Starting phenix.real_space_refine (version: dev) on Sun Feb 19 08:33:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sch_25035/02_2023/7sch_25035.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sch_25035/02_2023/7sch_25035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sch_25035/02_2023/7sch_25035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sch_25035/02_2023/7sch_25035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sch_25035/02_2023/7sch_25035.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sch_25035/02_2023/7sch_25035.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 9711 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4913 Classifications: {'peptide': 603} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 574} Chain breaks: 3 Chain: "B" Number of atoms: 4759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4759 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 38, 'TRANS': 548} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.86, per 1000 atoms: 0.60 Number of scatterers: 9711 At special positions: 0 Unit cell: (102.672, 87.768, 112.608, 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 47 16.00 O 1769 8.00 N 1645 7.00 C 6250 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 704 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 626 " - pdb=" SG CYS B 676 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG C 1 " - " ASN B 637 " Time building additional restraints: 4.01 Conformation dependent library (CDL) restraints added in 1.6 seconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 11 sheets defined 39.8% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 105 through 109 removed outlier: 3.689A pdb=" N LEU A 108 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 140 Processing helix chain 'A' and resid 173 through 180 removed outlier: 3.588A pdb=" N GLN A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 222 through 226 Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.578A pdb=" N ALA A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 4.295A pdb=" N VAL A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.875A pdb=" N GLN A 305 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 345 through 353 removed outlier: 3.750A pdb=" N GLU A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 377 removed outlier: 3.526A pdb=" N GLN A 376 " --> pdb=" O ASN A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 388 through 396 Processing helix chain 'A' and resid 397 through 416 Processing helix chain 'A' and resid 418 through 432 Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.884A pdb=" N TRP A 445 " --> pdb=" O ASN A 441 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 446' Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 496 through 506 Processing helix chain 'A' and resid 545 through 551 removed outlier: 3.911A pdb=" N ARG A 549 " --> pdb=" O MET A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 585 removed outlier: 3.607A pdb=" N SER A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 removed outlier: 3.647A pdb=" N TYR A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 650 removed outlier: 3.668A pdb=" N LYS A 643 " --> pdb=" O PRO A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 Processing helix chain 'A' and resid 697 through 713 removed outlier: 3.978A pdb=" N ARG A 701 " --> pdb=" O HIS A 697 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN A 702 " --> pdb=" O PHE A 698 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 127 through 139 Processing helix chain 'B' and resid 166 through 177 Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.932A pdb=" N LEU B 312 " --> pdb=" O TYR B 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 312' Processing helix chain 'B' and resid 329 through 338 removed outlier: 3.714A pdb=" N ASP B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 removed outlier: 3.616A pdb=" N ARG B 360 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.823A pdb=" N MET B 370 " --> pdb=" O GLU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 379 removed outlier: 3.529A pdb=" N SER B 379 " --> pdb=" O SER B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 399 Processing helix chain 'B' and resid 402 through 419 Processing helix chain 'B' and resid 420 through 423 Processing helix chain 'B' and resid 425 through 431 Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 468 through 478 removed outlier: 3.749A pdb=" N GLU B 475 " --> pdb=" O ARG B 471 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 524 removed outlier: 4.055A pdb=" N ARG B 522 " --> pdb=" O LEU B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 559 removed outlier: 3.711A pdb=" N GLU B 558 " --> pdb=" O GLU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 611 Processing helix chain 'B' and resid 615 through 624 Processing helix chain 'B' and resid 626 through 640 removed outlier: 3.513A pdb=" N ALA B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 685 Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 145 removed outlier: 5.898A pdb=" N VAL A 116 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TYR A 117 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N PHE A 154 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N PHE A 193 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N HIS A 190 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ALA A 217 " --> pdb=" O HIS A 190 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE A 192 " --> pdb=" O ALA A 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 297 removed outlier: 8.240A pdb=" N VAL A 293 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU A 264 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU A 295 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE A 266 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N THR A 297 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLY A 268 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N MET A 263 " --> pdb=" O PHE A 333 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU A 335 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL A 265 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR A 332 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL A 358 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N CYS A 334 " --> pdb=" O VAL A 358 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 536 through 540 removed outlier: 8.299A pdb=" N VAL A 537 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE A 513 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE A 539 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A 515 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N PHE A 480 " --> pdb=" O GLN A 512 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ILE A 514 " --> pdb=" O PHE A 480 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA A 482 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU A 516 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE A 484 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR A 481 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU A 564 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL A 483 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 605 through 609 removed outlier: 3.587A pdb=" N ARG A 605 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 722 through 726 Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 108 Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 189 removed outlier: 6.380A pdb=" N LEU B 212 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 280 through 283 removed outlier: 7.924A pdb=" N LEU B 281 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU B 254 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU B 283 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER B 256 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE B 253 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL B 319 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU B 255 " --> pdb=" O VAL B 319 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 509 through 513 removed outlier: 6.645A pdb=" N LEU B 485 " --> pdb=" O LYS B 510 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL B 512 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL B 487 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N PHE B 456 " --> pdb=" O LYS B 484 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU B 486 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ALA B 458 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL B 488 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL B 460 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 535 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 461 " --> pdb=" O ILE B 537 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 570 through 574 removed outlier: 3.565A pdb=" N LYS B 579 " --> pdb=" O ASP B 574 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 843 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: 2.87 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2883 1.34 - 1.46: 1881 1.46 - 1.58: 5134 1.58 - 1.70: 1 1.70 - 1.82: 73 Bond restraints: 9972 Sorted by residual: bond pdb=" N ASN B 430 " pdb=" CA ASN B 430 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.18e-02 7.18e+03 1.32e+01 bond pdb=" N PRO B 648 " pdb=" CA PRO B 648 " ideal model delta sigma weight residual 1.469 1.429 0.039 1.28e-02 6.10e+03 9.51e+00 bond pdb=" N SER B 425 " pdb=" CA SER B 425 " ideal model delta sigma weight residual 1.454 1.490 -0.035 1.27e-02 6.20e+03 7.74e+00 bond pdb=" N LYS B 645 " pdb=" CA LYS B 645 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.91e+00 bond pdb=" N ARG B 649 " pdb=" CA ARG B 649 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.25e-02 6.40e+03 6.70e+00 ... (remaining 9967 not shown) Histogram of bond angle deviations from ideal: 96.31 - 103.93: 166 103.93 - 111.55: 4395 111.55 - 119.17: 3638 119.17 - 126.79: 5156 126.79 - 134.41: 191 Bond angle restraints: 13546 Sorted by residual: angle pdb=" N LYS B 645 " pdb=" CA LYS B 645 " pdb=" C LYS B 645 " ideal model delta sigma weight residual 110.55 105.46 5.09 1.35e+00 5.49e-01 1.42e+01 angle pdb=" CA LYS B 645 " pdb=" C LYS B 645 " pdb=" O LYS B 645 " ideal model delta sigma weight residual 121.81 117.49 4.32 1.18e+00 7.18e-01 1.34e+01 angle pdb=" CA LYS B 645 " pdb=" C LYS B 645 " pdb=" N VAL B 646 " ideal model delta sigma weight residual 115.27 119.65 -4.38 1.30e+00 5.92e-01 1.14e+01 angle pdb=" C TRP B 429 " pdb=" N ASN B 430 " pdb=" CA ASN B 430 " ideal model delta sigma weight residual 122.73 117.40 5.33 1.61e+00 3.86e-01 1.10e+01 angle pdb=" N ASN B 430 " pdb=" CA ASN B 430 " pdb=" C ASN B 430 " ideal model delta sigma weight residual 112.72 116.33 -3.61 1.14e+00 7.69e-01 1.00e+01 ... (remaining 13541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5522 17.93 - 35.86: 379 35.86 - 53.78: 58 53.78 - 71.71: 8 71.71 - 89.64: 4 Dihedral angle restraints: 5971 sinusoidal: 2456 harmonic: 3515 Sorted by residual: dihedral pdb=" CB CYS B 85 " pdb=" SG CYS B 85 " pdb=" SG CYS B 90 " pdb=" CB CYS B 90 " ideal model delta sinusoidal sigma weight residual -86.00 -157.29 71.29 1 1.00e+01 1.00e-02 6.52e+01 dihedral pdb=" CB CYS B 96 " pdb=" SG CYS B 96 " pdb=" SG CYS B 151 " pdb=" CB CYS B 151 " ideal model delta sinusoidal sigma weight residual -86.00 -19.43 -66.57 1 1.00e+01 1.00e-02 5.78e+01 dihedral pdb=" CB CYS A 298 " pdb=" SG CYS A 298 " pdb=" SG CYS A 312 " pdb=" CB CYS A 312 " ideal model delta sinusoidal sigma weight residual 93.00 145.56 -52.56 1 1.00e+01 1.00e-02 3.76e+01 ... (remaining 5968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1098 0.046 - 0.091: 273 0.091 - 0.137: 99 0.137 - 0.182: 5 0.182 - 0.228: 1 Chirality restraints: 1476 Sorted by residual: chirality pdb=" CG LEU B 594 " pdb=" CB LEU B 594 " pdb=" CD1 LEU B 594 " pdb=" CD2 LEU B 594 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB VAL B 646 " pdb=" CA VAL B 646 " pdb=" CG1 VAL B 646 " pdb=" CG2 VAL B 646 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CG LEU A 161 " pdb=" CB LEU A 161 " pdb=" CD1 LEU A 161 " pdb=" CD2 LEU A 161 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 1473 not shown) Planarity restraints: 1726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 643 " -0.018 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C VAL B 643 " 0.064 2.00e-02 2.50e+03 pdb=" O VAL B 643 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE B 644 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 248 " -0.046 5.00e-02 4.00e+02 6.87e-02 7.54e+00 pdb=" N PRO B 249 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 249 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 249 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 559 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO B 560 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 560 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 560 " -0.025 5.00e-02 4.00e+02 ... (remaining 1723 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1264 2.75 - 3.29: 9392 3.29 - 3.83: 16123 3.83 - 4.36: 19715 4.36 - 4.90: 33561 Nonbonded interactions: 80055 Sorted by model distance: nonbonded pdb=" OG SER A 547 " pdb=" OD1 ASP A 647 " model vdw 2.218 2.440 nonbonded pdb=" ND2 ASN B 99 " pdb=" O LYS B 101 " model vdw 2.248 2.520 nonbonded pdb=" O TYR A 592 " pdb=" NZ LYS A 671 " model vdw 2.254 2.520 nonbonded pdb=" OG1 THR A 673 " pdb=" OD1 ASP A 725 " model vdw 2.257 2.440 nonbonded pdb=" OD2 ASP A 382 " pdb=" NH2 ARG A 384 " model vdw 2.271 2.520 ... (remaining 80050 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 6250 2.51 5 N 1645 2.21 5 O 1769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 4.290 Check model and map are aligned: 0.170 Process input model: 28.520 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 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 0.088 9972 Z= 0.201 Angle : 0.606 9.790 13546 Z= 0.337 Chirality : 0.044 0.228 1476 Planarity : 0.004 0.069 1725 Dihedral : 11.922 89.640 3672 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.02 (0.25), residues: 1174 helix: 0.94 (0.28), residues: 382 sheet: -0.48 (0.44), residues: 140 loop : -0.37 (0.24), residues: 652 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 317 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 318 average time/residue: 0.2577 time to fit residues: 109.5827 Evaluate side-chains 286 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 284 time to evaluate : 1.187 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1191 time to fit residues: 2.1306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 0.0030 chunk 47 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 107 optimal weight: 0.1980 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 362 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 HIS A 706 ASN B 415 ASN B 430 ASN B 550 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9972 Z= 0.166 Angle : 0.559 11.161 13546 Z= 0.281 Chirality : 0.043 0.138 1476 Planarity : 0.004 0.034 1725 Dihedral : 4.087 16.639 1329 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.22 (0.25), residues: 1174 helix: 1.20 (0.28), residues: 381 sheet: -0.25 (0.45), residues: 137 loop : -0.35 (0.25), residues: 656 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 294 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 299 average time/residue: 0.2567 time to fit residues: 102.6877 Evaluate side-chains 303 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 292 time to evaluate : 1.132 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1031 time to fit residues: 3.6827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 HIS A 706 ASN B 415 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 9972 Z= 0.371 Angle : 0.630 11.761 13546 Z= 0.321 Chirality : 0.047 0.157 1476 Planarity : 0.004 0.042 1725 Dihedral : 4.601 19.403 1329 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.05 (0.25), residues: 1174 helix: 1.03 (0.27), residues: 382 sheet: -0.06 (0.45), residues: 136 loop : -0.51 (0.24), residues: 656 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 294 time to evaluate : 1.216 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 299 average time/residue: 0.2549 time to fit residues: 101.9625 Evaluate side-chains 292 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 284 time to evaluate : 1.178 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1382 time to fit residues: 3.4703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.9980 chunk 80 optimal weight: 0.0170 chunk 55 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN B 415 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 9972 Z= 0.197 Angle : 0.559 9.048 13546 Z= 0.283 Chirality : 0.043 0.146 1476 Planarity : 0.004 0.043 1725 Dihedral : 4.315 17.667 1329 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.24 (0.25), residues: 1174 helix: 1.27 (0.28), residues: 381 sheet: -0.08 (0.47), residues: 126 loop : -0.41 (0.25), residues: 667 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 285 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 289 average time/residue: 0.2634 time to fit residues: 101.2821 Evaluate side-chains 287 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 276 time to evaluate : 1.186 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0968 time to fit residues: 3.6017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN B 415 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9972 Z= 0.193 Angle : 0.544 8.432 13546 Z= 0.275 Chirality : 0.043 0.143 1476 Planarity : 0.004 0.043 1725 Dihedral : 4.229 17.047 1329 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.24 (0.25), residues: 1174 helix: 1.29 (0.28), residues: 384 sheet: 0.14 (0.47), residues: 124 loop : -0.49 (0.25), residues: 666 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 284 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 290 average time/residue: 0.2503 time to fit residues: 97.8820 Evaluate side-chains 283 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 274 time to evaluate : 1.143 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1102 time to fit residues: 3.3868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.9980 chunk 102 optimal weight: 0.0770 chunk 22 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 388 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN B 415 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 9972 Z= 0.215 Angle : 0.554 8.059 13546 Z= 0.280 Chirality : 0.043 0.153 1476 Planarity : 0.004 0.043 1725 Dihedral : 4.239 16.841 1329 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.21 (0.25), residues: 1174 helix: 1.24 (0.28), residues: 385 sheet: 0.21 (0.47), residues: 124 loop : -0.51 (0.25), residues: 665 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 277 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 283 average time/residue: 0.2653 time to fit residues: 100.3442 Evaluate side-chains 283 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 271 time to evaluate : 1.392 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1047 time to fit residues: 3.9286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 0.0270 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 63 optimal weight: 0.0870 chunk 113 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN B 415 ASN B 550 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 9972 Z= 0.174 Angle : 0.547 9.020 13546 Z= 0.276 Chirality : 0.042 0.148 1476 Planarity : 0.004 0.042 1725 Dihedral : 4.153 15.758 1329 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.33 (0.25), residues: 1174 helix: 1.40 (0.28), residues: 379 sheet: 0.23 (0.48), residues: 124 loop : -0.45 (0.24), residues: 671 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 274 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 275 average time/residue: 0.2616 time to fit residues: 96.7803 Evaluate side-chains 276 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 270 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1070 time to fit residues: 2.7980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 0.0010 chunk 67 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 300 HIS A 388 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN B 415 ASN B 430 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 9972 Z= 0.186 Angle : 0.545 8.522 13546 Z= 0.275 Chirality : 0.043 0.145 1476 Planarity : 0.004 0.059 1725 Dihedral : 4.129 15.940 1329 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1174 helix: 1.33 (0.28), residues: 379 sheet: -0.00 (0.45), residues: 138 loop : -0.43 (0.25), residues: 657 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 272 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 279 average time/residue: 0.2633 time to fit residues: 98.7547 Evaluate side-chains 276 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 269 time to evaluate : 1.174 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1160 time to fit residues: 3.0452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 4.9990 chunk 99 optimal weight: 0.0270 chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 95 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.0444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 194 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN B 328 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 9972 Z= 0.263 Angle : 0.583 9.034 13546 Z= 0.294 Chirality : 0.044 0.148 1476 Planarity : 0.004 0.053 1725 Dihedral : 4.274 16.798 1329 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.26 (0.25), residues: 1174 helix: 1.29 (0.28), residues: 379 sheet: 0.08 (0.46), residues: 134 loop : -0.44 (0.25), residues: 661 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 274 time to evaluate : 1.068 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 277 average time/residue: 0.2661 time to fit residues: 98.7922 Evaluate side-chains 274 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 271 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1025 time to fit residues: 2.1953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 93 optimal weight: 0.0030 chunk 9 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 194 ASN A 388 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 9972 Z= 0.239 Angle : 0.591 9.205 13546 Z= 0.299 Chirality : 0.044 0.147 1476 Planarity : 0.004 0.049 1725 Dihedral : 4.303 16.487 1329 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.18 (0.25), residues: 1174 helix: 1.16 (0.27), residues: 385 sheet: 0.17 (0.48), residues: 124 loop : -0.49 (0.25), residues: 665 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 273 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 275 average time/residue: 0.2683 time to fit residues: 99.3426 Evaluate side-chains 277 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 273 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1157 time to fit residues: 2.4029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.0870 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 96 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 82 optimal weight: 0.0470 chunk 5 optimal weight: 0.5980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 194 ASN ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.142071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.121291 restraints weight = 13582.297| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.14 r_work: 0.3394 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9972 Z= 0.166 Angle : 0.569 9.438 13546 Z= 0.285 Chirality : 0.043 0.143 1476 Planarity : 0.004 0.046 1725 Dihedral : 4.132 14.942 1329 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1174 helix: 1.26 (0.28), residues: 385 sheet: 0.15 (0.47), residues: 136 loop : -0.43 (0.25), residues: 653 =============================================================================== Job complete usr+sys time: 2749.03 seconds wall clock time: 50 minutes 27.58 seconds (3027.58 seconds total)