Starting phenix.real_space_refine on Thu Feb 15 23:14:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlf_22242/02_2024/6xlf_22242_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlf_22242/02_2024/6xlf_22242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlf_22242/02_2024/6xlf_22242.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlf_22242/02_2024/6xlf_22242.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlf_22242/02_2024/6xlf_22242_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlf_22242/02_2024/6xlf_22242_updated.pdb" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 K 2 8.98 5 P 6 5.49 5 Mg 2 5.21 5 S 25 5.16 5 C 8721 2.51 5 N 2247 2.21 5 O 2650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4": "OE1" <-> "OE2" Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 76": "OE1" <-> "OE2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 113": "OD1" <-> "OD2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ASP 143": "OD1" <-> "OD2" Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A ASP 279": "OD1" <-> "OD2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A GLU 351": "OE1" <-> "OE2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 369": "OD1" <-> "OD2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A ASP 406": "OD1" <-> "OD2" Residue "A GLU 408": "OE1" <-> "OE2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A GLU 462": "OE1" <-> "OE2" Residue "A TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A ASP 523": "OD1" <-> "OD2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A ASP 530": "OD1" <-> "OD2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A GLU 537": "OE1" <-> "OE2" Residue "A ASP 552": "OD1" <-> "OD2" Residue "A ASP 556": "OD1" <-> "OD2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 569": "OD1" <-> "OD2" Residue "A GLU 586": "OE1" <-> "OE2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "A PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A GLU 620": "OE1" <-> "OE2" Residue "A ASP 626": "OD1" <-> "OD2" Residue "A ASP 632": "OD1" <-> "OD2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 113": "OD1" <-> "OD2" Residue "B ARG 133": "NH1" <-> "NH2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 149": "OE1" <-> "OE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 179": "OD1" <-> "OD2" Residue "B ASP 180": "OD1" <-> "OD2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B GLU 351": "OE1" <-> "OE2" Residue "B ASP 352": "OD1" <-> "OD2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 369": "OD1" <-> "OD2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B ARG 389": "NH1" <-> "NH2" Residue "B PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 448": "OD1" <-> "OD2" Residue "B TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 473": "OE1" <-> "OE2" Residue "B PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 502": "OD1" <-> "OD2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "B PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 513": "OE1" <-> "OE2" Residue "B ASP 523": "OD1" <-> "OD2" Residue "B PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B ASP 530": "OD1" <-> "OD2" Residue "B GLU 531": "OE1" <-> "OE2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B GLU 539": "OE1" <-> "OE2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 587": "NH1" <-> "NH2" Residue "B ARG 595": "NH1" <-> "NH2" Residue "B PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B GLU 620": "OE1" <-> "OE2" Residue "B ASP 637": "OD1" <-> "OD2" Residue "B GLU 644": "OE1" <-> "OE2" Residue "B PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 13": "OD1" <-> "OD2" Residue "C PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 76": "OE1" <-> "OE2" Residue "C PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 97": "OE1" <-> "OE2" Residue "C PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 219": "OE1" <-> "OE2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 333": "OE1" <-> "OE2" Residue "C TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 219": "OE1" <-> "OE2" Residue "D PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 228": "OE1" <-> "OE2" Residue "D GLU 231": "OE1" <-> "OE2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 307": "OE1" <-> "OE2" Residue "D PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 310": "OE1" <-> "OE2" Residue "D GLU 325": "OE1" <-> "OE2" Residue "D ASP 326": "OD1" <-> "OD2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13653 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4923 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 20, 'TRANS': 588} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4930 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 20, 'TRANS': 589} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2544 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 303} Chain breaks: 1 Chain: "D" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1190 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.20, per 1000 atoms: 0.53 Number of scatterers: 13653 At special positions: 0 Unit cell: (105.9, 110.136, 133.434, 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) K 2 19.00 S 25 16.00 P 6 15.00 Mg 2 11.99 O 2650 8.00 N 2247 7.00 C 8721 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.03 Conformation dependent library (CDL) restraints added in 2.4 seconds 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3202 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 61 helices and 14 sheets defined 34.5% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 removed outlier: 4.285A pdb=" N SER A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 51 removed outlier: 3.783A pdb=" N GLU A 33 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 36 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP A 40 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE A 45 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 48 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 50 " --> pdb=" O TYR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 56 Processing helix chain 'A' and resid 88 through 91 No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.761A pdb=" N LEU A 127 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE A 128 " --> pdb=" O TYR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 185 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 385 through 404 Processing helix chain 'A' and resid 407 through 416 removed outlier: 3.662A pdb=" N LYS A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.708A pdb=" N VAL A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 438 removed outlier: 3.735A pdb=" N LYS A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 489 removed outlier: 3.685A pdb=" N ASP A 485 " --> pdb=" O PRO A 482 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA A 486 " --> pdb=" O PHE A 483 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS A 488 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 489 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 509 removed outlier: 4.021A pdb=" N GLN A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 542 removed outlier: 3.974A pdb=" N ALA A 534 " --> pdb=" O ASP A 530 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A 535 " --> pdb=" O GLU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 557 removed outlier: 3.814A pdb=" N ILE A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLN A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 591 removed outlier: 3.503A pdb=" N ALA A 591 " --> pdb=" O ARG A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 626 removed outlier: 3.685A pdb=" N VAL A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP A 626 " --> pdb=" O LYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 650 removed outlier: 3.563A pdb=" N LEU A 648 " --> pdb=" O GLU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 671 Processing helix chain 'B' and resid 12 through 21 removed outlier: 4.825A pdb=" N SER B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 49 removed outlier: 3.607A pdb=" N GLU B 33 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 34 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN B 37 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 45 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 48 " --> pdb=" O ILE B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 56 Processing helix chain 'B' and resid 86 through 91 removed outlier: 3.777A pdb=" N ILE B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 124 through 129 removed outlier: 3.535A pdb=" N LEU B 127 " --> pdb=" O PHE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 185 Processing helix chain 'B' and resid 187 through 194 Processing helix chain 'B' and resid 282 through 292 Processing helix chain 'B' and resid 384 through 405 Processing helix chain 'B' and resid 408 through 416 removed outlier: 3.957A pdb=" N LYS B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 427 removed outlier: 3.637A pdb=" N VAL B 425 " --> pdb=" O ILE B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 438 removed outlier: 3.784A pdb=" N LYS B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.521A pdb=" N THR B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'B' and resid 502 through 509 removed outlier: 4.270A pdb=" N GLN B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 542 removed outlier: 3.593A pdb=" N LYS B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 539 " --> pdb=" O GLU B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 557 removed outlier: 3.538A pdb=" N ASP B 552 " --> pdb=" O LYS B 548 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASP B 556 " --> pdb=" O ASP B 552 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLN B 557 " --> pdb=" O ILE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 591 removed outlier: 3.558A pdb=" N ARG B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 626 removed outlier: 3.693A pdb=" N ASP B 626 " --> pdb=" O LYS B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 650 removed outlier: 3.521A pdb=" N ASP B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 638 " --> pdb=" O THR B 634 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 648 " --> pdb=" O GLU B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 671 Processing helix chain 'C' and resid 6 through 8 No H-bonds generated for 'chain 'C' and resid 6 through 8' Processing helix chain 'C' and resid 17 through 27 removed outlier: 3.530A pdb=" N GLN C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 4.512A pdb=" N GLU C 122 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS C 124 " --> pdb=" O SER C 121 " (cutoff:3.500A) Proline residue: C 125 - end of helix Processing helix chain 'C' and resid 131 through 149 removed outlier: 3.565A pdb=" N ILE C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY C 143 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU C 147 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.666A pdb=" N ASN C 169 " --> pdb=" O TYR C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 233 removed outlier: 3.774A pdb=" N GLU C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 243 removed outlier: 3.991A pdb=" N ALA C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP C 242 " --> pdb=" O ARG C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 removed outlier: 3.503A pdb=" N GLU C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'D' and resid 226 through 232 removed outlier: 3.511A pdb=" N GLU D 231 " --> pdb=" O SER D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 243 removed outlier: 4.182A pdb=" N ALA D 241 " --> pdb=" O GLN D 237 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 330 Processing helix chain 'D' and resid 332 through 335 No H-bonds generated for 'chain 'D' and resid 332 through 335' Processing helix chain 'D' and resid 337 through 343 Processing sheet with id= A, first strand: chain 'A' and resid 261 through 265 removed outlier: 6.107A pdb=" N ILE A 64 " --> pdb=" O GLN A 206 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU A 208 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE A 66 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N THR A 210 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG A 133 " --> pdb=" O PHE A 176 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 301 through 307 removed outlier: 3.738A pdb=" N ALA A 315 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 307 " --> pdb=" O PHE A 313 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 516 through 519 Processing sheet with id= D, first strand: chain 'A' and resid 560 through 564 removed outlier: 3.605A pdb=" N ILE A 611 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 156 through 160 removed outlier: 3.812A pdb=" N ARG B 174 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE B 66 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLN B 206 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU B 208 " --> pdb=" O PRO B 68 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 301 through 307 removed outlier: 3.617A pdb=" N PHE B 313 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR B 347 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL B 341 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N PHE B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 516 through 519 Processing sheet with id= H, first strand: chain 'B' and resid 560 through 564 removed outlier: 4.286A pdb=" N LYS B 560 " --> pdb=" O LYS B 607 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 611 " --> pdb=" O VAL B 562 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 131 through 134 removed outlier: 7.097A pdb=" N PHE B 176 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 12 through 15 removed outlier: 3.789A pdb=" N VAL C 12 " --> pdb=" O GLN C 58 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN C 58 " --> pdb=" O VAL C 12 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 32 through 34 removed outlier: 7.249A pdb=" N LEU C 74 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N VAL C 47 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR C 72 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 49 through 53 Processing sheet with id= M, first strand: chain 'C' and resid 246 through 248 removed outlier: 7.121A pdb=" N VAL C 282 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N CYS C 275 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS C 280 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS C 312 " --> pdb=" O HIS C 303 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N THR C 214 " --> pdb=" O GLY C 319 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 246 through 248 removed outlier: 3.793A pdb=" N GLU D 259 " --> pdb=" O LEU D 272 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 272 " --> pdb=" O GLU D 259 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL D 282 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N CYS D 275 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS D 280 " --> pdb=" O CYS D 275 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N THR D 214 " --> pdb=" O GLY D 319 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1275 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.11 Time building geometry restraints manager: 5.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4425 1.34 - 1.46: 2933 1.46 - 1.58: 6491 1.58 - 1.69: 10 1.69 - 1.81: 48 Bond restraints: 13907 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.695 0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" O5' ANP B 801 " pdb=" PA ANP B 801 " ideal model delta sigma weight residual 1.655 1.582 0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 13902 not shown) Histogram of bond angle deviations from ideal: 100.46 - 107.17: 320 107.17 - 113.88: 7840 113.88 - 120.59: 5638 120.59 - 127.29: 4850 127.29 - 134.00: 117 Bond angle restraints: 18765 Sorted by residual: angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 109.74 17.21 3.00e+00 1.11e-01 3.29e+01 angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 109.92 17.03 3.00e+00 1.11e-01 3.22e+01 angle pdb=" N VAL B 163 " pdb=" CA VAL B 163 " pdb=" C VAL B 163 " ideal model delta sigma weight residual 113.20 109.63 3.57 9.60e-01 1.09e+00 1.38e+01 angle pdb=" O1B ANP B 801 " pdb=" PB ANP B 801 " pdb=" O2B ANP B 801 " ideal model delta sigma weight residual 120.08 109.57 10.51 3.00e+00 1.11e-01 1.23e+01 angle pdb=" O1B ANP A 801 " pdb=" PB ANP A 801 " pdb=" O2B ANP A 801 " ideal model delta sigma weight residual 120.08 109.62 10.46 3.00e+00 1.11e-01 1.22e+01 ... (remaining 18760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.74: 8046 20.74 - 41.48: 365 41.48 - 62.23: 65 62.23 - 82.97: 18 82.97 - 103.71: 13 Dihedral angle restraints: 8507 sinusoidal: 3588 harmonic: 4919 Sorted by residual: dihedral pdb=" O1B ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PB ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sinusoidal sigma weight residual 35.15 -68.56 103.71 1 3.00e+01 1.11e-03 1.32e+01 dihedral pdb=" CB GLU B 644 " pdb=" CG GLU B 644 " pdb=" CD GLU B 644 " pdb=" OE1 GLU B 644 " ideal model delta sinusoidal sigma weight residual 0.00 89.41 -89.41 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" O1B ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PB ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sinusoidal sigma weight residual 35.15 -54.07 89.22 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 8504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1840 0.057 - 0.114: 230 0.114 - 0.171: 19 0.171 - 0.228: 0 0.228 - 0.285: 2 Chirality restraints: 2091 Sorted by residual: chirality pdb=" C3' ANP B 801 " pdb=" C2' ANP B 801 " pdb=" C4' ANP B 801 " pdb=" O3' ANP B 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA ILE C 154 " pdb=" N ILE C 154 " pdb=" C ILE C 154 " pdb=" CB ILE C 154 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 2088 not shown) Planarity restraints: 2395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 354 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO A 355 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 224 " 0.018 5.00e-02 4.00e+02 2.72e-02 1.19e+00 pdb=" N PRO C 225 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO C 225 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 225 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 320 " -0.017 5.00e-02 4.00e+02 2.55e-02 1.04e+00 pdb=" N PRO C 321 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 321 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 321 " -0.014 5.00e-02 4.00e+02 ... (remaining 2392 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.72: 547 2.72 - 3.32: 15199 3.32 - 3.93: 26597 3.93 - 4.53: 36412 4.53 - 5.14: 56921 Nonbonded interactions: 135676 Sorted by model distance: nonbonded pdb=" OD1 ASN B 37 " pdb="MG MG B 802 " model vdw 2.115 2.170 nonbonded pdb=" O3G ANP A 801 " pdb="MG MG A 802 " model vdw 2.115 2.170 nonbonded pdb=" O1B ANP B 801 " pdb="MG MG B 802 " model vdw 2.121 2.170 nonbonded pdb=" OD1 ASN A 37 " pdb="MG MG A 802 " model vdw 2.132 2.170 nonbonded pdb=" O3G ANP B 801 " pdb="MG MG B 802 " model vdw 2.163 2.170 ... (remaining 135671 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 'A' selection = (chain 'B' and (resid 3 through 212 or resid 259 through 675 or resid 801 throug \ h 803)) } 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.450 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 38.580 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.144 13907 Z= 0.171 Angle : 0.474 17.210 18765 Z= 0.234 Chirality : 0.040 0.285 2091 Planarity : 0.002 0.029 2395 Dihedral : 12.833 103.711 5305 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.20 % Allowed : 5.51 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.16), residues: 1658 helix: -3.56 (0.11), residues: 604 sheet: -1.50 (0.26), residues: 349 loop : -2.42 (0.18), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP D 242 HIS 0.001 0.000 HIS D 309 PHE 0.003 0.000 PHE A 660 TYR 0.003 0.000 TYR A 456 ARG 0.002 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 352 time to evaluate : 1.505 Fit side-chains TARDY: cannot create tardy model for: "LYS A 211 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS B 211 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 134 LYS cc_start: 0.6151 (mttt) cc_final: 0.5897 (ttpt) REVERT: C 162 LYS cc_start: 0.6304 (mttp) cc_final: 0.5858 (mmtp) REVERT: C 329 ARG cc_start: 0.7426 (ttp-170) cc_final: 0.7213 (ttm-80) REVERT: D 217 TYR cc_start: 0.6840 (t80) cc_final: 0.6551 (t80) outliers start: 18 outliers final: 11 residues processed: 366 average time/residue: 0.3202 time to fit residues: 158.7817 Evaluate side-chains 195 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 184 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 42 optimal weight: 0.3980 chunk 84 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 150 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 119 GLN A 135 GLN A 181 GLN A 380 GLN A 409 GLN A 430 GLN A 584 ASN A 592 GLN B 55 GLN B 135 GLN B 276 ASN B 578 GLN B 592 GLN C 57 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13907 Z= 0.150 Angle : 0.457 5.559 18765 Z= 0.240 Chirality : 0.042 0.152 2091 Planarity : 0.003 0.040 2395 Dihedral : 5.601 85.768 1873 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.86 % Allowed : 12.29 % Favored : 85.85 % 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: -2.53 (0.18), residues: 1658 helix: -1.78 (0.18), residues: 615 sheet: -1.12 (0.26), residues: 368 loop : -1.70 (0.21), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 285 HIS 0.004 0.001 HIS D 303 PHE 0.020 0.001 PHE A 104 TYR 0.013 0.001 TYR C 217 ARG 0.004 0.000 ARG B 666 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 192 time to evaluate : 1.536 Fit side-chains TARDY: cannot create tardy model for: "LYS A 211 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 310 GLN cc_start: 0.7301 (pm20) cc_final: 0.6608 (pm20) REVERT: A 532 GLU cc_start: 0.7083 (tt0) cc_final: 0.6801 (tt0) REVERT: A 585 MET cc_start: 0.8502 (tpt) cc_final: 0.7553 (tpt) REVERT: A 589 MET cc_start: 0.8065 (mmm) cc_final: 0.7749 (mmt) REVERT: B 314 ARG cc_start: 0.7002 (mtp85) cc_final: 0.6789 (mtp180) REVERT: C 162 LYS cc_start: 0.6321 (mttp) cc_final: 0.5850 (mmtp) REVERT: D 217 TYR cc_start: 0.7120 (t80) cc_final: 0.6834 (t80) outliers start: 28 outliers final: 13 residues processed: 214 average time/residue: 0.2749 time to fit residues: 84.8325 Evaluate side-chains 172 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 159 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 278 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 151 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 121 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 ASN D 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13907 Z= 0.146 Angle : 0.440 7.881 18765 Z= 0.229 Chirality : 0.042 0.162 2091 Planarity : 0.003 0.044 2395 Dihedral : 5.345 80.269 1858 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.19 % Allowed : 14.29 % Favored : 83.52 % 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: -1.58 (0.20), residues: 1658 helix: -0.81 (0.20), residues: 619 sheet: -0.74 (0.26), residues: 377 loop : -1.27 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 285 HIS 0.003 0.001 HIS C 303 PHE 0.015 0.001 PHE A 643 TYR 0.007 0.001 TYR B 469 ARG 0.003 0.000 ARG C 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 163 time to evaluate : 1.652 Fit side-chains TARDY: cannot create tardy model for: "LYS A 211 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 310 GLN cc_start: 0.7500 (pm20) cc_final: 0.6987 (pm20) REVERT: A 532 GLU cc_start: 0.7247 (tt0) cc_final: 0.6867 (tt0) REVERT: A 585 MET cc_start: 0.8621 (tpt) cc_final: 0.7701 (tpt) REVERT: A 589 MET cc_start: 0.8002 (mmm) cc_final: 0.7715 (mmp) REVERT: B 11 GLU cc_start: 0.7004 (tp30) cc_final: 0.6784 (tp30) REVERT: C 162 LYS cc_start: 0.6315 (mttp) cc_final: 0.6002 (mmtp) REVERT: D 217 TYR cc_start: 0.6872 (t80) cc_final: 0.6619 (t80) outliers start: 33 outliers final: 23 residues processed: 186 average time/residue: 0.2634 time to fit residues: 70.9623 Evaluate side-chains 168 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 145 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 349 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 0.2980 chunk 113 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13907 Z= 0.228 Angle : 0.478 6.175 18765 Z= 0.250 Chirality : 0.043 0.167 2091 Planarity : 0.003 0.048 2395 Dihedral : 5.676 80.395 1857 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.72 % Allowed : 15.15 % Favored : 82.13 % 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: -1.21 (0.20), residues: 1658 helix: -0.50 (0.21), residues: 623 sheet: -0.63 (0.26), residues: 382 loop : -1.02 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 285 HIS 0.004 0.001 HIS C 303 PHE 0.024 0.001 PHE C 89 TYR 0.010 0.001 TYR A 125 ARG 0.004 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 160 time to evaluate : 1.534 Fit side-chains TARDY: cannot create tardy model for: "LYS A 211 " (corrupted residue). Skipping it. REVERT: A 585 MET cc_start: 0.8707 (tpt) cc_final: 0.7980 (tpt) REVERT: B 349 GLU cc_start: 0.6054 (tp30) cc_final: 0.5779 (mm-30) REVERT: C 28 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7090 (mt) REVERT: C 162 LYS cc_start: 0.6343 (mttp) cc_final: 0.5923 (mmtp) REVERT: C 244 ARG cc_start: 0.8371 (mtt180) cc_final: 0.8038 (mtt180) REVERT: D 217 TYR cc_start: 0.7161 (t80) cc_final: 0.6756 (t80) REVERT: D 327 ARG cc_start: 0.8103 (ttt180) cc_final: 0.7866 (ttt180) outliers start: 41 outliers final: 27 residues processed: 186 average time/residue: 0.2859 time to fit residues: 76.5908 Evaluate side-chains 176 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 119 optimal weight: 0.0370 chunk 66 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13907 Z= 0.217 Angle : 0.473 6.885 18765 Z= 0.246 Chirality : 0.043 0.158 2091 Planarity : 0.003 0.048 2395 Dihedral : 5.738 77.997 1857 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.79 % Allowed : 16.21 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.21), residues: 1658 helix: -0.34 (0.21), residues: 623 sheet: -0.50 (0.27), residues: 374 loop : -0.90 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 285 HIS 0.003 0.001 HIS C 303 PHE 0.019 0.001 PHE C 89 TYR 0.008 0.001 TYR B 543 ARG 0.003 0.000 ARG D 244 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 148 time to evaluate : 1.646 Fit side-chains TARDY: cannot create tardy model for: "LYS A 211 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 585 MET cc_start: 0.8698 (tpt) cc_final: 0.8033 (tpt) REVERT: B 312 GLU cc_start: 0.6416 (mm-30) cc_final: 0.6212 (mm-30) REVERT: C 28 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7155 (mt) REVERT: C 162 LYS cc_start: 0.6428 (mttp) cc_final: 0.6017 (mmtp) REVERT: C 317 TRP cc_start: 0.8861 (t60) cc_final: 0.8393 (t60) REVERT: D 217 TYR cc_start: 0.7169 (t80) cc_final: 0.6800 (t80) REVERT: D 327 ARG cc_start: 0.7990 (ttt180) cc_final: 0.7511 (ttt180) outliers start: 42 outliers final: 31 residues processed: 179 average time/residue: 0.2568 time to fit residues: 67.7994 Evaluate side-chains 177 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 145 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 320 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13907 Z= 0.241 Angle : 0.486 6.808 18765 Z= 0.253 Chirality : 0.044 0.157 2091 Planarity : 0.003 0.048 2395 Dihedral : 5.820 77.441 1857 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.86 % Allowed : 16.74 % Favored : 80.40 % 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: -0.94 (0.21), residues: 1658 helix: -0.29 (0.21), residues: 628 sheet: -0.52 (0.27), residues: 373 loop : -0.82 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 285 HIS 0.004 0.001 HIS A 197 PHE 0.016 0.001 PHE C 89 TYR 0.008 0.001 TYR B 203 ARG 0.013 0.001 ARG B 666 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 150 time to evaluate : 1.711 Fit side-chains TARDY: cannot create tardy model for: "LYS A 211 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 585 MET cc_start: 0.8735 (tpt) cc_final: 0.8078 (tpt) REVERT: B 314 ARG cc_start: 0.7123 (mtp85) cc_final: 0.6912 (mtp180) REVERT: C 28 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7144 (mt) REVERT: C 317 TRP cc_start: 0.8861 (OUTLIER) cc_final: 0.8359 (t-100) REVERT: D 217 TYR cc_start: 0.7207 (t80) cc_final: 0.6794 (t80) outliers start: 43 outliers final: 33 residues processed: 177 average time/residue: 0.2554 time to fit residues: 66.9251 Evaluate side-chains 166 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 131 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 317 TRP Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 90 optimal weight: 0.0770 chunk 135 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 592 GLN ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13907 Z= 0.262 Angle : 0.496 6.874 18765 Z= 0.258 Chirality : 0.044 0.157 2091 Planarity : 0.003 0.048 2395 Dihedral : 5.895 76.668 1857 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.06 % Allowed : 17.01 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.21), residues: 1658 helix: -0.20 (0.21), residues: 622 sheet: -0.60 (0.27), residues: 368 loop : -0.74 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 285 HIS 0.004 0.001 HIS A 197 PHE 0.015 0.001 PHE C 89 TYR 0.009 0.001 TYR B 543 ARG 0.008 0.001 ARG B 666 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 138 time to evaluate : 1.752 Fit side-chains TARDY: cannot create tardy model for: "LYS A 211 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 385 MET cc_start: 0.8030 (tpp) cc_final: 0.7712 (tpp) REVERT: A 585 MET cc_start: 0.8701 (tpt) cc_final: 0.8007 (tpt) REVERT: B 314 ARG cc_start: 0.7096 (mtp85) cc_final: 0.6892 (mtp180) REVERT: B 349 GLU cc_start: 0.6317 (mm-30) cc_final: 0.6052 (mm-30) REVERT: C 28 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7095 (mt) REVERT: C 113 ILE cc_start: 0.3749 (mt) cc_final: 0.3545 (mt) REVERT: C 127 ILE cc_start: 0.5431 (OUTLIER) cc_final: 0.5220 (mp) REVERT: C 317 TRP cc_start: 0.8888 (OUTLIER) cc_final: 0.8371 (t-100) REVERT: D 217 TYR cc_start: 0.7297 (t80) cc_final: 0.6841 (t80) outliers start: 46 outliers final: 35 residues processed: 172 average time/residue: 0.2506 time to fit residues: 64.6418 Evaluate side-chains 174 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 136 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 317 TRP Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 0.6980 chunk 95 optimal weight: 0.3980 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 0.0570 chunk 30 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13907 Z= 0.126 Angle : 0.444 7.227 18765 Z= 0.231 Chirality : 0.042 0.155 2091 Planarity : 0.003 0.045 2395 Dihedral : 5.678 74.964 1857 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.46 % Allowed : 18.14 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.21), residues: 1658 helix: -0.07 (0.21), residues: 629 sheet: -0.41 (0.27), residues: 373 loop : -0.73 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 148 HIS 0.004 0.001 HIS A 197 PHE 0.015 0.001 PHE C 89 TYR 0.007 0.001 TYR B 203 ARG 0.006 0.000 ARG B 666 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 152 time to evaluate : 1.637 Fit side-chains TARDY: cannot create tardy model for: "LYS A 211 " (corrupted residue). Skipping it. REVERT: A 585 MET cc_start: 0.8692 (tpt) cc_final: 0.8049 (tpt) REVERT: B 314 ARG cc_start: 0.7026 (mtp85) cc_final: 0.6786 (mtp180) REVERT: B 349 GLU cc_start: 0.6075 (mm-30) cc_final: 0.5860 (mm-30) REVERT: C 28 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7263 (mt) REVERT: C 134 LYS cc_start: 0.6462 (mttt) cc_final: 0.5701 (mtmt) REVERT: C 317 TRP cc_start: 0.8838 (OUTLIER) cc_final: 0.8512 (t60) outliers start: 37 outliers final: 24 residues processed: 176 average time/residue: 0.2515 time to fit residues: 65.6039 Evaluate side-chains 160 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 317 TRP Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 89 optimal weight: 0.0980 chunk 64 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13907 Z= 0.161 Angle : 0.463 8.457 18765 Z= 0.240 Chirality : 0.042 0.151 2091 Planarity : 0.003 0.046 2395 Dihedral : 5.648 74.183 1853 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.13 % Allowed : 19.47 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.21), residues: 1658 helix: -0.06 (0.21), residues: 627 sheet: -0.39 (0.27), residues: 368 loop : -0.70 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 581 HIS 0.004 0.001 HIS A 197 PHE 0.019 0.001 PHE A 643 TYR 0.006 0.001 TYR B 203 ARG 0.006 0.000 ARG B 666 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 1.680 Fit side-chains TARDY: cannot create tardy model for: "LYS A 211 " (corrupted residue). Skipping it. REVERT: A 585 MET cc_start: 0.8595 (tpt) cc_final: 0.7861 (tpt) REVERT: B 314 ARG cc_start: 0.7042 (mtp85) cc_final: 0.6810 (mtp180) REVERT: B 349 GLU cc_start: 0.6228 (mm-30) cc_final: 0.6014 (mm-30) REVERT: C 28 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7320 (mt) REVERT: C 134 LYS cc_start: 0.6521 (mttt) cc_final: 0.5682 (mtmt) REVERT: C 317 TRP cc_start: 0.8869 (OUTLIER) cc_final: 0.8409 (t60) outliers start: 32 outliers final: 28 residues processed: 162 average time/residue: 0.2497 time to fit residues: 61.8002 Evaluate side-chains 164 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 134 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 317 TRP Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 131 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13907 Z= 0.238 Angle : 0.500 7.785 18765 Z= 0.260 Chirality : 0.044 0.152 2091 Planarity : 0.003 0.046 2395 Dihedral : 5.806 76.693 1853 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.06 % Allowed : 19.67 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1658 helix: -0.08 (0.21), residues: 625 sheet: -0.50 (0.27), residues: 367 loop : -0.69 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 581 HIS 0.004 0.001 HIS A 197 PHE 0.014 0.001 PHE A 643 TYR 0.008 0.001 TYR B 184 ARG 0.006 0.000 ARG B 666 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 129 time to evaluate : 1.808 Fit side-chains TARDY: cannot create tardy model for: "LYS A 211 " (corrupted residue). Skipping it. REVERT: A 585 MET cc_start: 0.8596 (tpt) cc_final: 0.7704 (tpt) REVERT: B 314 ARG cc_start: 0.7151 (mtp85) cc_final: 0.6928 (mtp180) REVERT: B 349 GLU cc_start: 0.6365 (mm-30) cc_final: 0.6164 (mm-30) REVERT: C 28 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7402 (mt) REVERT: C 134 LYS cc_start: 0.6429 (mttt) cc_final: 0.5721 (mtmt) REVERT: C 317 TRP cc_start: 0.8875 (OUTLIER) cc_final: 0.8339 (t-100) outliers start: 31 outliers final: 27 residues processed: 150 average time/residue: 0.2582 time to fit residues: 59.1208 Evaluate side-chains 155 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 317 TRP Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.120570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.100828 restraints weight = 24436.005| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.26 r_work: 0.3205 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13907 Z= 0.234 Angle : 0.500 8.581 18765 Z= 0.259 Chirality : 0.044 0.151 2091 Planarity : 0.003 0.046 2395 Dihedral : 5.803 75.649 1853 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.33 % Allowed : 19.53 % Favored : 78.14 % 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: -0.75 (0.21), residues: 1658 helix: -0.08 (0.21), residues: 616 sheet: -0.58 (0.27), residues: 368 loop : -0.65 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 581 HIS 0.004 0.001 HIS A 197 PHE 0.014 0.001 PHE A 643 TYR 0.007 0.001 TYR C 107 ARG 0.005 0.000 ARG B 666 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2937.20 seconds wall clock time: 54 minutes 18.80 seconds (3258.80 seconds total)