Starting phenix.real_space_refine on Tue Feb 13 13:27:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9i_32367/02_2024/7w9i_32367.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9i_32367/02_2024/7w9i_32367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9i_32367/02_2024/7w9i_32367.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9i_32367/02_2024/7w9i_32367.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9i_32367/02_2024/7w9i_32367.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9i_32367/02_2024/7w9i_32367.pdb" } resolution = 3.4 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= 0.076 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4101 2.51 5 N 1066 2.21 5 O 1208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 57": "OE1" <-> "OE2" Residue "A ASP 67": "OD1" <-> "OD2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 206": "OD1" <-> "OD2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ASP 225": "OD1" <-> "OD2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 292": "OD1" <-> "OD2" Residue "A ASP 303": "OD1" <-> "OD2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ASP 367": "OD1" <-> "OD2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A ASP 494": "OD1" <-> "OD2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A TYR 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A ASP 543": "OD1" <-> "OD2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A ASP 597": "OD1" <-> "OD2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 389": "OD1" <-> "OD2" Residue "E PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 442": "OD1" <-> "OD2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 467": "OD1" <-> "OD2" Residue "E TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6412 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "E" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1542 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 183} Time building chain proxies: 3.88, per 1000 atoms: 0.61 Number of scatterers: 6412 At special positions: 0 Unit cell: (91.812, 84.161, 119.137, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1208 8.00 N 1066 7.00 C 4101 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 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: 2.07 Conformation dependent library (CDL) restraints added in 1.3 seconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 6 sheets defined 48.3% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 20 through 34 removed outlier: 3.711A pdb=" N LYS A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 53 removed outlier: 3.577A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 80 removed outlier: 3.667A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.655A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.122A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.552A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.508A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 152' Processing helix chain 'A' and resid 158 through 167 removed outlier: 3.831A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.923A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.683A pdb=" N ARG A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 248 removed outlier: 3.589A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.829A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 297 removed outlier: 3.607A pdb=" N MET A 297 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 4.188A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.979A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 331' Processing helix chain 'A' and resid 368 through 378 removed outlier: 3.609A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.536A pdb=" N ALA A 387 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.668A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 removed outlier: 3.720A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 405' Processing helix chain 'A' and resid 431 through 444 removed outlier: 3.700A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.650A pdb=" N LEU A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 482 removed outlier: 4.040A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N MET A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 515 Processing helix chain 'A' and resid 516 through 533 removed outlier: 3.671A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.668A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.696A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.925A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 598 removed outlier: 3.623A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 4.001A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 removed outlier: 3.766A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 365 through 370' Processing helix chain 'E' and resid 385 through 389 removed outlier: 3.897A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP E 389 " --> pdb=" O LYS E 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 385 through 389' Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.621A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 506 removed outlier: 3.530A pdb=" N TYR E 505 " --> pdb=" O GLY E 502 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN E 506 " --> pdb=" O VAL E 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 502 through 506' Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 removed outlier: 4.638A pdb=" N VAL A 132 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 142 " --> pdb=" O VAL A 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.409A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.200A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.528A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 197 hydrogen bonds defined for protein. 543 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: 1.51 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2065 1.34 - 1.46: 1673 1.46 - 1.58: 2796 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6592 Sorted by residual: bond pdb=" C VAL A 488 " pdb=" N GLU A 489 " ideal model delta sigma weight residual 1.331 1.279 0.052 2.07e-02 2.33e+03 6.20e+00 bond pdb=" C LYS E 478 " pdb=" N PRO E 479 " ideal model delta sigma weight residual 1.338 1.364 -0.026 1.90e-02 2.77e+03 1.80e+00 bond pdb=" C ARG A 177 " pdb=" N PRO A 178 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.25e-02 6.40e+03 1.49e+00 bond pdb=" C ASP A 499 " pdb=" N PRO A 500 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.25e-02 6.40e+03 1.44e+00 bond pdb=" CB VAL A 581 " pdb=" CG2 VAL A 581 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.43e+00 ... (remaining 6587 not shown) Histogram of bond angle deviations from ideal: 99.48 - 107.34: 266 107.34 - 115.20: 3708 115.20 - 123.06: 4605 123.06 - 130.93: 336 130.93 - 138.79: 43 Bond angle restraints: 8958 Sorted by residual: angle pdb=" C LYS E 478 " pdb=" N PRO E 479 " pdb=" CA PRO E 479 " ideal model delta sigma weight residual 127.00 138.79 -11.79 2.40e+00 1.74e-01 2.41e+01 angle pdb=" C LYS E 478 " pdb=" N PRO E 479 " pdb=" CD PRO E 479 " ideal model delta sigma weight residual 120.60 111.48 9.12 2.20e+00 2.07e-01 1.72e+01 angle pdb=" N ARG A 582 " pdb=" CA ARG A 582 " pdb=" C ARG A 582 " ideal model delta sigma weight residual 109.81 117.59 -7.78 2.21e+00 2.05e-01 1.24e+01 angle pdb=" N ASP A 499 " pdb=" CA ASP A 499 " pdb=" C ASP A 499 " ideal model delta sigma weight residual 109.81 116.86 -7.05 2.21e+00 2.05e-01 1.02e+01 angle pdb=" CA LEU A 143 " pdb=" CB LEU A 143 " pdb=" CG LEU A 143 " ideal model delta sigma weight residual 116.30 126.28 -9.98 3.50e+00 8.16e-02 8.13e+00 ... (remaining 8953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 3450 17.85 - 35.71: 365 35.71 - 53.56: 58 53.56 - 71.41: 15 71.41 - 89.27: 5 Dihedral angle restraints: 3893 sinusoidal: 1573 harmonic: 2320 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 134.75 -41.75 1 1.00e+01 1.00e-02 2.44e+01 dihedral pdb=" CA CYS A 344 " pdb=" C CYS A 344 " pdb=" N HIS A 345 " pdb=" CA HIS A 345 " ideal model delta harmonic sigma weight residual 180.00 158.21 21.79 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA LEU E 461 " pdb=" C LEU E 461 " pdb=" N LYS E 462 " pdb=" CA LYS E 462 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 3890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 744 0.056 - 0.111: 166 0.111 - 0.167: 22 0.167 - 0.222: 1 0.222 - 0.278: 1 Chirality restraints: 934 Sorted by residual: chirality pdb=" CB ILE A 291 " pdb=" CA ILE A 291 " pdb=" CG1 ILE A 291 " pdb=" CG2 ILE A 291 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CB VAL A 364 " pdb=" CA VAL A 364 " pdb=" CG1 VAL A 364 " pdb=" CG2 VAL A 364 " both_signs ideal model delta sigma weight residual False -2.63 -2.80 0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CB VAL E 350 " pdb=" CA VAL E 350 " pdb=" CG1 VAL E 350 " pdb=" CG2 VAL E 350 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 931 not shown) Planarity restraints: 1165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " 0.044 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO A 583 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " 0.042 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO A 235 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 520 " 0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO E 521 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO E 521 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 521 " 0.033 5.00e-02 4.00e+02 ... (remaining 1162 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1967 2.81 - 3.33: 5129 3.33 - 3.86: 10439 3.86 - 4.38: 12633 4.38 - 4.90: 21601 Nonbonded interactions: 51769 Sorted by model distance: nonbonded pdb=" O ALA A 501 " pdb=" OG SER A 507 " model vdw 2.289 2.440 nonbonded pdb=" OD1 ASP A 543 " pdb=" OG SER A 545 " model vdw 2.319 2.440 nonbonded pdb=" OG SER A 170 " pdb=" OE1 GLU A 171 " model vdw 2.344 2.440 nonbonded pdb=" OG SER E 371 " pdb=" OG SER E 373 " model vdw 2.348 2.440 nonbonded pdb=" OD1 ASP A 382 " pdb=" OH TYR A 385 " model vdw 2.360 2.440 ... (remaining 51764 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 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: 0.000 Extract box with map and model: 10.070 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 20.230 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 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 : 0.005 0.052 6592 Z= 0.292 Angle : 0.724 11.787 8958 Z= 0.382 Chirality : 0.049 0.278 934 Planarity : 0.006 0.065 1165 Dihedral : 14.898 89.268 2384 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -5.48 (0.21), residues: 787 helix: -4.83 (0.08), residues: 351 sheet: -2.24 (0.72), residues: 49 loop : -2.53 (0.25), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 566 HIS 0.004 0.001 HIS E 519 PHE 0.015 0.002 PHE A 452 TYR 0.025 0.002 TYR E 453 ARG 0.007 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 50 TYR cc_start: 0.8635 (t80) cc_final: 0.8433 (t80) REVERT: A 62 MET cc_start: 0.7878 (ptm) cc_final: 0.7601 (ptm) REVERT: A 255 TYR cc_start: 0.7287 (m-80) cc_final: 0.7075 (m-10) REVERT: A 375 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7260 (mm-30) REVERT: A 398 GLU cc_start: 0.8189 (pt0) cc_final: 0.7875 (pt0) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2140 time to fit residues: 34.5730 Evaluate side-chains 86 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 0.0570 chunk 20 optimal weight: 0.1980 chunk 39 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 0.0470 chunk 45 optimal weight: 0.3980 chunk 70 optimal weight: 0.4980 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 58 ASN A 64 ASN A 81 GLN A 89 GLN A 96 GLN A 103 ASN A 277 ASN A 330 ASN A 373 HIS A 378 HIS E 450 ASN E 474 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6592 Z= 0.131 Angle : 0.488 7.477 8958 Z= 0.247 Chirality : 0.041 0.154 934 Planarity : 0.004 0.045 1165 Dihedral : 4.261 16.657 861 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.30 % Allowed : 10.95 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -3.79 (0.25), residues: 787 helix: -3.14 (0.19), residues: 349 sheet: -1.80 (0.71), residues: 50 loop : -1.88 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 566 HIS 0.003 0.001 HIS A 505 PHE 0.012 0.001 PHE E 377 TYR 0.016 0.001 TYR A 202 ARG 0.003 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.8085 (tp30) cc_final: 0.7699 (tp30) REVERT: A 255 TYR cc_start: 0.7306 (m-80) cc_final: 0.7036 (m-10) REVERT: A 332 MET cc_start: 0.8374 (ttp) cc_final: 0.8163 (ttp) REVERT: A 375 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6914 (mm-30) REVERT: A 479 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7295 (tm-30) REVERT: E 452 ARG cc_start: 0.7942 (mtm-85) cc_final: 0.7736 (mtm180) REVERT: E 508 TYR cc_start: 0.8092 (m-80) cc_final: 0.7541 (m-80) outliers start: 9 outliers final: 6 residues processed: 103 average time/residue: 0.1554 time to fit residues: 22.2700 Evaluate side-chains 90 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6592 Z= 0.255 Angle : 0.529 6.815 8958 Z= 0.264 Chirality : 0.043 0.160 934 Planarity : 0.004 0.038 1165 Dihedral : 4.251 17.859 861 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.73 % Allowed : 14.27 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -2.93 (0.27), residues: 787 helix: -2.16 (0.24), residues: 354 sheet: -1.38 (0.69), residues: 47 loop : -1.71 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 566 HIS 0.004 0.001 HIS E 519 PHE 0.013 0.001 PHE E 377 TYR 0.020 0.001 TYR E 453 ARG 0.003 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.741 Fit side-chains REVERT: A 157 ASP cc_start: 0.7156 (t0) cc_final: 0.6845 (t0) REVERT: A 166 GLU cc_start: 0.8063 (tp30) cc_final: 0.7597 (tp30) REVERT: A 255 TYR cc_start: 0.7365 (m-80) cc_final: 0.7097 (m-10) REVERT: A 332 MET cc_start: 0.8533 (ttp) cc_final: 0.7352 (ttp) REVERT: A 375 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7060 (mm-30) REVERT: A 479 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7241 (tm-30) outliers start: 12 outliers final: 11 residues processed: 93 average time/residue: 0.1548 time to fit residues: 20.4447 Evaluate side-chains 96 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 0.0470 chunk 71 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 0.0070 chunk 42 optimal weight: 1.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6592 Z= 0.182 Angle : 0.483 7.457 8958 Z= 0.238 Chirality : 0.042 0.146 934 Planarity : 0.003 0.035 1165 Dihedral : 3.964 15.419 861 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.31 % Allowed : 14.27 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -2.36 (0.28), residues: 787 helix: -1.59 (0.26), residues: 354 sheet: -1.47 (0.67), residues: 50 loop : -1.43 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 566 HIS 0.002 0.001 HIS E 519 PHE 0.011 0.001 PHE A 369 TYR 0.016 0.001 TYR A 202 ARG 0.002 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.718 Fit side-chains REVERT: A 157 ASP cc_start: 0.7190 (t0) cc_final: 0.6910 (t0) REVERT: A 166 GLU cc_start: 0.8003 (tp30) cc_final: 0.7532 (tp30) REVERT: A 255 TYR cc_start: 0.7392 (m-80) cc_final: 0.7143 (m-10) REVERT: A 332 MET cc_start: 0.8488 (ttp) cc_final: 0.7359 (ttp) REVERT: A 375 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7165 (mm-30) REVERT: A 479 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7171 (tm-30) outliers start: 16 outliers final: 12 residues processed: 96 average time/residue: 0.1644 time to fit residues: 22.2184 Evaluate side-chains 97 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 31 optimal weight: 5.9990 chunk 64 optimal weight: 0.0010 chunk 52 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6592 Z= 0.148 Angle : 0.473 8.055 8958 Z= 0.229 Chirality : 0.041 0.120 934 Planarity : 0.003 0.038 1165 Dihedral : 3.790 14.588 861 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.45 % Allowed : 15.13 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.29), residues: 787 helix: -1.23 (0.27), residues: 360 sheet: -1.30 (0.68), residues: 49 loop : -1.27 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 566 HIS 0.002 0.001 HIS E 519 PHE 0.008 0.001 PHE A 369 TYR 0.015 0.001 TYR A 202 ARG 0.001 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.751 Fit side-chains REVERT: A 157 ASP cc_start: 0.7217 (t0) cc_final: 0.7012 (t0) REVERT: A 166 GLU cc_start: 0.7995 (tp30) cc_final: 0.7505 (tp30) REVERT: A 332 MET cc_start: 0.8466 (ttp) cc_final: 0.7352 (ttp) REVERT: A 375 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7196 (mm-30) REVERT: A 479 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7092 (tm-30) outliers start: 17 outliers final: 13 residues processed: 95 average time/residue: 0.1495 time to fit residues: 20.3021 Evaluate side-chains 96 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6592 Z= 0.248 Angle : 0.523 8.091 8958 Z= 0.255 Chirality : 0.043 0.122 934 Planarity : 0.003 0.042 1165 Dihedral : 4.048 16.654 861 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.59 % Allowed : 16.43 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.86 (0.29), residues: 787 helix: -1.13 (0.27), residues: 362 sheet: -0.92 (0.70), residues: 48 loop : -1.26 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.004 0.001 HIS E 519 PHE 0.011 0.001 PHE A 369 TYR 0.019 0.001 TYR E 453 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 0.788 Fit side-chains REVERT: A 157 ASP cc_start: 0.7341 (t0) cc_final: 0.7068 (t0) REVERT: A 323 MET cc_start: 0.7204 (mmm) cc_final: 0.6717 (tpp) REVERT: A 332 MET cc_start: 0.8481 (ttp) cc_final: 0.7378 (ttp) REVERT: A 375 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7186 (mm-30) REVERT: A 479 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7137 (tm-30) outliers start: 18 outliers final: 16 residues processed: 96 average time/residue: 0.1587 time to fit residues: 21.9005 Evaluate side-chains 100 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6592 Z= 0.243 Angle : 0.527 7.906 8958 Z= 0.256 Chirality : 0.043 0.121 934 Planarity : 0.003 0.046 1165 Dihedral : 4.064 16.174 861 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.45 % Allowed : 17.58 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.76 (0.29), residues: 787 helix: -1.00 (0.28), residues: 361 sheet: -1.09 (0.70), residues: 50 loop : -1.23 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 566 HIS 0.004 0.001 HIS E 519 PHE 0.011 0.001 PHE A 369 TYR 0.017 0.001 TYR A 202 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.726 Fit side-chains REVERT: A 157 ASP cc_start: 0.7314 (t0) cc_final: 0.7079 (t0) REVERT: A 323 MET cc_start: 0.7341 (mmm) cc_final: 0.6852 (tpp) REVERT: A 332 MET cc_start: 0.8499 (ttp) cc_final: 0.7404 (ttp) REVERT: A 375 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7182 (mm-30) REVERT: A 479 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7116 (tm-30) outliers start: 17 outliers final: 15 residues processed: 94 average time/residue: 0.1501 time to fit residues: 20.0695 Evaluate side-chains 93 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 65 optimal weight: 0.0870 chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6592 Z= 0.175 Angle : 0.501 8.047 8958 Z= 0.242 Chirality : 0.042 0.166 934 Planarity : 0.003 0.046 1165 Dihedral : 3.852 14.313 861 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.16 % Allowed : 18.44 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.51 (0.30), residues: 787 helix: -0.76 (0.28), residues: 359 sheet: -1.06 (0.71), residues: 50 loop : -1.13 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 566 HIS 0.002 0.001 HIS E 519 PHE 0.010 0.001 PHE A 369 TYR 0.016 0.001 TYR A 202 ARG 0.002 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.726 Fit side-chains REVERT: A 157 ASP cc_start: 0.7356 (t0) cc_final: 0.7077 (t0) REVERT: A 332 MET cc_start: 0.8483 (ttp) cc_final: 0.7409 (ttp) REVERT: A 375 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7222 (mm-30) REVERT: A 479 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7022 (tm-30) outliers start: 15 outliers final: 15 residues processed: 92 average time/residue: 0.1547 time to fit residues: 20.3138 Evaluate side-chains 95 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 45 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 GLN ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6592 Z= 0.210 Angle : 0.525 8.031 8958 Z= 0.253 Chirality : 0.043 0.160 934 Planarity : 0.003 0.048 1165 Dihedral : 3.918 15.736 861 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.16 % Allowed : 18.88 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.46 (0.30), residues: 787 helix: -0.70 (0.28), residues: 360 sheet: -1.13 (0.70), residues: 50 loop : -1.10 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 566 HIS 0.003 0.001 HIS E 519 PHE 0.011 0.001 PHE A 369 TYR 0.018 0.001 TYR A 202 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 0.562 Fit side-chains REVERT: A 332 MET cc_start: 0.8462 (ttp) cc_final: 0.7394 (ttp) REVERT: A 375 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7217 (mm-30) REVERT: A 479 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7022 (tm-30) outliers start: 15 outliers final: 15 residues processed: 88 average time/residue: 0.1559 time to fit residues: 19.5369 Evaluate side-chains 92 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.0770 chunk 71 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 47 optimal weight: 0.4980 chunk 37 optimal weight: 0.0970 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6592 Z= 0.158 Angle : 0.505 8.751 8958 Z= 0.243 Chirality : 0.041 0.135 934 Planarity : 0.003 0.049 1165 Dihedral : 3.731 13.945 861 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.02 % Allowed : 19.02 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.26 (0.30), residues: 787 helix: -0.50 (0.29), residues: 358 sheet: -1.01 (0.71), residues: 50 loop : -1.05 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 566 HIS 0.002 0.001 HIS E 519 PHE 0.010 0.001 PHE A 369 TYR 0.018 0.001 TYR A 202 ARG 0.001 0.000 ARG A 460 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 0.760 Fit side-chains REVERT: A 332 MET cc_start: 0.8483 (ttp) cc_final: 0.7422 (ttp) REVERT: A 375 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7220 (mm-30) REVERT: A 479 GLU cc_start: 0.7494 (tm-30) cc_final: 0.6998 (tm-30) outliers start: 14 outliers final: 14 residues processed: 87 average time/residue: 0.1601 time to fit residues: 19.8396 Evaluate side-chains 91 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.0270 chunk 63 optimal weight: 0.0020 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 70 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.3646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.186770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.154712 restraints weight = 7838.826| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.07 r_work: 0.3486 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6592 Z= 0.147 Angle : 0.492 8.848 8958 Z= 0.236 Chirality : 0.041 0.124 934 Planarity : 0.003 0.048 1165 Dihedral : 3.624 14.335 861 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.31 % Allowed : 19.02 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.08 (0.30), residues: 787 helix: -0.31 (0.29), residues: 358 sheet: -0.94 (0.71), residues: 49 loop : -1.00 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 566 HIS 0.002 0.001 HIS E 519 PHE 0.010 0.001 PHE A 369 TYR 0.017 0.001 TYR A 202 ARG 0.002 0.000 ARG A 460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1849.05 seconds wall clock time: 34 minutes 7.44 seconds (2047.44 seconds total)