F' and resid 0 through 254) selection = (chain 'G' and ((resid 0 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 1 through 254)) selection = (chain 'H' and ((resid 0 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 1 through 254)) } 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: 2.740 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: 0.620 Extract box with map and model: 13.960 Check model and map are aligned: 0.650 Set scattering table: 0.390 Process input model: 150.550 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.120 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:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 182.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 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 : 0.002 0.033 22470 Z= 0.146 Angle : 0.521 9.069 30653 Z= 0.298 Chirality : 0.038 0.150 3569 Planarity : 0.003 0.061 3672 Dihedral : 17.749 177.260 8574 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.95 % Allowed : 18.00 % Favored : 81.05 % 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: 2.01 (0.17), residues: 2590 helix: 2.11 (0.16), residues: 1227 sheet: 0.97 (0.22), residues: 521 loop : 0.53 (0.23), residues: 842 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 311 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 289 time to evaluate : 3.289 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 outliers start: 22 outliers final: 17 residues processed: 309 average time/residue: 3.3190 time to fit residues: 1156.9340 Evaluate side-chains 224 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 207 time to evaluate : 3.677 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 2 average time/residue: 0.5514 time to fit residues: 6.4545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 0.5980 chunk 198 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 205 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 237 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 ASN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 GLN F 84 ASN G 29 GLN G 255 ASN H 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22470 Z= 0.196 Angle : 0.503 5.837 30653 Z= 0.270 Chirality : 0.039 0.171 3569 Planarity : 0.003 0.050 3672 Dihedral : 14.563 177.219 3458 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.86 % Allowed : 18.22 % Favored : 79.92 % 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: 1.99 (0.17), residues: 2590 helix: 2.05 (0.16), residues: 1229 sheet: 1.07 (0.22), residues: 520 loop : 0.52 (0.23), residues: 841 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 253 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 210 time to evaluate : 3.374 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 outliers start: 43 outliers final: 23 residues processed: 246 average time/residue: 3.2209 time to fit residues: 897.6523 Evaluate side-chains 220 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 197 time to evaluate : 3.440 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 3 average time/residue: 1.1773 time to fit residues: 9.0938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 238 optimal weight: 9.9990 chunk 257 optimal weight: 10.0000 chunk 212 optimal weight: 2.9990 chunk 236 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 ASN D 317 ASN F 38 GLN F 159 ASN H 84 ASN H 153 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 22470 Z= 0.317 Angle : 0.527 7.528 30653 Z= 0.283 Chirality : 0.041 0.157 3569 Planarity : 0.003 0.040 3672 Dihedral : 14.876 176.949 3458 Min Nonbonded Distance : 1.578 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.21 % Allowed : 17.35 % Favored : 80.44 % 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: 1.72 (0.17), residues: 2590 helix: 1.76 (0.16), residues: 1236 sheet: 1.08 (0.22), residues: 519 loop : 0.37 (0.22), residues: 835 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 199 time to evaluate : 3.642 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 outliers start: 51 outliers final: 31 residues processed: 239 average time/residue: 3.2015 time to fit residues: 869.8228 Evaluate side-chains 220 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 189 time to evaluate : 3.378 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 29 residues processed: 3 average time/residue: 0.5631 time to fit residues: 7.1997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 235 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 160 optimal weight: 2.9990 chunk 239 optimal weight: 5.9990 chunk 253 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 212 GLN H 84 ASN H 153 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 22470 Z= 0.299 Angle : 0.518 6.093 30653 Z= 0.278 Chirality : 0.041 0.159 3569 Planarity : 0.004 0.062 3672 Dihedral : 14.960 177.721 3458 Min Nonbonded Distance : 1.633 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.08 % Allowed : 16.88 % Favored : 81.05 % 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: 1.63 (0.17), residues: 2590 helix: 1.68 (0.16), residues: 1234 sheet: 1.01 (0.22), residues: 529 loop : 0.35 (0.22), residues: 827 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 203 time to evaluate : 3.390 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 outliers start: 48 outliers final: 33 residues processed: 243 average time/residue: 3.1888 time to fit residues: 878.1810 Evaluate side-chains 223 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 190 time to evaluate : 3.272 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 30 residues processed: 3 average time/residue: 0.9857 time to fit residues: 8.1438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 188 optimal weight: 0.3980 chunk 104 optimal weight: 2.9990 chunk 216 optimal weight: 0.0050 chunk 175 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22470 Z= 0.154 Angle : 0.485 5.687 30653 Z= 0.258 Chirality : 0.039 0.160 3569 Planarity : 0.003 0.053 3672 Dihedral : 14.914 177.611 3458 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.77 % Allowed : 17.40 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.17), residues: 2590 helix: 1.88 (0.16), residues: 1233 sheet: 1.04 (0.22), residues: 529 loop : 0.43 (0.22), residues: 828 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 243 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 202 time to evaluate : 3.869 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 outliers start: 41 outliers final: 35 residues processed: 234 average time/residue: 3.1860 time to fit residues: 847.2125 Evaluate side-chains 228 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 193 time to evaluate : 3.370 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 35 outliers final: 31 residues processed: 6 average time/residue: 1.1206 time to fit residues: 13.4897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 85 optimal weight: 0.5980 chunk 228 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 148 optimal weight: 0.0570 chunk 62 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 212 GLN G 29 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22470 Z= 0.153 Angle : 0.479 5.892 30653 Z= 0.254 Chirality : 0.039 0.158 3569 Planarity : 0.003 0.041 3672 Dihedral : 14.852 177.516 3458 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.77 % Allowed : 17.61 % Favored : 80.61 % 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: 1.93 (0.17), residues: 2590 helix: 1.99 (0.16), residues: 1231 sheet: 1.06 (0.22), residues: 529 loop : 0.46 (0.22), residues: 830 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 246 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 205 time to evaluate : 3.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 29 residues processed: 238 average time/residue: 3.2173 time to fit residues: 870.5340 Evaluate side-chains 222 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 193 time to evaluate : 3.336 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 27 residues processed: 2 average time/residue: 0.5418 time to fit residues: 6.1882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 0.0060 chunk 28 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 chunk 185 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 213 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 252 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22470 Z= 0.166 Angle : 0.484 6.179 30653 Z= 0.256 Chirality : 0.039 0.155 3569 Planarity : 0.003 0.044 3672 Dihedral : 14.831 177.549 3458 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.64 % Allowed : 17.74 % Favored : 80.61 % 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: 1.94 (0.17), residues: 2590 helix: 2.01 (0.16), residues: 1232 sheet: 1.12 (0.22), residues: 519 loop : 0.41 (0.22), residues: 839 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 241 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 203 time to evaluate : 3.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 30 residues processed: 236 average time/residue: 3.3402 time to fit residues: 903.4891 Evaluate side-chains 222 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 192 time to evaluate : 3.633 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 29 residues processed: 1 average time/residue: 2.0057 time to fit residues: 6.8923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 156 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 160 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN E 212 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22470 Z= 0.258 Angle : 0.505 5.931 30653 Z= 0.269 Chirality : 0.040 0.152 3569 Planarity : 0.003 0.046 3672 Dihedral : 14.913 177.928 3458 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.69 % Allowed : 17.87 % Favored : 80.44 % 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: 1.81 (0.17), residues: 2590 helix: 1.90 (0.16), residues: 1233 sheet: 1.06 (0.22), residues: 523 loop : 0.36 (0.22), residues: 834 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 192 time to evaluate : 3.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 31 residues processed: 224 average time/residue: 3.2304 time to fit residues: 823.4817 Evaluate side-chains 220 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 189 time to evaluate : 3.409 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 28 residues processed: 3 average time/residue: 1.0618 time to fit residues: 8.6327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 4.9990 chunk 241 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 235 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 222 optimal weight: 4.9990 chunk 234 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22470 Z= 0.313 Angle : 0.532 7.716 30653 Z= 0.283 Chirality : 0.041 0.154 3569 Planarity : 0.004 0.075 3672 Dihedral : 15.058 178.477 3458 Min Nonbonded Distance : 1.668 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.56 % Allowed : 18.26 % Favored : 80.18 % 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: 1.67 (0.17), residues: 2590 helix: 1.77 (0.15), residues: 1234 sheet: 1.05 (0.22), residues: 523 loop : 0.27 (0.22), residues: 833 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 191 time to evaluate : 4.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 32 residues processed: 222 average time/residue: 2.5930 time to fit residues: 655.6988 Evaluate side-chains 220 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 188 time to evaluate : 2.244 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 30 residues processed: 2 average time/residue: 0.9078 time to fit residues: 5.1559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 0.0970 chunk 248 optimal weight: 0.0970 chunk 151 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN E 212 GLN F 132 GLN H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2507 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: