Starting phenix.real_space_refine (version: dev) on Thu Feb 23 23:54:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tib_25616/02_2023/7tib_25616_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tib_25616/02_2023/7tib_25616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tib_25616/02_2023/7tib_25616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tib_25616/02_2023/7tib_25616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tib_25616/02_2023/7tib_25616_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tib_25616/02_2023/7tib_25616_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 Process input model Symmetric amino acids flipped Residue "A GLU 293": "OE1" <-> "OE2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 373": "OD1" <-> "OD2" Residue "A ASP 381": "OD1" <-> "OD2" Residue "A ASP 397": "OD1" <-> "OD2" Residue "A TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 479": "OD1" <-> "OD2" Residue "A ASP 504": "OD1" <-> "OD2" Residue "A ASP 513": "OD1" <-> "OD2" Residue "A GLU 538": "OE1" <-> "OE2" Residue "A ASP 560": "OD1" <-> "OD2" Residue "A ASP 566": "OD1" <-> "OD2" Residue "A PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 616": "OE1" <-> "OE2" Residue "A GLU 635": "OE1" <-> "OE2" Residue "A TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 704": "OD1" <-> "OD2" Residue "A TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 715": "OD1" <-> "OD2" Residue "A ASP 723": "OD1" <-> "OD2" Residue "A ASP 733": "OD1" <-> "OD2" Residue "A PHE 749": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 22": "OD1" <-> "OD2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ASP 31": "OD1" <-> "OD2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B ASP 168": "OD1" <-> "OD2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B ASP 189": "OD1" <-> "OD2" Residue "B ASP 201": "OD1" <-> "OD2" Residue "B PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 287": "OE1" <-> "OE2" Residue "C GLU 11": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C ASP 230": "OD1" <-> "OD2" Residue "C ASP 243": "OD1" <-> "OD2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "C ASP 255": "OD1" <-> "OD2" Residue "C ASP 276": "OD1" <-> "OD2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C GLU 293": "OE1" <-> "OE2" Residue "C GLU 332": "OE1" <-> "OE2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D ASP 143": "OD1" <-> "OD2" Residue "D ASP 178": "OD1" <-> "OD2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "D ASP 213": "OD1" <-> "OD2" 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 GLU 273": "OE1" <-> "OE2" Residue "D ASP 279": "OD1" <-> "OD2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D GLU 306": "OE1" <-> "OE2" Residue "D ASP 312": "OD1" <-> "OD2" Residue "D ASP 315": "OD1" <-> "OD2" Residue "E TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "E GLU 115": "OE1" <-> "OE2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "E ASP 149": "OD1" <-> "OD2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E GLU 302": "OE1" <-> "OE2" Residue "E ASP 309": "OD1" <-> "OD2" Residue "E GLU 323": "OE1" <-> "OE2" Residue "E PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 330": "OE1" <-> "OE2" Residue "F GLU 7": "OE1" <-> "OE2" Residue "F ASP 21": "OD1" <-> "OD2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F ASP 33": "OD1" <-> "OD2" Residue "F ASP 41": "OD1" <-> "OD2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F GLU 59": "OE1" <-> "OE2" Residue "F ASP 71": "OD1" <-> "OD2" Residue "F ASP 86": "OD1" <-> "OD2" Residue "F ASP 93": "OD1" <-> "OD2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F ASP 109": "OD1" <-> "OD2" Residue "F TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 122": "OD1" <-> "OD2" Residue "F GLU 129": "OE1" <-> "OE2" Residue "F GLU 143": "OE1" <-> "OE2" Residue "F ASP 150": "OD1" <-> "OD2" Residue "F ASP 187": "OD1" <-> "OD2" Residue "F GLU 192": "OE1" <-> "OE2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "F ASP 204": "OD1" <-> "OD2" Residue "F ASP 214": "OD1" <-> "OD2" Residue "F ASP 223": "OD1" <-> "OD2" Residue "F GLU 232": "OE1" <-> "OE2" Residue "F PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 240": "OD1" <-> "OD2" Residue "F PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 17": "OD1" <-> "OD2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G ASP 33": "OD1" <-> "OD2" Residue "G ASP 42": "OD1" <-> "OD2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 59": "OE1" <-> "OE2" Residue "G ASP 63": "OD1" <-> "OD2" Residue "G ASP 86": "OD1" <-> "OD2" Residue "G ASP 93": "OD1" <-> "OD2" Residue "G GLU 104": "OE1" <-> "OE2" Residue "G ASP 122": "OD1" <-> "OD2" Residue "G ASP 150": "OD1" <-> "OD2" Residue "G ASP 156": "OD1" <-> "OD2" Residue "G PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 187": "OD1" <-> "OD2" Residue "G GLU 198": "OE1" <-> "OE2" Residue "G ASP 200": "OD1" <-> "OD2" Residue "G ASP 204": "OD1" <-> "OD2" Residue "G ASP 223": "OD1" <-> "OD2" Residue "G PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 8": "OE1" <-> "OE2" Residue "H ASP 17": "OD1" <-> "OD2" Residue "H PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 21": "OD1" <-> "OD2" Residue "H PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H ASP 33": "OD1" <-> "OD2" Residue "H GLU 51": "OE1" <-> "OE2" Residue "H PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 59": "OE1" <-> "OE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 71": "OD1" <-> "OD2" Residue "H ASP 93": "OD1" <-> "OD2" Residue "H PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 109": "OD1" <-> "OD2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 122": "OD1" <-> "OD2" Residue "H PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 129": "OE1" <-> "OE2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "H ASP 150": "OD1" <-> "OD2" Residue "H ASP 156": "OD1" <-> "OD2" Residue "H PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 198": "OE1" <-> "OE2" Residue "H ASP 200": "OD1" <-> "OD2" Residue "H TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 232": "OE1" <-> "OE2" Residue "H PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 240": "OD1" <-> "OD2" Residue "H PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 256": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 21377 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3923 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 19, 'TRANS': 475} Chain: "B" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2505 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain: "C" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2586 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain: "D" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2687 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 327} Chain: "E" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2716 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 14, 'TRANS': 328} Chain breaks: 1 Chain: "F" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2003 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "G" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1983 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain breaks: 1 Chain: "H" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1964 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 8, 'TRANS': 241} Chain breaks: 3 Chain: "I" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 488 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "J" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 367 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} 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} Time building chain proxies: 12.36, per 1000 atoms: 0.58 Number of scatterers: 21377 At special positions: 0 Unit cell: (127.2, 133.56, 125.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 101 16.00 P 55 15.00 Mg 4 11.99 O 4205 8.00 N 3631 7.00 C 13381 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.88 Conformation dependent library (CDL) restraints added in 3.0 seconds 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4910 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 118 helices and 17 sheets defined 45.6% alpha, 15.1% beta 8 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 6.92 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 333 removed outlier: 3.708A pdb=" N ASN A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 369 Processing helix chain 'A' and resid 385 through 391 Processing helix chain 'A' and resid 393 through 395 No H-bonds generated for 'chain 'A' and resid 393 through 395' Processing helix chain 'A' and resid 402 through 406 Processing helix chain 'A' and resid 414 through 417 removed outlier: 3.974A pdb=" N LYS A 417 " --> pdb=" O LEU A 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 414 through 417' 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 436 through 445 removed outlier: 3.892A pdb=" N ARG A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 467 Proline residue: A 465 - end of helix No H-bonds generated for 'chain 'A' and resid 462 through 467' Processing helix chain 'A' and resid 480 through 493 Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 514 through 524 Processing helix chain 'A' and resid 536 through 542 Processing helix chain 'A' and resid 553 through 558 Processing helix chain 'A' and resid 566 through 569 No H-bonds generated for 'chain 'A' and resid 566 through 569' Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'A' and resid 588 through 594 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: 3.929A pdb=" N LEU A 647 " --> pdb=" O HIS A 644 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER A 648 " --> pdb=" O ALA A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 656 Processing helix chain 'A' and resid 669 through 694 removed outlier: 5.442A pdb=" N LEU A 692 " --> pdb=" O TYR A 688 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLY A 693 " --> pdb=" O HIS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 702 Processing helix chain 'A' and resid 706 through 713 removed outlier: 4.104A pdb=" N LYS A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 720 removed outlier: 3.586A pdb=" N LYS A 719 " --> pdb=" O ASP A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 734 Processing helix chain 'A' and resid 739 through 747 removed outlier: 3.709A pdb=" N MET A 746 " --> pdb=" O TRP A 742 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 761 No H-bonds generated for 'chain 'A' and resid 758 through 761' Processing helix chain 'A' and resid 764 through 774 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 56 through 74 removed outlier: 7.454A pdb=" N ARG B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N SER B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ALA B 72 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ASP B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 98 removed outlier: 4.079A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.316A 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: 3.767A pdb=" N ARG B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 3.653A 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: 3.775A 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 216 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 254 Processing helix chain 'B' and resid 263 through 275 Processing helix chain 'B' and resid 282 through 299 removed outlier: 3.624A pdb=" N ARG B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 321 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 32 through 43 removed outlier: 3.508A pdb=" N THR C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 78 removed outlier: 7.568A pdb=" N LYS C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ASN C 74 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N TYR C 75 " --> pdb=" O TYR C 71 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N SER C 76 " --> pdb=" O GLY C 72 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASN C 77 " --> pdb=" O LYS C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 removed outlier: 4.016A 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: 4.410A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 No H-bonds generated for 'chain 'C' and resid 155 through 158' Processing helix chain 'C' and resid 171 through 184 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 252 Processing helix chain 'C' and resid 256 through 269 Processing helix chain 'C' and resid 274 through 285 Processing helix chain 'C' and resid 294 through 312 removed outlier: 3.776A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 333 removed outlier: 3.952A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 23 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 43 through 54 removed outlier: 3.704A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 89 Proline residue: D 85 - end of helix removed outlier: 4.797A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.870A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 removed outlier: 3.786A pdb=" N GLU D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN D 128 " --> pdb=" O HIS D 124 " (cutoff:3.500A) No H-bonds generated for '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: 3.571A pdb=" N LEU D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG D 154 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (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 194 through 207 removed outlier: 5.155A pdb=" N ASP D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 224 Processing helix chain 'D' and resid 228 through 245 removed outlier: 3.700A pdb=" N LEU D 245 " --> pdb=" O GLY D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 259 removed outlier: 3.958A pdb=" N LEU D 259 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 276 Processing helix chain 'D' and resid 280 through 292 removed outlier: 3.602A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 310 Processing helix chain 'D' and resid 316 through 335 removed outlier: 4.102A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'E' and resid 13 through 15 No H-bonds generated for 'chain 'E' and resid 13 through 15' Processing helix chain 'E' and resid 20 through 31 Processing helix chain 'E' and resid 49 through 60 Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 103 through 118 removed outlier: 4.379A pdb=" N ARG E 106 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE E 107 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU E 111 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU E 112 " --> pdb=" O ILE E 109 " (cutoff:3.500A) 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: 4.045A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 195 through 208 Processing helix chain 'E' and resid 217 through 226 Processing helix chain 'E' and resid 230 through 243 Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 276 through 292 removed outlier: 3.539A pdb=" N GLU E 281 " --> pdb=" O ASN E 277 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 308 Processing helix chain 'E' and resid 315 through 334 Processing helix chain 'E' and resid 338 through 352 removed outlier: 3.821A pdb=" N GLY E 344 " --> pdb=" O PHE E 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 19 removed outlier: 4.216A pdb=" N PHE F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 81 removed outlier: 3.575A pdb=" N CYS F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 151 Processing helix chain 'F' and resid 209 through 220 removed outlier: 3.830A pdb=" N ASP F 214 " --> pdb=" O LYS F 210 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS F 217 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY F 218 " --> pdb=" O ASP F 214 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER F 219 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER F 220 " --> pdb=" O ILE F 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 19 removed outlier: 4.114A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) 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 73 through 79 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 218 removed outlier: 3.580A pdb=" N LYS G 217 " --> pdb=" O LEU G 213 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY G 218 " --> pdb=" O ASP G 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 18 Processing helix chain 'H' and resid 72 through 81 Processing helix chain 'H' and resid 141 through 151 Processing helix chain 'H' and resid 209 through 220 removed outlier: 3.699A pdb=" N ASP H 214 " --> pdb=" O LYS H 210 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS H 217 " --> pdb=" O LEU H 213 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY H 218 " --> pdb=" O ASP H 214 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER H 219 " --> pdb=" O ILE H 215 " (cutoff:3.500A) removed outlier: 5.471A 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: 6.208A pdb=" N LEU A 451 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU A 351 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU A 453 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N GLY A 353 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N CYS A 455 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP A 373 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE A 422 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 375 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ASP A 424 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN A 377 " --> pdb=" O ASP A 424 " (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: 6.305A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.728A 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: 6.570A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 7.149A 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: 3.592A pdb=" N GLY D 65 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.594A 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: 6.604A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.385A 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 111 through 116 removed outlier: 4.940A pdb=" N LEU F 88 " --> pdb=" O PHE F 6 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 66 through 71 removed outlier: 5.649A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASN F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLN F 38 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 6.542A 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: 5.543A pdb=" N SER F 157 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP F 172 " --> pdb=" O SER F 157 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 111 through 117 removed outlier: 4.509A pdb=" N LEU G 88 " --> pdb=" O PHE G 6 " (cutoff:3.500A) removed outlier: 3.577A 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: 6.362A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.958A 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 207 Processing sheet with id= N, first strand: chain 'H' and resid 100 through 104 removed outlier: 3.672A pdb=" N GLU H 59 " --> pdb=" O LYS H 5 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 66 through 71 removed outlier: 6.039A pdb=" N LEU H 25 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N VAL H 40 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 196 through 199 Processing sheet with id= Q, first strand: chain 'H' and resid 203 through 208 removed outlier: 6.127A pdb=" N SER H 157 " --> pdb=" O ASP H 172 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP H 172 " --> pdb=" O SER H 157 " (cutoff:3.500A) 929 hydrogen bonds defined for protein. 2643 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 7.94 Time building geometry restraints manager: 9.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7004 1.36 - 1.51: 5611 1.51 - 1.66: 9032 1.66 - 1.80: 96 1.80 - 1.95: 63 Bond restraints: 21806 Sorted by residual: bond pdb=" C4 ADP E 401 " pdb=" C5 ADP E 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.01e+00 bond pdb=" C3' DT J 19 " pdb=" C2' DT J 19 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 8.51e-01 bond pdb=" CA ILE G 195 " pdb=" CB ILE G 195 " ideal model delta sigma weight residual 1.530 1.540 -0.009 1.05e-02 9.07e+03 7.89e-01 bond pdb=" CA ILE F 111 " pdb=" CB ILE F 111 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.36e-02 5.41e+03 7.84e-01 bond pdb=" N PRO A 780 " pdb=" CA PRO A 780 " ideal model delta sigma weight residual 1.469 1.480 -0.011 1.28e-02 6.10e+03 7.79e-01 ... (remaining 21801 not shown) Histogram of bond angle deviations from ideal: 99.42 - 106.76: 796 106.76 - 114.09: 12934 114.09 - 121.43: 10755 121.43 - 128.77: 5046 128.77 - 136.10: 128 Bond angle restraints: 29659 Sorted by residual: angle pdb=" N VAL B 303 " pdb=" CA VAL B 303 " pdb=" C VAL B 303 " ideal model delta sigma weight residual 111.91 108.30 3.61 8.90e-01 1.26e+00 1.64e+01 angle pdb=" N VAL H 45 " pdb=" CA VAL H 45 " pdb=" C VAL H 45 " ideal model delta sigma weight residual 113.53 109.91 3.62 9.80e-01 1.04e+00 1.36e+01 angle pdb=" C SER A 634 " pdb=" N GLU A 635 " pdb=" CA GLU A 635 " ideal model delta sigma weight residual 121.54 128.22 -6.68 1.91e+00 2.74e-01 1.22e+01 angle pdb=" N ASN B 321 " pdb=" CA ASN B 321 " pdb=" C ASN B 321 " ideal model delta sigma weight residual 112.97 109.89 3.08 1.06e+00 8.90e-01 8.42e+00 angle pdb=" CA GLU F 129 " pdb=" CB GLU F 129 " pdb=" CG GLU F 129 " ideal model delta sigma weight residual 114.10 119.66 -5.56 2.00e+00 2.50e-01 7.74e+00 ... (remaining 29654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.56: 12328 26.56 - 53.12: 767 53.12 - 79.68: 94 79.68 - 106.25: 18 106.25 - 132.81: 4 Dihedral angle restraints: 13211 sinusoidal: 5669 harmonic: 7542 Sorted by residual: dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 72.81 -132.81 1 2.00e+01 2.50e-03 4.03e+01 dihedral pdb=" O2A ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PA ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 46.54 -106.54 1 2.00e+01 2.50e-03 3.08e+01 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 -60.00 29.75 -89.75 1 2.00e+01 2.50e-03 2.39e+01 ... (remaining 13208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2139 0.028 - 0.056: 861 0.056 - 0.085: 282 0.085 - 0.113: 144 0.113 - 0.141: 25 Chirality restraints: 3451 Sorted by residual: chirality pdb=" CA VAL E 122 " pdb=" N VAL E 122 " pdb=" C VAL E 122 " pdb=" CB VAL E 122 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA GLU F 129 " pdb=" N GLU F 129 " pdb=" C GLU F 129 " pdb=" CB GLU F 129 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA ILE G 111 " pdb=" N ILE G 111 " pdb=" C ILE G 111 " pdb=" CB ILE G 111 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 3448 not shown) Planarity restraints: 3618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 221 " -0.034 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO C 222 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 222 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 222 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 10 " 0.019 2.00e-02 2.50e+03 1.02e-02 2.61e+00 pdb=" N1 DT I 10 " -0.025 2.00e-02 2.50e+03 pdb=" C2 DT I 10 " -0.000 2.00e-02 2.50e+03 pdb=" O2 DT I 10 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DT I 10 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DT I 10 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT I 10 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DT I 10 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 10 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT I 10 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN H 201 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO H 202 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO H 202 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 202 " 0.020 5.00e-02 4.00e+02 ... (remaining 3615 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 314 2.66 - 3.22: 19699 3.22 - 3.78: 33444 3.78 - 4.34: 46539 4.34 - 4.90: 75191 Nonbonded interactions: 175187 Sorted by model distance: nonbonded pdb=" OG1 THR B 56 " pdb="MG MG B 402 " model vdw 2.099 2.170 nonbonded pdb=" O3G AGS B 401 " pdb="MG MG B 402 " model vdw 2.104 2.170 nonbonded pdb=" OG1 THR C 60 " pdb="MG MG C 402 " model vdw 2.106 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 2.146 2.170 nonbonded pdb=" O3G AGS C 401 " pdb="MG MG C 402 " model vdw 2.150 2.170 ... (remaining 175182 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 1 through 82 or resid 85 through 104 or resid 106 through \ 173 or resid 177 through 240 or resid 244 through 255)) selection = (chain 'G' and (resid 1 through 82 or resid 85 through 104 or resid 106 through \ 240 or resid 244 through 255)) selection = (chain 'H' and (resid 1 through 173 or resid 177 through 255)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 55 5.49 5 Mg 4 5.21 5 S 101 5.16 5 C 13381 2.51 5 N 3631 2.21 5 O 4205 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.690 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: 0.020 Extract box with map and model: 5.010 Check model and map are aligned: 0.330 Process input model: 60.520 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.200 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 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 0.032 21806 Z= 0.136 Angle : 0.530 8.499 29659 Z= 0.317 Chirality : 0.038 0.141 3451 Planarity : 0.003 0.052 3618 Dihedral : 16.657 132.807 8301 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.15), residues: 2555 helix: -0.62 (0.14), residues: 1202 sheet: -1.27 (0.20), residues: 525 loop : -2.12 (0.19), residues: 828 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 644 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 17 residues processed: 664 average time/residue: 0.4050 time to fit residues: 393.8091 Evaluate side-chains 524 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 507 time to evaluate : 2.589 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2019 time to fit residues: 10.0537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 150 optimal weight: 0.0020 chunk 234 optimal weight: 0.6980 overall best weight: 1.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 313 ASN A 322 ASN A 398 ASN A 413 ASN A 501 ASN A 537 ASN A 672 GLN A 775 ASN B 18 GLN B 92 GLN B 279 GLN B 296 HIS B 317 HIS B 320 ASN C 180 ASN C 221 ASN C 317 GLN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN D 236 GLN D 303 GLN D 352 GLN E 18 HIS E 19 ASN E 86 ASN E 103 ASN E 133 HIS E 317 ASN F 27 ASN F 38 GLN F 58 GLN G 94 ASN G 201 GLN H 27 ASN H 153 GLN H 247 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 21806 Z= 0.266 Angle : 0.573 10.411 29659 Z= 0.289 Chirality : 0.042 0.156 3451 Planarity : 0.004 0.056 3618 Dihedral : 14.155 126.211 3216 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 2.92 % 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: -0.76 (0.16), residues: 2555 helix: 0.39 (0.15), residues: 1189 sheet: -0.77 (0.21), residues: 524 loop : -1.45 (0.20), residues: 842 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 523 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 39 residues processed: 554 average time/residue: 0.3573 time to fit residues: 298.0220 Evaluate side-chains 524 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 485 time to evaluate : 2.314 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.2141 time to fit residues: 18.4005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 194 optimal weight: 0.0870 chunk 159 optimal weight: 0.0670 chunk 64 optimal weight: 2.9990 chunk 234 optimal weight: 9.9990 chunk 253 optimal weight: 8.9990 chunk 209 optimal weight: 4.9990 chunk 232 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 overall best weight: 1.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 ASN ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS B 26 ASN B 108 HIS B 317 HIS C 171 GLN C 333 ASN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN D 311 ASN E 74 GLN E 104 ASN E 317 ASN F 27 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 21806 Z= 0.272 Angle : 0.562 12.428 29659 Z= 0.282 Chirality : 0.042 0.150 3451 Planarity : 0.004 0.042 3618 Dihedral : 14.156 129.238 3216 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 2.31 % 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: -0.38 (0.16), residues: 2555 helix: 0.58 (0.15), residues: 1190 sheet: -0.54 (0.22), residues: 522 loop : -1.10 (0.21), residues: 843 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 500 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 22 residues processed: 532 average time/residue: 0.3642 time to fit residues: 291.6891 Evaluate side-chains 495 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 473 time to evaluate : 2.451 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2028 time to fit residues: 11.7367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 9.9990 chunk 176 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 235 optimal weight: 40.0000 chunk 249 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 223 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 HIS C 171 GLN E 317 ASN F 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 21806 Z= 0.262 Angle : 0.556 14.206 29659 Z= 0.281 Chirality : 0.041 0.150 3451 Planarity : 0.004 0.044 3618 Dihedral : 14.133 129.209 3216 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 2.31 % 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: -0.16 (0.17), residues: 2555 helix: 0.70 (0.15), residues: 1187 sheet: -0.38 (0.22), residues: 523 loop : -0.93 (0.21), residues: 845 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 484 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 39 residues processed: 512 average time/residue: 0.3675 time to fit residues: 282.6044 Evaluate side-chains 505 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 466 time to evaluate : 2.412 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.1943 time to fit residues: 17.6584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 185 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 212 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN F 27 ASN ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 21806 Z= 0.236 Angle : 0.551 15.123 29659 Z= 0.275 Chirality : 0.041 0.173 3451 Planarity : 0.004 0.044 3618 Dihedral : 14.095 129.758 3216 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 1.35 % 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: -0.03 (0.17), residues: 2555 helix: 0.74 (0.15), residues: 1201 sheet: -0.26 (0.22), residues: 524 loop : -0.79 (0.22), residues: 830 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 479 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 499 average time/residue: 0.3564 time to fit residues: 269.5921 Evaluate side-chains 474 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 459 time to evaluate : 2.400 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2011 time to fit residues: 9.1767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 0.8980 chunk 224 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 249 optimal weight: 8.9990 chunk 207 optimal weight: 0.2980 chunk 115 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN E 317 ASN F 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 21806 Z= 0.167 Angle : 0.534 15.826 29659 Z= 0.265 Chirality : 0.040 0.151 3451 Planarity : 0.004 0.046 3618 Dihedral : 13.992 129.648 3216 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 1.26 % 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: 0.20 (0.17), residues: 2555 helix: 0.90 (0.15), residues: 1209 sheet: -0.12 (0.23), residues: 523 loop : -0.67 (0.22), residues: 823 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 492 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 503 average time/residue: 0.3686 time to fit residues: 280.3960 Evaluate side-chains 484 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 466 time to evaluate : 2.563 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2235 time to fit residues: 10.4627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 182 optimal weight: 0.4980 chunk 141 optimal weight: 3.9990 chunk 210 optimal weight: 7.9990 chunk 139 optimal weight: 0.5980 chunk 248 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 210 ASN E 74 GLN E 317 ASN F 27 ASN F 29 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 21806 Z= 0.300 Angle : 0.588 15.958 29659 Z= 0.293 Chirality : 0.042 0.145 3451 Planarity : 0.004 0.055 3618 Dihedral : 14.153 130.851 3216 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 1.61 % 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: 0.17 (0.17), residues: 2555 helix: 0.82 (0.15), residues: 1200 sheet: -0.07 (0.23), residues: 513 loop : -0.62 (0.22), residues: 842 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 476 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 19 residues processed: 494 average time/residue: 0.3602 time to fit residues: 268.7361 Evaluate side-chains 489 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 470 time to evaluate : 2.329 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2070 time to fit residues: 10.7030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 153 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 122 optimal weight: 0.0470 chunk 23 optimal weight: 0.0570 chunk 195 optimal weight: 5.9990 chunk 226 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN E 74 GLN F 27 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 21806 Z= 0.162 Angle : 0.545 16.157 29659 Z= 0.269 Chirality : 0.040 0.186 3451 Planarity : 0.004 0.053 3618 Dihedral : 14.074 129.342 3216 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.92 % 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: 0.38 (0.17), residues: 2555 helix: 0.98 (0.16), residues: 1209 sheet: 0.06 (0.23), residues: 512 loop : -0.55 (0.22), residues: 834 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 485 time to evaluate : 2.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 496 average time/residue: 0.3601 time to fit residues: 270.3201 Evaluate side-chains 475 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 463 time to evaluate : 2.584 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2337 time to fit residues: 8.5501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 238 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 231 optimal weight: 30.0000 chunk 139 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 219 optimal weight: 0.9990 chunk 230 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 21806 Z= 0.369 Angle : 0.635 16.003 29659 Z= 0.316 Chirality : 0.044 0.159 3451 Planarity : 0.004 0.048 3618 Dihedral : 14.242 133.247 3216 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.96 % 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: 0.12 (0.17), residues: 2555 helix: 0.73 (0.15), residues: 1211 sheet: -0.08 (0.23), residues: 513 loop : -0.60 (0.22), residues: 831 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 471 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 481 average time/residue: 0.3602 time to fit residues: 263.6348 Evaluate side-chains 482 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 467 time to evaluate : 2.394 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1948 time to fit residues: 8.9509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 245 optimal weight: 0.9990 chunk 149 optimal weight: 0.5980 chunk 116 optimal weight: 0.0570 chunk 170 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 chunk 236 optimal weight: 0.0970 chunk 204 optimal weight: 0.8980 chunk 21 optimal weight: 0.0270 chunk 158 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN E 74 GLN E 317 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 21806 Z= 0.149 Angle : 0.559 16.200 29659 Z= 0.276 Chirality : 0.040 0.198 3451 Planarity : 0.004 0.051 3618 Dihedral : 13.972 129.017 3216 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 0.44 % 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: 0.44 (0.17), residues: 2555 helix: 1.00 (0.16), residues: 1206 sheet: 0.15 (0.23), residues: 512 loop : -0.51 (0.22), residues: 837 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 489 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 494 average time/residue: 0.3590 time to fit residues: 269.6850 Evaluate side-chains 477 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 470 time to evaluate : 2.487 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2091 time to fit residues: 6.1808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 218 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 188 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 205 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 179 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN B 102 HIS E 317 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.163906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.117040 restraints weight = 24465.240| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.82 r_work: 0.2946 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 21806 Z= 0.327 Angle : 0.625 16.315 29659 Z= 0.309 Chirality : 0.043 0.215 3451 Planarity : 0.004 0.051 3618 Dihedral : 14.077 128.732 3216 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.52 % 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: 0.27 (0.17), residues: 2555 helix: 0.84 (0.15), residues: 1222 sheet: 0.04 (0.23), residues: 513 loop : -0.55 (0.22), residues: 820 =============================================================================== Job complete usr+sys time: 5663.02 seconds wall clock time: 102 minutes 24.29 seconds (6144.29 seconds total)