Starting phenix.real_space_refine on Fri Mar 15 17:18:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xle_22241/03_2024/6xle_22241_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xle_22241/03_2024/6xle_22241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xle_22241/03_2024/6xle_22241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xle_22241/03_2024/6xle_22241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xle_22241/03_2024/6xle_22241_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xle_22241/03_2024/6xle_22241_updated.pdb" } resolution = 2.74 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= 0.006 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 22 5.16 5 C 7824 2.51 5 N 2008 2.21 5 O 2376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 76": "OE1" <-> "OE2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "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 76": "OE1" <-> "OE2" Residue "B ASP 132": "OD1" <-> "OD2" Residue "B ARG 133": "NH1" <-> "NH2" Residue "B TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B ARG 389": "NH1" <-> "NH2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 502": "OD1" <-> "OD2" Residue "B PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B TYR 565": "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 PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C GLU 325": "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 335": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 244": "NH1" <-> "NH2" Residue "D PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 308": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12240 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4897 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 20, 'TRANS': 585} Chain breaks: 3 Chain: "B" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4897 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 20, 'TRANS': 585} Chain breaks: 3 Chain: "C" 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: "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: 6.69, per 1000 atoms: 0.55 Number of scatterers: 12240 At special positions: 0 Unit cell: (104.841, 92.133, 132.375, 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 22 16.00 P 6 15.00 Mg 2 11.99 O 2376 8.00 N 2008 7.00 C 7824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.86 Conformation dependent library (CDL) restraints added in 2.0 seconds 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2868 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 10 sheets defined 35.4% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 12 through 18 removed outlier: 4.321A pdb=" N SER A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 49 removed outlier: 3.578A pdb=" N LEU A 31 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 34 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE A 35 " --> pdb=" O ARG A 32 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 41 " --> pdb=" O ALA A 38 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE A 45 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 48 " --> pdb=" O ILE A 45 " (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 106 Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.614A pdb=" N PHE A 128 " --> pdb=" O TYR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 185 removed outlier: 3.903A pdb=" N LEU A 182 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU A 183 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR A 184 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 282 through 292 removed outlier: 3.643A pdb=" N SER A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 404 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.602A pdb=" N VAL A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 438 removed outlier: 3.892A pdb=" N LYS A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 4.200A 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 485 through 489 Processing helix chain 'A' and resid 502 through 509 removed outlier: 3.824A pdb=" N GLN A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 540 removed outlier: 3.920A pdb=" N GLU A 535 " --> pdb=" O GLU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 557 removed outlier: 3.501A pdb=" N ILE A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLN A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 591 removed outlier: 3.818A pdb=" N ARG A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 626 removed outlier: 3.668A pdb=" N LYS A 623 " --> pdb=" O LYS A 619 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 624 " --> pdb=" O GLU A 620 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A 626 " --> pdb=" O LYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 650 removed outlier: 3.892A pdb=" N ASP A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 638 " --> pdb=" O THR A 634 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 648 " --> pdb=" O GLU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 672 Processing helix chain 'B' and resid 12 through 21 removed outlier: 4.492A pdb=" N SER B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 49 removed outlier: 3.523A pdb=" N GLU B 33 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 34 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN B 37 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 45 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.572A 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 88 through 91 No H-bonds generated for 'chain 'B' and resid 88 through 91' Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 123 through 129 removed outlier: 3.528A pdb=" N LEU B 127 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE B 128 " --> pdb=" O TYR B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 185 Processing helix chain 'B' and resid 187 through 197 Processing helix chain 'B' and resid 277 through 279 No H-bonds generated for 'chain 'B' and resid 277 through 279' Processing helix chain 'B' and resid 282 through 292 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 384 through 404 Processing helix chain 'B' and resid 408 through 416 removed outlier: 3.683A pdb=" N LYS B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 427 removed outlier: 3.592A pdb=" N VAL B 425 " --> pdb=" O ILE B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 438 removed outlier: 3.698A pdb=" N LYS B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.559A 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: 4.081A pdb=" N GLN B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 542 removed outlier: 3.632A pdb=" N LYS B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 539 " --> pdb=" O GLU B 535 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B 542 " --> pdb=" O LYS B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 557 removed outlier: 3.577A pdb=" N ASP B 552 " --> pdb=" O LYS B 548 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASP B 556 " --> pdb=" O ASP B 552 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLN B 557 " --> pdb=" O ILE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 589 removed outlier: 3.825A pdb=" N ARG B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 626 removed outlier: 3.715A pdb=" N LYS B 623 " --> pdb=" O LYS B 619 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 625 " --> pdb=" O LEU B 621 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP B 626 " --> pdb=" O LYS B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 650 removed outlier: 3.742A pdb=" N ASP B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU B 638 " --> pdb=" O THR B 634 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 641 " --> pdb=" O ASP B 637 " (cutoff:3.500A) removed outlier: 3.569A 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 226 through 232 removed outlier: 3.982A pdb=" N GLU C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 243 removed outlier: 3.896A pdb=" N ALA C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TRP C 242 " --> pdb=" O ARG C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 324 No H-bonds generated for 'chain 'C' and resid 322 through 324' Processing helix chain 'C' and resid 327 through 335 removed outlier: 3.580A pdb=" N GLU C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'D' and resid 226 through 232 Processing helix chain 'D' and resid 236 through 243 removed outlier: 3.994A pdb=" N ALA D 241 " --> pdb=" O GLN D 237 " (cutoff:3.500A) removed outlier: 3.927A 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 156 through 160 removed outlier: 7.535A pdb=" N PHE A 176 " --> pdb=" O ASP A 132 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL A 134 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG A 174 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL A 136 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL A 172 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N SER A 138 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY A 170 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE A 66 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLN A 206 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU A 208 " --> pdb=" O PRO A 68 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 301 through 308 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 561 through 563 removed outlier: 6.332A pdb=" N PHE A 609 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 156 through 160 removed outlier: 7.169A pdb=" N PHE B 176 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL B 134 " --> pdb=" O ARG B 174 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ARG B 174 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL B 136 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 172 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER B 138 " --> pdb=" O GLY B 170 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLY B 170 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE B 66 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN B 206 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.138A 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: 3.877A pdb=" N THR B 347 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL B 341 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 5.181A 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 561 through 564 removed outlier: 8.891A pdb=" N VAL B 562 " --> pdb=" O LYS B 607 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE B 609 " --> pdb=" O VAL B 562 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N SER B 564 " --> pdb=" O PHE B 609 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ILE B 611 " --> pdb=" O SER B 564 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 246 through 248 removed outlier: 3.634A pdb=" N GLU C 259 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C 282 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N CYS C 275 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LYS C 280 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS C 312 " --> pdb=" O HIS C 303 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N THR C 214 " --> pdb=" O GLY C 319 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 246 through 248 removed outlier: 3.644A pdb=" N GLU D 259 " --> pdb=" O LEU D 272 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL D 282 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N CYS D 275 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS D 280 " --> pdb=" O CYS D 275 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N THR D 214 " --> pdb=" O GLY D 319 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1083 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.59 Time building geometry restraints manager: 5.22 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: 3962 1.34 - 1.46: 2647 1.46 - 1.58: 5807 1.58 - 1.69: 10 1.69 - 1.81: 42 Bond restraints: 12468 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" O5' ANP A 801 " pdb=" PA ANP A 801 " ideal model delta sigma weight residual 1.655 1.581 0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 12463 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.07: 282 107.07 - 113.80: 6942 113.80 - 120.52: 5068 120.52 - 127.25: 4440 127.25 - 133.98: 98 Bond angle restraints: 16830 Sorted by residual: angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 109.64 17.31 3.00e+00 1.11e-01 3.33e+01 angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 109.85 17.10 3.00e+00 1.11e-01 3.25e+01 angle pdb=" O1B ANP B 801 " pdb=" PB ANP B 801 " pdb=" O2B ANP B 801 " ideal model delta sigma weight residual 120.08 109.54 10.54 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 120.08 109.58 10.50 3.00e+00 1.11e-01 1.22e+01 angle pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " pdb=" O2G ANP B 801 " ideal model delta sigma weight residual 101.05 109.72 -8.67 3.00e+00 1.11e-01 8.35e+00 ... (remaining 16825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.24: 7358 18.24 - 36.49: 195 36.49 - 54.73: 40 54.73 - 72.98: 13 72.98 - 91.22: 20 Dihedral angle restraints: 7626 sinusoidal: 3222 harmonic: 4404 Sorted by residual: dihedral pdb=" CA ASP B 132 " pdb=" CB ASP B 132 " pdb=" CG ASP B 132 " pdb=" OD1 ASP B 132 " ideal model delta sinusoidal sigma weight residual -30.00 -88.36 58.36 1 2.00e+01 2.50e-03 1.14e+01 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 -56.07 91.22 1 3.00e+01 1.11e-03 1.09e+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 -53.01 88.16 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 7623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1645 0.055 - 0.109: 207 0.109 - 0.164: 26 0.164 - 0.218: 0 0.218 - 0.273: 2 Chirality restraints: 1880 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 -2.63 0.27 2.00e-01 2.50e+01 1.86e+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 A 64 " pdb=" N ILE A 64 " pdb=" C ILE A 64 " pdb=" CB ILE A 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 ... (remaining 1877 not shown) Planarity restraints: 2146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 354 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.91e+00 pdb=" N PRO A 355 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 354 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.12e+00 pdb=" N PRO B 355 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 355 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 355 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 570 " -0.017 5.00e-02 4.00e+02 2.58e-02 1.07e+00 pdb=" N PRO B 571 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 571 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 571 " -0.015 5.00e-02 4.00e+02 ... (remaining 2143 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.70: 326 2.70 - 3.31: 13643 3.31 - 3.92: 24147 3.92 - 4.53: 33119 4.53 - 5.14: 51594 Nonbonded interactions: 122829 Sorted by model distance: nonbonded pdb=" OD1 ASN B 37 " pdb="MG MG B 802 " model vdw 2.095 2.170 nonbonded pdb=" OD1 ASN A 37 " pdb="MG MG A 802 " model vdw 2.096 2.170 nonbonded pdb=" OE2 GLU B 33 " pdb="MG MG B 802 " model vdw 2.110 2.170 nonbonded pdb=" O1B ANP B 801 " pdb="MG MG B 802 " model vdw 2.127 2.170 nonbonded pdb=" O1A ANP B 801 " pdb="MG MG B 802 " model vdw 2.213 2.170 ... (remaining 122824 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' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.380 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 33.880 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 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 0.143 12468 Z= 0.216 Angle : 0.488 17.312 16830 Z= 0.237 Chirality : 0.039 0.273 1880 Planarity : 0.003 0.035 2146 Dihedral : 10.218 91.219 4758 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.07 % Allowed : 3.19 % Favored : 96.73 % 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: -3.54 (0.18), residues: 1482 helix: -3.59 (0.12), residues: 528 sheet: -1.42 (0.28), residues: 326 loop : -1.46 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 273 HIS 0.001 0.000 HIS D 284 PHE 0.005 0.001 PHE D 283 TYR 0.006 0.001 TYR A 285 ARG 0.001 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 357 time to evaluate : 1.287 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 358 average time/residue: 1.6457 time to fit residues: 625.6410 Evaluate side-chains 162 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.7980 chunk 112 optimal weight: 0.0470 chunk 62 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 0.4980 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 151 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN A 431 ASN A 557 GLN A 592 GLN B 197 HIS B 442 ASN ** B 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 GLN C 207 GLN C 223 ASN C 284 HIS D 303 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12468 Z= 0.217 Angle : 0.526 6.002 16830 Z= 0.273 Chirality : 0.042 0.151 1880 Planarity : 0.004 0.040 2146 Dihedral : 6.068 64.262 1666 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.57 % Allowed : 14.64 % Favored : 81.80 % 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: -2.13 (0.19), residues: 1482 helix: -1.76 (0.18), residues: 560 sheet: -1.21 (0.27), residues: 310 loop : -0.91 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 285 HIS 0.003 0.001 HIS B 463 PHE 0.015 0.002 PHE A 660 TYR 0.016 0.002 TYR A 456 ARG 0.004 0.001 ARG B 663 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 179 time to evaluate : 1.476 Fit side-chains REVERT: B 11 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6896 (tm-30) REVERT: B 14 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7359 (tm-30) REVERT: B 268 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7276 (mptp) REVERT: B 356 GLU cc_start: 0.7506 (tp30) cc_final: 0.7276 (tp30) REVERT: B 589 MET cc_start: 0.8436 (mmm) cc_final: 0.8176 (mmm) REVERT: C 316 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7704 (mmmt) REVERT: D 247 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7717 (tt0) REVERT: D 331 ASN cc_start: 0.8996 (m110) cc_final: 0.8758 (m110) outliers start: 48 outliers final: 9 residues processed: 211 average time/residue: 1.3443 time to fit residues: 308.1837 Evaluate side-chains 142 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 247 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 134 optimal weight: 0.0020 chunk 145 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN B 373 ASN B 466 ASN C 223 ASN D 284 HIS D 314 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12468 Z= 0.149 Angle : 0.456 7.736 16830 Z= 0.239 Chirality : 0.040 0.140 1880 Planarity : 0.003 0.044 2146 Dihedral : 5.913 68.984 1666 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.15 % Allowed : 18.20 % Favored : 79.64 % 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: -1.33 (0.20), residues: 1482 helix: -0.82 (0.21), residues: 562 sheet: -0.83 (0.27), residues: 326 loop : -0.73 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 148 HIS 0.002 0.000 HIS B 463 PHE 0.012 0.001 PHE A 6 TYR 0.008 0.001 TYR A 203 ARG 0.002 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 1.465 Fit side-chains REVERT: A 356 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7448 (tp30) REVERT: B 268 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7208 (mptp) REVERT: B 308 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6317 (mm-30) REVERT: B 356 GLU cc_start: 0.7540 (tp30) cc_final: 0.7290 (tp30) REVERT: B 548 LYS cc_start: 0.8323 (ptpt) cc_final: 0.8070 (mtmm) REVERT: D 247 GLN cc_start: 0.8025 (mt0) cc_final: 0.7765 (tt0) REVERT: D 331 ASN cc_start: 0.8954 (m110) cc_final: 0.8697 (m110) outliers start: 29 outliers final: 7 residues processed: 162 average time/residue: 1.3113 time to fit residues: 230.2542 Evaluate side-chains 129 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain D residue 218 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 2.9990 chunk 101 optimal weight: 0.0570 chunk 69 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN C 223 ASN D 223 ASN D 314 GLN D 331 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12468 Z= 0.255 Angle : 0.522 7.358 16830 Z= 0.269 Chirality : 0.042 0.138 1880 Planarity : 0.004 0.043 2146 Dihedral : 6.429 73.880 1666 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.19 % Allowed : 16.94 % Favored : 79.87 % 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: 1482 helix: -0.29 (0.22), residues: 542 sheet: -0.72 (0.26), residues: 326 loop : -0.67 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 285 HIS 0.003 0.001 HIS B 463 PHE 0.015 0.002 PHE C 344 TYR 0.025 0.002 TYR C 230 ARG 0.004 0.000 ARG B 663 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 136 time to evaluate : 1.847 Fit side-chains revert: symmetry clash REVERT: A 539 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7008 (tp30) REVERT: B 268 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7552 (mptp) REVERT: B 356 GLU cc_start: 0.7676 (tp30) cc_final: 0.7410 (tp30) REVERT: B 548 LYS cc_start: 0.8387 (ptpt) cc_final: 0.8163 (mtmm) REVERT: D 238 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7334 (ttp-170) REVERT: D 247 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7898 (tt0) outliers start: 43 outliers final: 11 residues processed: 169 average time/residue: 1.2838 time to fit residues: 234.1352 Evaluate side-chains 139 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 247 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 12468 Z= 0.353 Angle : 0.572 7.962 16830 Z= 0.295 Chirality : 0.045 0.138 1880 Planarity : 0.004 0.044 2146 Dihedral : 6.809 72.428 1666 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.01 % Allowed : 16.42 % Favored : 79.57 % 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: 1482 helix: -0.12 (0.22), residues: 554 sheet: -0.76 (0.27), residues: 318 loop : -0.73 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 285 HIS 0.005 0.001 HIS B 463 PHE 0.018 0.002 PHE C 344 TYR 0.016 0.002 TYR C 230 ARG 0.006 0.001 ARG B 663 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 129 time to evaluate : 1.243 Fit side-chains REVERT: A 384 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7666 (tp) REVERT: B 268 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7555 (mptp) REVERT: B 312 GLU cc_start: 0.6763 (tt0) cc_final: 0.6562 (tt0) REVERT: B 548 LYS cc_start: 0.8297 (ptpt) cc_final: 0.8069 (mtmm) REVERT: D 238 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7412 (ttp-170) REVERT: D 247 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7857 (tt0) REVERT: D 316 LYS cc_start: 0.8084 (tptt) cc_final: 0.7753 (mmmt) outliers start: 54 outliers final: 21 residues processed: 165 average time/residue: 1.4750 time to fit residues: 261.5622 Evaluate side-chains 144 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain B residue 623 LYS Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 247 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.0570 chunk 128 optimal weight: 0.0030 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 overall best weight: 0.4508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 ASN C 314 GLN D 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12468 Z= 0.131 Angle : 0.451 7.095 16830 Z= 0.234 Chirality : 0.040 0.138 1880 Planarity : 0.003 0.044 2146 Dihedral : 6.260 78.915 1666 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.71 % Allowed : 19.47 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.21), residues: 1482 helix: 0.11 (0.22), residues: 566 sheet: -0.57 (0.27), residues: 326 loop : -0.59 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 148 HIS 0.003 0.001 HIS C 303 PHE 0.013 0.001 PHE B 6 TYR 0.016 0.001 TYR C 230 ARG 0.002 0.000 ARG B 663 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 1.551 Fit side-chains REVERT: A 384 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7602 (tp) REVERT: A 539 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7148 (tp30) REVERT: B 312 GLU cc_start: 0.6636 (tt0) cc_final: 0.6410 (tt0) REVERT: C 247 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7891 (tp-100) REVERT: C 311 THR cc_start: 0.8811 (t) cc_final: 0.8596 (t) REVERT: D 238 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7433 (ttp-170) REVERT: D 316 LYS cc_start: 0.8003 (tptt) cc_final: 0.7722 (mmmt) outliers start: 23 outliers final: 7 residues processed: 155 average time/residue: 1.4734 time to fit residues: 245.9013 Evaluate side-chains 134 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 245 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 120 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 89 optimal weight: 0.0870 chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12468 Z= 0.150 Angle : 0.460 6.574 16830 Z= 0.238 Chirality : 0.040 0.134 1880 Planarity : 0.003 0.043 2146 Dihedral : 6.211 77.398 1666 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.56 % Allowed : 19.76 % Favored : 78.68 % 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: -0.47 (0.21), residues: 1482 helix: 0.21 (0.22), residues: 574 sheet: -0.52 (0.27), residues: 330 loop : -0.51 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 148 HIS 0.003 0.001 HIS D 284 PHE 0.012 0.001 PHE B 6 TYR 0.009 0.001 TYR A 203 ARG 0.002 0.000 ARG B 663 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 1.436 Fit side-chains REVERT: A 539 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7059 (tp30) REVERT: B 312 GLU cc_start: 0.6621 (tt0) cc_final: 0.6401 (tt0) REVERT: C 247 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7898 (tp-100) REVERT: C 316 LYS cc_start: 0.7812 (mmmt) cc_final: 0.7044 (mmmt) REVERT: D 238 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7443 (ttp-170) REVERT: D 316 LYS cc_start: 0.7939 (tptt) cc_final: 0.7652 (mmmt) outliers start: 21 outliers final: 9 residues processed: 146 average time/residue: 1.4845 time to fit residues: 233.0689 Evaluate side-chains 132 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 245 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN D 314 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12468 Z= 0.298 Angle : 0.541 6.638 16830 Z= 0.279 Chirality : 0.043 0.134 1880 Planarity : 0.004 0.043 2146 Dihedral : 6.584 73.735 1666 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.49 % Allowed : 19.99 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.21), residues: 1482 helix: 0.21 (0.22), residues: 568 sheet: -0.61 (0.27), residues: 332 loop : -0.63 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 285 HIS 0.004 0.001 HIS B 463 PHE 0.012 0.002 PHE C 344 TYR 0.012 0.002 TYR A 203 ARG 0.004 0.000 ARG B 663 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 1.432 Fit side-chains REVERT: A 57 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: A 539 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7029 (tp30) REVERT: B 312 GLU cc_start: 0.6721 (tt0) cc_final: 0.6517 (tt0) REVERT: C 247 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7946 (tp-100) REVERT: C 316 LYS cc_start: 0.7878 (mmmt) cc_final: 0.7048 (mmmt) REVERT: D 238 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7460 (ttp-170) REVERT: D 316 LYS cc_start: 0.8000 (tptt) cc_final: 0.7690 (mmmt) outliers start: 20 outliers final: 12 residues processed: 134 average time/residue: 1.4803 time to fit residues: 213.3706 Evaluate side-chains 131 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 245 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 120 optimal weight: 9.9990 chunk 125 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12468 Z= 0.162 Angle : 0.476 6.502 16830 Z= 0.246 Chirality : 0.041 0.130 1880 Planarity : 0.003 0.043 2146 Dihedral : 6.299 77.178 1666 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.56 % Allowed : 20.13 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.21), residues: 1482 helix: 0.32 (0.22), residues: 572 sheet: -0.55 (0.27), residues: 334 loop : -0.48 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 148 HIS 0.003 0.001 HIS D 284 PHE 0.012 0.001 PHE B 6 TYR 0.010 0.001 TYR A 203 ARG 0.002 0.000 ARG B 663 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 1.223 Fit side-chains REVERT: A 57 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7717 (mt-10) REVERT: A 539 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7049 (tp30) REVERT: B 312 GLU cc_start: 0.6692 (tt0) cc_final: 0.6485 (tt0) REVERT: B 548 LYS cc_start: 0.8282 (mtmm) cc_final: 0.7870 (ttpp) REVERT: C 247 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7909 (tp-100) REVERT: C 258 LYS cc_start: 0.7824 (mmtp) cc_final: 0.7617 (mmtt) REVERT: D 238 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7437 (ttp-170) REVERT: D 316 LYS cc_start: 0.7962 (tptt) cc_final: 0.7689 (mmmt) outliers start: 21 outliers final: 12 residues processed: 137 average time/residue: 1.5303 time to fit residues: 224.9385 Evaluate side-chains 134 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 245 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 97 optimal weight: 0.0040 chunk 147 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 223 ASN D 303 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12468 Z= 0.165 Angle : 0.478 6.693 16830 Z= 0.246 Chirality : 0.041 0.131 1880 Planarity : 0.003 0.042 2146 Dihedral : 6.263 76.413 1666 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.41 % Allowed : 20.36 % Favored : 78.23 % 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: -0.30 (0.21), residues: 1482 helix: 0.38 (0.22), residues: 572 sheet: -0.51 (0.28), residues: 324 loop : -0.41 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 148 HIS 0.004 0.001 HIS D 284 PHE 0.012 0.001 PHE B 6 TYR 0.009 0.001 TYR A 203 ARG 0.003 0.000 ARG A 389 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 1.522 Fit side-chains revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7710 (mt-10) REVERT: A 539 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7121 (tp30) REVERT: B 261 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7722 (mt0) REVERT: B 548 LYS cc_start: 0.8246 (mtmm) cc_final: 0.7888 (ttpp) REVERT: C 247 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7912 (tp-100) REVERT: C 258 LYS cc_start: 0.7824 (mmtp) cc_final: 0.7619 (mmtt) REVERT: D 238 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7455 (ttp-170) REVERT: D 316 LYS cc_start: 0.7959 (tptt) cc_final: 0.7679 (mmmt) outliers start: 19 outliers final: 11 residues processed: 141 average time/residue: 1.5185 time to fit residues: 230.5889 Evaluate side-chains 138 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 245 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 117 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 120 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 303 HIS D 314 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.125390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.102965 restraints weight = 16579.010| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.92 r_work: 0.3066 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12468 Z= 0.297 Angle : 0.554 6.838 16830 Z= 0.285 Chirality : 0.044 0.136 1880 Planarity : 0.004 0.042 2146 Dihedral : 6.611 73.255 1666 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.34 % Allowed : 20.65 % Favored : 78.01 % 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: -0.46 (0.21), residues: 1482 helix: 0.29 (0.22), residues: 568 sheet: -0.55 (0.28), residues: 320 loop : -0.57 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 285 HIS 0.004 0.001 HIS B 463 PHE 0.013 0.002 PHE B 30 TYR 0.011 0.002 TYR A 565 ARG 0.005 0.000 ARG B 663 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4785.95 seconds wall clock time: 85 minutes 21.85 seconds (5121.85 seconds total)