Starting phenix.real_space_refine on Fri Jul 19 11:51:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4h_41031/07_2024/8t4h_41031.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4h_41031/07_2024/8t4h_41031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4h_41031/07_2024/8t4h_41031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4h_41031/07_2024/8t4h_41031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4h_41031/07_2024/8t4h_41031.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4h_41031/07_2024/8t4h_41031.cif" } resolution = 3.8 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= 0.027 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 31 5.16 5 C 4874 2.51 5 N 1354 2.21 5 O 1443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 201": "OE1" <-> "OE2" Residue "A ASP 218": "OD1" <-> "OD2" Residue "A ASP 297": "OD1" <-> "OD2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "C GLU 7": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7702 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 3442 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 192} Link IDs: {'PTRANS': 18, 'TRANS': 514} Chain breaks: 2 Unresolved non-hydrogen bonds: 693 Unresolved non-hydrogen angles: 894 Unresolved non-hydrogen dihedrals: 554 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLN:plan1': 24, 'ARG:plan': 11, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 7, 'GLU:plan': 16, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 406 Chain: "B" Number of atoms: 4186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4186 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 19, 'TRANS': 527} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 68 Chain: "C" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 74 Classifications: {'peptide': 8} Modifications used: {'COO': 1} Link IDs: {'TRANS': 7} Time building chain proxies: 5.40, per 1000 atoms: 0.70 Number of scatterers: 7702 At special positions: 0 Unit cell: (68.798, 112.426, 135.918, 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 31 16.00 O 1443 8.00 N 1354 7.00 C 4874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.73 Conformation dependent library (CDL) restraints added in 1.7 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2006 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 6 sheets defined 73.0% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 183 through 202 removed outlier: 4.451A pdb=" N LEU A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 218 removed outlier: 4.154A pdb=" N PHE A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 250 removed outlier: 4.016A pdb=" N PHE A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 270 Processing helix chain 'A' and resid 292 through 323 Processing helix chain 'A' and resid 324 through 373 removed outlier: 3.735A pdb=" N THR A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Proline residue: A 336 - end of helix removed outlier: 4.074A pdb=" N LEU A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Proline residue: A 342 - end of helix removed outlier: 3.703A pdb=" N LYS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TRP A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 382 through 437 removed outlier: 3.619A pdb=" N LYS A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 482 removed outlier: 3.713A pdb=" N LEU A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Proline residue: A 466 - end of helix removed outlier: 4.100A pdb=" N LYS A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 542 Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 573 through 581 Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 608 through 619 removed outlier: 3.514A pdb=" N ILE A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 628 Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 637 through 641 removed outlier: 3.728A pdb=" N GLY A 640 " --> pdb=" O ASP A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 659 removed outlier: 3.583A pdb=" N ARG A 659 " --> pdb=" O ARG A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 687 Processing helix chain 'A' and resid 702 through 709 removed outlier: 3.709A pdb=" N LEU A 705 " --> pdb=" O HIS A 702 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 708 " --> pdb=" O LEU A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 732 Processing helix chain 'A' and resid 734 through 742 Processing helix chain 'B' and resid 132 through 146 Processing helix chain 'B' and resid 148 through 182 removed outlier: 3.680A pdb=" N GLY B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 185 through 235 removed outlier: 3.626A pdb=" N GLY B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.854A pdb=" N PHE B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 261 removed outlier: 3.579A pdb=" N LEU B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 259 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER B 261 " --> pdb=" O THR B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 289 removed outlier: 4.099A pdb=" N VAL B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 338 removed outlier: 3.598A pdb=" N THR B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) Proline residue: B 301 - end of helix removed outlier: 3.702A pdb=" N GLY B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 347 through 402 removed outlier: 4.583A pdb=" N LEU B 390 " --> pdb=" O GLY B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 448 removed outlier: 3.824A pdb=" N GLY B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU B 434 " --> pdb=" O TYR B 430 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR B 446 " --> pdb=" O LYS B 442 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET B 447 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 517 removed outlier: 4.243A pdb=" N ALA B 513 " --> pdb=" O LYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 537 Processing helix chain 'B' and resid 538 through 545 removed outlier: 3.576A pdb=" N HIS B 543 " --> pdb=" O HIS B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 572 through 583 removed outlier: 3.800A pdb=" N VAL B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 591 removed outlier: 3.751A pdb=" N GLU B 591 " --> pdb=" O ASP B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 598 removed outlier: 3.986A pdb=" N THR B 598 " --> pdb=" O GLY B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 605 Processing helix chain 'B' and resid 608 through 623 removed outlier: 3.723A pdb=" N ARG B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 637 Processing helix chain 'B' and resid 638 through 646 Processing helix chain 'B' and resid 648 through 653 removed outlier: 4.437A pdb=" N ASP B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 519 through 524 removed outlier: 6.664A pdb=" N PHE A 510 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN A 522 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL A 508 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU A 524 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 503 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 519 through 524 removed outlier: 6.664A pdb=" N PHE A 510 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN A 522 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL A 508 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU A 524 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL A 508 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY A 559 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 533 through 535 removed outlier: 6.614A pdb=" N THR A 534 " --> pdb=" O LEU A 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 712 through 716 removed outlier: 6.425A pdb=" N ILE A 712 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY A 723 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE A 714 " --> pdb=" O ARG A 721 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 484 through 493 removed outlier: 7.374A pdb=" N VAL B 485 " --> pdb=" O ALA B 476 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ALA B 476 " --> pdb=" O VAL B 485 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS B 487 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER B 474 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU B 489 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL B 468 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN B 471 " --> pdb=" O GLN B 526 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN B 526 " --> pdb=" O GLN B 471 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL B 473 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLY B 524 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 546 through 549 removed outlier: 6.891A pdb=" N VAL B 547 " --> pdb=" O ILE B 629 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N ASP B 631 " --> pdb=" O VAL B 547 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL B 549 " --> pdb=" O ASP B 631 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL B 498 " --> pdb=" O GLN B 671 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU B 673 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA B 500 " --> pdb=" O LEU B 673 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1713 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: 2.27 Time building geometry restraints manager: 4.06 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: 2608 1.34 - 1.46: 1670 1.46 - 1.58: 3493 1.58 - 1.70: 0 1.70 - 1.82: 53 Bond restraints: 7824 Sorted by residual: bond pdb=" CA LEU B 286 " pdb=" C LEU B 286 " ideal model delta sigma weight residual 1.524 1.502 0.022 1.27e-02 6.20e+03 3.02e+00 bond pdb=" CB THR A 235 " pdb=" CG2 THR A 235 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.50e+00 bond pdb=" CA MET B 285 " pdb=" C MET B 285 " ideal model delta sigma weight residual 1.523 1.503 0.020 1.30e-02 5.92e+03 2.47e+00 bond pdb=" CA ASN A 251 " pdb=" CB ASN A 251 " ideal model delta sigma weight residual 1.530 1.553 -0.023 1.69e-02 3.50e+03 1.85e+00 bond pdb=" SD MET B 196 " pdb=" CE MET B 196 " ideal model delta sigma weight residual 1.791 1.758 0.033 2.50e-02 1.60e+03 1.77e+00 ... (remaining 7819 not shown) Histogram of bond angle deviations from ideal: 97.13 - 104.50: 109 104.50 - 111.86: 3851 111.86 - 119.23: 2543 119.23 - 126.59: 4066 126.59 - 133.95: 87 Bond angle restraints: 10656 Sorted by residual: angle pdb=" C VAL B 576 " pdb=" N MET B 577 " pdb=" CA MET B 577 " ideal model delta sigma weight residual 121.58 112.36 9.22 1.95e+00 2.63e-01 2.24e+01 angle pdb=" CB MET A 420 " pdb=" CG MET A 420 " pdb=" SD MET A 420 " ideal model delta sigma weight residual 112.70 98.53 14.17 3.00e+00 1.11e-01 2.23e+01 angle pdb=" N LEU B 286 " pdb=" CA LEU B 286 " pdb=" C LEU B 286 " ideal model delta sigma weight residual 111.07 106.13 4.94 1.07e+00 8.73e-01 2.13e+01 angle pdb=" CB MET B 260 " pdb=" CG MET B 260 " pdb=" SD MET B 260 " ideal model delta sigma weight residual 112.70 125.54 -12.84 3.00e+00 1.11e-01 1.83e+01 angle pdb=" CB MET B 592 " pdb=" CG MET B 592 " pdb=" SD MET B 592 " ideal model delta sigma weight residual 112.70 124.34 -11.64 3.00e+00 1.11e-01 1.51e+01 ... (remaining 10651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 4101 16.79 - 33.57: 423 33.57 - 50.36: 113 50.36 - 67.15: 21 67.15 - 83.93: 11 Dihedral angle restraints: 4669 sinusoidal: 1554 harmonic: 3115 Sorted by residual: dihedral pdb=" CA MET A 420 " pdb=" C MET A 420 " pdb=" N LEU A 421 " pdb=" CA LEU A 421 " ideal model delta harmonic sigma weight residual 180.00 162.75 17.25 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ASP B 237 " pdb=" CB ASP B 237 " pdb=" CG ASP B 237 " pdb=" OD1 ASP B 237 " ideal model delta sinusoidal sigma weight residual -30.00 -87.81 57.81 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ILE A 319 " pdb=" C ILE A 319 " pdb=" N MET A 320 " pdb=" CA MET A 320 " ideal model delta harmonic sigma weight residual 180.00 163.97 16.03 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 4666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 917 0.039 - 0.078: 264 0.078 - 0.116: 77 0.116 - 0.155: 12 0.155 - 0.194: 6 Chirality restraints: 1276 Sorted by residual: chirality pdb=" CB ILE B 169 " pdb=" CA ILE B 169 " pdb=" CG1 ILE B 169 " pdb=" CG2 ILE B 169 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" CG LEU A 316 " pdb=" CB LEU A 316 " pdb=" CD1 LEU A 316 " pdb=" CD2 LEU A 316 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.74e-01 chirality pdb=" CA MET B 577 " pdb=" N MET B 577 " pdb=" C MET B 577 " pdb=" CB MET B 577 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.19e-01 ... (remaining 1273 not shown) Planarity restraints: 1391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 251 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C ASN A 251 " -0.035 2.00e-02 2.50e+03 pdb=" O ASN A 251 " 0.013 2.00e-02 2.50e+03 pdb=" N THR A 252 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 257 " -0.011 2.00e-02 2.50e+03 1.58e-02 3.74e+00 pdb=" CG HIS A 257 " 0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS A 257 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 HIS A 257 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 HIS A 257 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS A 257 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 404 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" CD GLU A 404 " -0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU A 404 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 404 " 0.011 2.00e-02 2.50e+03 ... (remaining 1388 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1938 2.79 - 3.32: 7749 3.32 - 3.85: 12888 3.85 - 4.37: 12954 4.37 - 4.90: 23270 Nonbonded interactions: 58799 Sorted by model distance: nonbonded pdb=" OE1 GLU B 307 " pdb=" OH TYR B 376 " model vdw 2.267 2.440 nonbonded pdb=" O LEU B 253 " pdb=" OG1 THR B 257 " model vdw 2.295 2.440 nonbonded pdb=" O ASN A 443 " pdb=" OG1 THR A 446 " model vdw 2.331 2.440 nonbonded pdb=" NH1 ARG A 186 " pdb=" OG1 THR A 252 " model vdw 2.337 2.520 nonbonded pdb=" NH2 ARG A 378 " pdb=" O GLN B 236 " model vdw 2.340 2.520 ... (remaining 58794 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 group one per residue 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: 4.100 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 26.080 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 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 : 0.004 0.052 7824 Z= 0.229 Angle : 0.760 14.168 10656 Z= 0.371 Chirality : 0.042 0.194 1276 Planarity : 0.004 0.044 1391 Dihedral : 15.551 83.931 2663 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.57 % Allowed : 20.43 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.25), residues: 1076 helix: 1.78 (0.19), residues: 720 sheet: -1.23 (0.75), residues: 54 loop : -0.31 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 322 HIS 0.021 0.002 HIS A 257 PHE 0.011 0.001 PHE A 224 TYR 0.010 0.001 TYR B 422 ARG 0.009 0.000 ARG C 2 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 329 MET cc_start: 0.8048 (mmm) cc_final: 0.7595 (mmt) REVERT: A 339 PHE cc_start: 0.7991 (m-80) cc_final: 0.7595 (m-10) REVERT: A 408 TYR cc_start: 0.8111 (t80) cc_final: 0.7789 (t80) REVERT: B 166 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7723 (mt-10) REVERT: B 269 ASN cc_start: 0.8235 (t0) cc_final: 0.7876 (t0) REVERT: B 294 LEU cc_start: 0.7505 (mt) cc_final: 0.7088 (tp) REVERT: B 298 LEU cc_start: 0.8840 (mm) cc_final: 0.8466 (mp) outliers start: 4 outliers final: 2 residues processed: 128 average time/residue: 0.2104 time to fit residues: 36.1123 Evaluate side-chains 91 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 419 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 43 optimal weight: 20.0000 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 0.0060 chunk 50 optimal weight: 20.0000 chunk 62 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7824 Z= 0.162 Angle : 0.519 7.135 10656 Z= 0.265 Chirality : 0.036 0.142 1276 Planarity : 0.003 0.029 1391 Dihedral : 3.713 34.883 1157 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.40 % Allowed : 20.43 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.26), residues: 1076 helix: 2.27 (0.19), residues: 736 sheet: -1.05 (0.76), residues: 54 loop : -0.22 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 322 HIS 0.009 0.001 HIS A 257 PHE 0.022 0.001 PHE A 224 TYR 0.009 0.001 TYR A 309 ARG 0.005 0.000 ARG C 1 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 0.821 Fit side-chains REVERT: A 202 MET cc_start: 0.7428 (tpp) cc_final: 0.6887 (ttm) REVERT: A 339 PHE cc_start: 0.8028 (m-80) cc_final: 0.7681 (m-10) REVERT: A 408 TYR cc_start: 0.8122 (t80) cc_final: 0.7793 (t80) REVERT: A 420 MET cc_start: 0.8023 (ttt) cc_final: 0.7680 (mtp) REVERT: B 166 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7701 (mt-10) REVERT: B 269 ASN cc_start: 0.8335 (t0) cc_final: 0.8119 (t0) REVERT: B 298 LEU cc_start: 0.8863 (mm) cc_final: 0.8583 (mp) outliers start: 24 outliers final: 14 residues processed: 114 average time/residue: 0.1687 time to fit residues: 27.6845 Evaluate side-chains 101 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 4 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 96 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7824 Z= 0.170 Angle : 0.497 6.260 10656 Z= 0.253 Chirality : 0.037 0.125 1276 Planarity : 0.003 0.030 1391 Dihedral : 3.536 33.844 1157 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.97 % Allowed : 21.13 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.26), residues: 1076 helix: 2.43 (0.19), residues: 736 sheet: -1.03 (0.77), residues: 54 loop : -0.12 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 322 HIS 0.006 0.001 HIS A 257 PHE 0.023 0.001 PHE A 224 TYR 0.009 0.001 TYR B 422 ARG 0.003 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 93 time to evaluate : 0.796 Fit side-chains REVERT: A 339 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: A 408 TYR cc_start: 0.8209 (t80) cc_final: 0.7838 (t80) REVERT: B 166 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7703 (mt-10) REVERT: B 298 LEU cc_start: 0.8846 (mm) cc_final: 0.8503 (mp) REVERT: B 517 GLN cc_start: 0.8424 (mm110) cc_final: 0.7929 (mt0) outliers start: 28 outliers final: 18 residues processed: 112 average time/residue: 0.1662 time to fit residues: 26.7411 Evaluate side-chains 104 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 4 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 30.0000 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN A 257 HIS B 416 GLN B 517 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7824 Z= 0.309 Angle : 0.602 8.638 10656 Z= 0.307 Chirality : 0.040 0.131 1276 Planarity : 0.003 0.032 1391 Dihedral : 3.694 31.328 1156 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 5.11 % Allowed : 21.28 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.26), residues: 1076 helix: 2.25 (0.19), residues: 730 sheet: -1.23 (0.77), residues: 54 loop : -0.27 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 322 HIS 0.007 0.001 HIS A 257 PHE 0.020 0.002 PHE A 224 TYR 0.016 0.002 TYR B 282 ARG 0.004 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 91 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 199 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8053 (mm) REVERT: A 339 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7861 (m-80) REVERT: B 166 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7760 (mt-10) REVERT: B 298 LEU cc_start: 0.8917 (mm) cc_final: 0.8631 (mp) REVERT: B 300 MET cc_start: 0.8406 (tpp) cc_final: 0.7976 (tpp) REVERT: B 572 GLU cc_start: 0.8288 (mp0) cc_final: 0.8075 (mp0) outliers start: 36 outliers final: 28 residues processed: 121 average time/residue: 0.1724 time to fit residues: 30.3269 Evaluate side-chains 112 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 82 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 4 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 52 optimal weight: 50.0000 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7824 Z= 0.208 Angle : 0.533 7.555 10656 Z= 0.268 Chirality : 0.038 0.146 1276 Planarity : 0.003 0.033 1391 Dihedral : 3.645 30.681 1156 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.68 % Allowed : 22.84 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.26), residues: 1076 helix: 2.47 (0.19), residues: 728 sheet: -1.24 (0.76), residues: 54 loop : -0.30 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 322 HIS 0.003 0.001 HIS B 543 PHE 0.019 0.001 PHE A 224 TYR 0.015 0.001 TYR B 282 ARG 0.003 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 88 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 199 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7970 (mm) REVERT: A 339 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7967 (m-80) REVERT: A 420 MET cc_start: 0.8119 (mtt) cc_final: 0.7789 (mmm) REVERT: B 166 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7737 (mt-10) REVERT: B 298 LEU cc_start: 0.8887 (mm) cc_final: 0.8600 (mp) REVERT: B 300 MET cc_start: 0.8355 (tpp) cc_final: 0.7930 (tpp) REVERT: B 388 GLN cc_start: 0.8267 (tp40) cc_final: 0.8002 (tp40) outliers start: 33 outliers final: 23 residues processed: 115 average time/residue: 0.1557 time to fit residues: 26.3637 Evaluate side-chains 108 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 83 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain C residue 4 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7824 Z= 0.257 Angle : 0.579 10.740 10656 Z= 0.290 Chirality : 0.039 0.140 1276 Planarity : 0.003 0.033 1391 Dihedral : 3.774 36.799 1156 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 6.10 % Allowed : 22.70 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.26), residues: 1076 helix: 2.38 (0.19), residues: 728 sheet: -1.32 (0.76), residues: 54 loop : -0.32 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 322 HIS 0.006 0.001 HIS A 257 PHE 0.018 0.002 PHE A 224 TYR 0.018 0.001 TYR B 282 ARG 0.004 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 89 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 199 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7994 (mm) REVERT: A 329 MET cc_start: 0.7980 (mmt) cc_final: 0.7756 (tpp) REVERT: B 298 LEU cc_start: 0.8938 (mm) cc_final: 0.8623 (mp) REVERT: B 300 MET cc_start: 0.8357 (tpp) cc_final: 0.7909 (tpp) outliers start: 43 outliers final: 32 residues processed: 124 average time/residue: 0.1542 time to fit residues: 28.4985 Evaluate side-chains 114 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 81 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 4 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 103 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7824 Z= 0.177 Angle : 0.523 7.415 10656 Z= 0.264 Chirality : 0.037 0.146 1276 Planarity : 0.003 0.033 1391 Dihedral : 3.598 43.318 1154 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 5.39 % Allowed : 24.54 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.26), residues: 1076 helix: 2.61 (0.19), residues: 725 sheet: -1.25 (0.75), residues: 54 loop : -0.36 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 322 HIS 0.009 0.001 HIS A 257 PHE 0.017 0.001 PHE A 224 TYR 0.012 0.001 TYR B 282 ARG 0.003 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 90 time to evaluate : 0.898 Fit side-chains REVERT: A 202 MET cc_start: 0.7482 (tpp) cc_final: 0.6924 (ttm) REVERT: A 329 MET cc_start: 0.7962 (mmt) cc_final: 0.7748 (tpp) REVERT: A 408 TYR cc_start: 0.8444 (t80) cc_final: 0.8009 (t80) REVERT: A 417 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7647 (tp) REVERT: A 420 MET cc_start: 0.8051 (mtt) cc_final: 0.7812 (mmm) REVERT: B 298 LEU cc_start: 0.8899 (mm) cc_final: 0.8608 (mp) REVERT: B 300 MET cc_start: 0.8367 (tpp) cc_final: 0.7938 (tpp) REVERT: B 416 GLN cc_start: 0.8794 (tp40) cc_final: 0.8547 (tp40) REVERT: C 3 TYR cc_start: 0.8492 (t80) cc_final: 0.8217 (t80) outliers start: 38 outliers final: 30 residues processed: 122 average time/residue: 0.1534 time to fit residues: 27.3060 Evaluate side-chains 120 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 89 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain C residue 4 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.8980 chunk 31 optimal weight: 40.0000 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 50 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7824 Z= 0.230 Angle : 0.571 10.034 10656 Z= 0.285 Chirality : 0.038 0.141 1276 Planarity : 0.003 0.034 1391 Dihedral : 3.727 48.581 1154 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 5.25 % Allowed : 24.68 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.26), residues: 1076 helix: 2.56 (0.19), residues: 723 sheet: -1.32 (0.75), residues: 54 loop : -0.33 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 322 HIS 0.009 0.001 HIS A 257 PHE 0.016 0.001 PHE A 224 TYR 0.016 0.001 TYR B 282 ARG 0.004 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 88 time to evaluate : 0.976 Fit side-chains REVERT: A 199 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7982 (mm) REVERT: A 347 LYS cc_start: 0.8016 (mmmm) cc_final: 0.7637 (mtmm) REVERT: A 417 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7699 (tp) REVERT: B 298 LEU cc_start: 0.8948 (mm) cc_final: 0.8626 (mp) REVERT: B 300 MET cc_start: 0.8397 (tpp) cc_final: 0.7957 (tpp) REVERT: C 3 TYR cc_start: 0.8470 (t80) cc_final: 0.8142 (t80) outliers start: 37 outliers final: 33 residues processed: 120 average time/residue: 0.1471 time to fit residues: 25.9232 Evaluate side-chains 119 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 84 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain C residue 4 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 41 optimal weight: 20.0000 chunk 75 optimal weight: 0.9980 chunk 29 optimal weight: 30.0000 chunk 86 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 HIS B 517 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7824 Z= 0.278 Angle : 0.609 12.317 10656 Z= 0.304 Chirality : 0.039 0.140 1276 Planarity : 0.003 0.033 1391 Dihedral : 3.951 56.773 1154 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 5.96 % Allowed : 24.11 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.26), residues: 1076 helix: 2.39 (0.19), residues: 722 sheet: -1.47 (0.73), residues: 54 loop : -0.35 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 322 HIS 0.009 0.001 HIS A 257 PHE 0.016 0.002 PHE A 224 TYR 0.021 0.001 TYR B 282 ARG 0.004 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 87 time to evaluate : 0.883 Fit side-chains REVERT: A 199 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8020 (mm) REVERT: A 202 MET cc_start: 0.7465 (tpp) cc_final: 0.7161 (ttp) REVERT: A 417 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7712 (tp) REVERT: B 298 LEU cc_start: 0.8918 (mm) cc_final: 0.8593 (mp) REVERT: B 300 MET cc_start: 0.8403 (tpp) cc_final: 0.7951 (tpp) REVERT: C 3 TYR cc_start: 0.8453 (t80) cc_final: 0.8128 (t80) outliers start: 42 outliers final: 37 residues processed: 121 average time/residue: 0.1641 time to fit residues: 28.8991 Evaluate side-chains 122 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 83 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 571 CYS Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 4 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 52 optimal weight: 30.0000 chunk 67 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7824 Z= 0.214 Angle : 0.580 12.427 10656 Z= 0.287 Chirality : 0.038 0.140 1276 Planarity : 0.003 0.036 1391 Dihedral : 3.870 57.402 1154 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.39 % Allowed : 24.54 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.26), residues: 1076 helix: 2.49 (0.19), residues: 722 sheet: -1.51 (0.72), residues: 54 loop : -0.33 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 322 HIS 0.009 0.001 HIS A 257 PHE 0.016 0.001 PHE A 224 TYR 0.015 0.001 TYR B 282 ARG 0.004 0.000 ARG B 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 88 time to evaluate : 0.838 Fit side-chains REVERT: A 199 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7906 (mm) REVERT: A 202 MET cc_start: 0.7432 (tpp) cc_final: 0.7126 (ttp) REVERT: A 408 TYR cc_start: 0.8446 (t80) cc_final: 0.8097 (t80) REVERT: A 417 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7656 (tp) REVERT: B 294 LEU cc_start: 0.8194 (tp) cc_final: 0.7968 (tp) REVERT: B 298 LEU cc_start: 0.8959 (mm) cc_final: 0.8535 (mp) REVERT: B 300 MET cc_start: 0.8388 (tpp) cc_final: 0.7935 (tpp) outliers start: 38 outliers final: 35 residues processed: 119 average time/residue: 0.1631 time to fit residues: 27.7783 Evaluate side-chains 122 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 85 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 571 CYS Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 4 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 74 optimal weight: 0.0030 chunk 4 optimal weight: 0.7980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 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 = 0.3961 r_free = 0.3961 target = 0.141674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.111936 restraints weight = 13372.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.115421 restraints weight = 6615.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.117698 restraints weight = 4127.751| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7824 Z= 0.168 Angle : 0.553 8.630 10656 Z= 0.274 Chirality : 0.037 0.132 1276 Planarity : 0.003 0.035 1391 Dihedral : 3.784 59.922 1154 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.68 % Allowed : 25.53 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.26), residues: 1076 helix: 2.62 (0.19), residues: 726 sheet: -1.62 (0.70), residues: 56 loop : -0.25 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 322 HIS 0.011 0.001 HIS A 257 PHE 0.016 0.001 PHE A 224 TYR 0.008 0.001 TYR B 282 ARG 0.003 0.000 ARG B 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1631.12 seconds wall clock time: 29 minutes 56.59 seconds (1796.59 seconds total)