Starting phenix.real_space_refine on Fri Nov 15 14:24:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snm_40629/11_2024/8snm_40629.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snm_40629/11_2024/8snm_40629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snm_40629/11_2024/8snm_40629.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snm_40629/11_2024/8snm_40629.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snm_40629/11_2024/8snm_40629.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snm_40629/11_2024/8snm_40629.cif" } resolution = 3.84 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= 0.001 sd= 0.059 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 Zn 1 6.06 5 S 69 5.16 5 C 5719 2.51 5 N 1529 2.21 5 O 1667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8986 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 3929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3929 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 467} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1406 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 170} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3649 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 450} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5195 SG CYS A 184 44.254 25.694 36.116 1.00 74.22 S Time building chain proxies: 6.34, per 1000 atoms: 0.71 Number of scatterers: 8986 At special positions: 0 Unit cell: (70.992, 110.432, 152.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Ca 1 19.99 S 69 16.00 O 1667 8.00 N 1529 7.00 C 5719 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS C 447 " - pdb=" SG CYS C 611 " distance=2.03 Simple disulfide: pdb=" SG CYS C 470 " - pdb=" SG CYS C 520 " distance=2.03 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS C 487 " distance=2.03 Simple disulfide: pdb=" SG CYS C 479 " - pdb=" SG CYS C 564 " distance=2.03 Simple disulfide: pdb=" SG CYS C 527 " - pdb=" SG CYS C 548 " distance=2.03 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 572 " - pdb=" SG CYS C 606 " distance=2.03 Simple disulfide: pdb=" SG CYS C 579 " - pdb=" SG CYS C 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 225 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 469 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 506 " distance=2.03 Simple disulfide: pdb=" SG CYS B 489 " - pdb=" SG CYS B 502 " distance=2.02 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 514 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 521 " - pdb=" SG CYS B 548 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 578 " distance=2.03 Simple disulfide: pdb=" SG CYS B 582 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 591 " - pdb=" SG CYS B 611 " distance=2.03 Simple disulfide: pdb=" SG CYS B 593 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 641 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 415 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 409 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 405 " pdb="ZN ZN B 901 " - pdb=" SG CYS A 184 " Number of angles added : 3 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 11 sheets defined 37.8% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'C' and resid 343 through 349 Processing helix chain 'C' and resid 361 through 367 Processing helix chain 'C' and resid 373 through 395 removed outlier: 3.710A pdb=" N TYR C 377 " --> pdb=" O PRO C 373 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY C 395 " --> pdb=" O ILE C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 441 Processing helix chain 'C' and resid 444 through 449 Processing helix chain 'C' and resid 451 through 467 removed outlier: 4.049A pdb=" N ASP C 467 " --> pdb=" O ASP C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 537 removed outlier: 3.816A pdb=" N ILE C 537 " --> pdb=" O GLY C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 545 Processing helix chain 'C' and resid 559 through 564 removed outlier: 3.769A pdb=" N CYS C 564 " --> pdb=" O LEU C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 590 Processing helix chain 'C' and resid 600 through 604 Processing helix chain 'C' and resid 605 through 612 removed outlier: 4.062A pdb=" N LYS C 609 " --> pdb=" O HIS C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 631 removed outlier: 3.524A pdb=" N SER C 631 " --> pdb=" O ARG C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 660 removed outlier: 4.455A pdb=" N ARG C 653 " --> pdb=" O MET C 649 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP C 654 " --> pdb=" O THR C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 683 Processing helix chain 'C' and resid 691 through 709 Processing helix chain 'C' and resid 715 through 735 removed outlier: 4.210A pdb=" N ALA C 719 " --> pdb=" O ARG C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 756 removed outlier: 3.764A pdb=" N HIS C 744 " --> pdb=" O ASP C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 795 Processing helix chain 'C' and resid 801 through 803 No H-bonds generated for 'chain 'C' and resid 801 through 803' Processing helix chain 'C' and resid 804 through 809 removed outlier: 3.879A pdb=" N THR C 808 " --> pdb=" O ILE C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 820 Processing helix chain 'A' and resid 32 through 39 removed outlier: 4.071A pdb=" N SER A 37 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.827A pdb=" N ARG A 89 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 153 through 156 removed outlier: 3.758A pdb=" N VAL A 156 " --> pdb=" O TRP A 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 153 through 156' Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 243 through 265 Processing helix chain 'B' and resid 313 through 325 Processing helix chain 'B' and resid 343 through 347 removed outlier: 3.508A pdb=" N GLY B 346 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 347 " --> pdb=" O ASP B 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 343 through 347' Processing helix chain 'B' and resid 395 through 410 Processing helix chain 'B' and resid 451 through 465 removed outlier: 3.816A pdb=" N SER B 457 " --> pdb=" O CYS B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 585 Processing helix chain 'B' and resid 647 through 658 removed outlier: 3.596A pdb=" N GLN B 658 " --> pdb=" O ASP B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 671 through 698 removed outlier: 3.528A pdb=" N SER B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) Proline residue: B 686 - end of helix Processing sheet with id=AA1, first strand: chain 'C' and resid 403 through 411 Processing sheet with id=AA2, first strand: chain 'C' and resid 481 through 482 Processing sheet with id=AA3, first strand: chain 'C' and resid 579 through 582 removed outlier: 3.515A pdb=" N TYR C 593 " --> pdb=" O CYS C 572 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.829A pdb=" N ARG A 126 " --> pdb=" O ASN A 141 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N SER A 125 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL A 119 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 104 through 107 removed outlier: 4.355A pdb=" N VAL A 96 " --> pdb=" O TYR A 107 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N CYS B 225 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE B 279 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LEU B 227 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN B 281 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N LEU B 334 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS B 226 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N HIS B 336 " --> pdb=" O LYS B 226 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU B 228 " --> pdb=" O HIS B 336 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N PHE B 338 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL B 230 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 368 through 371 Processing sheet with id=AA7, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AA8, first strand: chain 'B' and resid 522 through 523 Processing sheet with id=AA9, first strand: chain 'B' and resid 533 through 535 Processing sheet with id=AB1, first strand: chain 'B' and resid 589 through 590 removed outlier: 4.111A pdb=" N GLU B 589 " --> pdb=" O ARG B 605 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 612 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 633 through 635 344 hydrogen bonds defined for protein. 984 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: 2.89 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2049 1.33 - 1.46: 2684 1.46 - 1.59: 4383 1.59 - 1.72: 0 1.72 - 1.85: 83 Bond restraints: 9199 Sorted by residual: bond pdb=" C TRP B 684 " pdb=" O TRP B 684 " ideal model delta sigma weight residual 1.236 1.199 0.037 1.15e-02 7.56e+03 1.02e+01 bond pdb=" CA GLY C 517 " pdb=" C GLY C 517 " ideal model delta sigma weight residual 1.509 1.481 0.028 1.04e-02 9.25e+03 7.50e+00 bond pdb=" CA SER C 516 " pdb=" CB SER C 516 " ideal model delta sigma weight residual 1.530 1.490 0.040 1.57e-02 4.06e+03 6.54e+00 bond pdb=" CA SER C 516 " pdb=" C SER C 516 " ideal model delta sigma weight residual 1.524 1.494 0.030 1.24e-02 6.50e+03 5.94e+00 bond pdb=" CA THR C 515 " pdb=" C THR C 515 " ideal model delta sigma weight residual 1.521 1.493 0.029 1.31e-02 5.83e+03 4.77e+00 ... (remaining 9194 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 12096 1.99 - 3.98: 316 3.98 - 5.97: 39 5.97 - 7.95: 7 7.95 - 9.94: 5 Bond angle restraints: 12463 Sorted by residual: angle pdb=" N GLY C 517 " pdb=" CA GLY C 517 " pdb=" C GLY C 517 " ideal model delta sigma weight residual 111.09 102.51 8.58 1.33e+00 5.65e-01 4.16e+01 angle pdb=" N ASN A 174 " pdb=" CA ASN A 174 " pdb=" C ASN A 174 " ideal model delta sigma weight residual 108.08 117.42 -9.34 1.69e+00 3.50e-01 3.05e+01 angle pdb=" CA ASN A 174 " pdb=" C ASN A 174 " pdb=" N VAL A 175 " ideal model delta sigma weight residual 119.63 115.16 4.47 8.10e-01 1.52e+00 3.04e+01 angle pdb=" C ASN A 174 " pdb=" CA ASN A 174 " pdb=" CB ASN A 174 " ideal model delta sigma weight residual 116.63 110.23 6.40 1.16e+00 7.43e-01 3.04e+01 angle pdb=" C ALA B 270 " pdb=" CA ALA B 270 " pdb=" CB ALA B 270 " ideal model delta sigma weight residual 116.54 110.56 5.98 1.15e+00 7.56e-01 2.71e+01 ... (remaining 12458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5039 17.72 - 35.44: 401 35.44 - 53.16: 63 53.16 - 70.88: 21 70.88 - 88.60: 8 Dihedral angle restraints: 5532 sinusoidal: 2239 harmonic: 3293 Sorted by residual: dihedral pdb=" CB CYS B 582 " pdb=" SG CYS B 582 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual -86.00 -174.60 88.60 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS B 591 " pdb=" SG CYS B 591 " pdb=" SG CYS B 611 " pdb=" CB CYS B 611 " ideal model delta sinusoidal sigma weight residual -86.00 -150.88 64.88 1 1.00e+01 1.00e-02 5.52e+01 dihedral pdb=" CB CYS B 514 " pdb=" SG CYS B 514 " pdb=" SG CYS B 522 " pdb=" CB CYS B 522 " ideal model delta sinusoidal sigma weight residual -86.00 -142.84 56.84 1 1.00e+01 1.00e-02 4.35e+01 ... (remaining 5529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1068 0.052 - 0.104: 254 0.104 - 0.156: 39 0.156 - 0.207: 3 0.207 - 0.259: 2 Chirality restraints: 1366 Sorted by residual: chirality pdb=" CA ASN A 174 " pdb=" N ASN A 174 " pdb=" C ASN A 174 " pdb=" CB ASN A 174 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA VAL C 430 " pdb=" N VAL C 430 " pdb=" C VAL C 430 " pdb=" CB VAL C 430 " both_signs ideal model delta sigma weight residual False 2.44 2.22 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA SER B 608 " pdb=" N SER B 608 " pdb=" C SER B 608 " pdb=" CB SER B 608 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.36e-01 ... (remaining 1363 not shown) Planarity restraints: 1602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 612 " -0.089 5.00e-02 4.00e+02 1.33e-01 2.82e+01 pdb=" N PRO B 613 " 0.229 5.00e-02 4.00e+02 pdb=" CA PRO B 613 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO B 613 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 312 " -0.014 2.00e-02 2.50e+03 1.95e-02 9.55e+00 pdb=" CG TRP B 312 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 312 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP B 312 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 312 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 312 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 312 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 312 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 312 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 312 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 685 " 0.049 5.00e-02 4.00e+02 7.34e-02 8.62e+00 pdb=" N PRO B 686 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 686 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 686 " 0.042 5.00e-02 4.00e+02 ... (remaining 1599 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 511 2.73 - 3.27: 9305 3.27 - 3.81: 14987 3.81 - 4.36: 18810 4.36 - 4.90: 31509 Nonbonded interactions: 75122 Sorted by model distance: nonbonded pdb=" OE1 GLN C 624 " pdb=" OH TYR C 626 " model vdw 2.183 3.040 nonbonded pdb=" OD2 ASP C 475 " pdb=" OG1 THR A 62 " model vdw 2.187 3.040 nonbonded pdb=" OH TYR B 340 " pdb=" OG1 THR B 393 " model vdw 2.207 3.040 nonbonded pdb=" NH1 ARG A 89 " pdb=" OG1 THR A 116 " model vdw 2.207 3.120 nonbonded pdb=" OG1 THR C 376 " pdb=" OE1 GLU C 656 " model vdw 2.209 3.040 ... (remaining 75117 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 5.380 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.070 Process input model: 26.190 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 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 0.080 9199 Z= 0.269 Angle : 0.743 9.942 12463 Z= 0.444 Chirality : 0.046 0.259 1366 Planarity : 0.006 0.133 1602 Dihedral : 13.051 83.445 3344 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.67 (0.24), residues: 1126 helix: 0.98 (0.27), residues: 358 sheet: -0.21 (0.48), residues: 111 loop : -1.36 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 312 HIS 0.009 0.001 HIS B 405 PHE 0.015 0.001 PHE B 323 TYR 0.012 0.001 TYR C 797 ARG 0.008 0.001 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 434 SER cc_start: 0.8184 (m) cc_final: 0.7874 (p) REVERT: C 515 THR cc_start: 0.8782 (p) cc_final: 0.8226 (t) REVERT: C 529 GLU cc_start: 0.7222 (tt0) cc_final: 0.6675 (tt0) REVERT: C 694 SER cc_start: 0.8856 (m) cc_final: 0.8547 (p) REVERT: C 728 LEU cc_start: 0.7914 (tp) cc_final: 0.7714 (mm) REVERT: B 224 THR cc_start: 0.9035 (m) cc_final: 0.8532 (p) REVERT: B 564 ASP cc_start: 0.6807 (m-30) cc_final: 0.5906 (t0) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.2714 time to fit residues: 92.3151 Evaluate side-chains 110 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0010 chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 0.0470 chunk 28 optimal weight: 0.0570 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 101 optimal weight: 3.9990 overall best weight: 0.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN ** C 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN A 92 GLN B 320 GLN B 444 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9199 Z= 0.198 Angle : 0.619 8.753 12463 Z= 0.323 Chirality : 0.043 0.159 1366 Planarity : 0.005 0.085 1602 Dihedral : 4.629 24.186 1221 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.82 % Allowed : 10.51 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 (0.24), residues: 1126 helix: 1.57 (0.27), residues: 362 sheet: -0.17 (0.47), residues: 120 loop : -1.27 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 312 HIS 0.005 0.001 HIS B 692 PHE 0.017 0.001 PHE B 655 TYR 0.023 0.001 TYR C 685 ARG 0.005 0.001 ARG C 412 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 412 ARG cc_start: 0.8689 (mmm-85) cc_final: 0.7876 (mmm-85) REVERT: C 515 THR cc_start: 0.8243 (p) cc_final: 0.7876 (t) REVERT: C 529 GLU cc_start: 0.7526 (tt0) cc_final: 0.7143 (tt0) REVERT: C 555 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.8004 (t0) REVERT: C 618 ASN cc_start: 0.8698 (t0) cc_final: 0.8416 (t0) REVERT: C 694 SER cc_start: 0.8809 (m) cc_final: 0.8437 (p) REVERT: C 740 ASP cc_start: 0.6072 (p0) cc_final: 0.5581 (p0) REVERT: A 61 GLN cc_start: 0.8322 (tt0) cc_final: 0.8017 (tm-30) REVERT: B 267 TRP cc_start: 0.7574 (m100) cc_final: 0.7259 (m100) REVERT: B 345 MET cc_start: 0.7728 (mmp) cc_final: 0.7503 (mmm) REVERT: B 564 ASP cc_start: 0.6243 (m-30) cc_final: 0.5338 (t0) REVERT: B 693 CYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7599 (t) outliers start: 18 outliers final: 8 residues processed: 142 average time/residue: 0.2381 time to fit residues: 46.6546 Evaluate side-chains 98 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 463 ASP Chi-restraints excluded: chain C residue 555 ASN Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 687 PHE Chi-restraints excluded: chain B residue 693 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 GLN ** C 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 HIS C 648 GLN C 695 GLN C 800 ASN A 65 HIS A 92 GLN B 535 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9199 Z= 0.327 Angle : 0.645 10.076 12463 Z= 0.336 Chirality : 0.044 0.166 1366 Planarity : 0.005 0.065 1602 Dihedral : 4.635 23.593 1221 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.53 % Allowed : 12.93 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 (0.24), residues: 1126 helix: 1.70 (0.27), residues: 357 sheet: -0.17 (0.46), residues: 124 loop : -1.34 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 153 HIS 0.006 0.001 HIS B 336 PHE 0.015 0.002 PHE B 321 TYR 0.017 0.001 TYR C 685 ARG 0.005 0.001 ARG C 412 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8218 (t0) cc_final: 0.7200 (p0) REVERT: C 515 THR cc_start: 0.8212 (p) cc_final: 0.7888 (t) REVERT: C 562 MET cc_start: 0.8431 (mmm) cc_final: 0.8123 (ttm) REVERT: C 694 SER cc_start: 0.8982 (m) cc_final: 0.8620 (p) REVERT: B 435 MET cc_start: 0.9000 (mmm) cc_final: 0.8285 (mmm) REVERT: B 693 CYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7658 (t) outliers start: 25 outliers final: 10 residues processed: 121 average time/residue: 0.2076 time to fit residues: 35.4362 Evaluate side-chains 96 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 762 ILE Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 693 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 48 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 GLN C 556 HIS ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 ASN A 92 GLN B 497 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9199 Z= 0.278 Angle : 0.599 7.823 12463 Z= 0.313 Chirality : 0.044 0.177 1366 Planarity : 0.004 0.058 1602 Dihedral : 4.597 23.668 1221 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.83 % Allowed : 14.55 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 (0.24), residues: 1126 helix: 1.77 (0.28), residues: 359 sheet: -0.01 (0.49), residues: 112 loop : -1.34 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 153 HIS 0.006 0.001 HIS C 635 PHE 0.024 0.002 PHE B 655 TYR 0.010 0.001 TYR C 685 ARG 0.007 0.001 ARG C 412 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8331 (t0) cc_final: 0.7541 (p0) REVERT: C 515 THR cc_start: 0.8224 (p) cc_final: 0.7897 (t) REVERT: C 562 MET cc_start: 0.8546 (mmm) cc_final: 0.8230 (ttm) REVERT: C 694 SER cc_start: 0.8985 (m) cc_final: 0.8554 (p) REVERT: C 703 PHE cc_start: 0.8655 (m-80) cc_final: 0.8096 (m-10) REVERT: B 435 MET cc_start: 0.8926 (mmm) cc_final: 0.8215 (mmm) outliers start: 28 outliers final: 15 residues processed: 120 average time/residue: 0.2139 time to fit residues: 36.1863 Evaluate side-chains 102 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 463 ASP Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 790 LEU Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 0.0020 chunk 0 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 97 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 556 HIS ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9199 Z= 0.190 Angle : 0.588 14.726 12463 Z= 0.295 Chirality : 0.042 0.138 1366 Planarity : 0.004 0.055 1602 Dihedral : 4.443 23.760 1221 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.12 % Allowed : 16.46 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.04 (0.24), residues: 1126 helix: 1.93 (0.28), residues: 359 sheet: 0.09 (0.50), residues: 108 loop : -1.24 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 267 HIS 0.009 0.001 HIS C 556 PHE 0.021 0.001 PHE B 652 TYR 0.009 0.001 TYR B 298 ARG 0.006 0.000 ARG C 412 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8304 (t0) cc_final: 0.7697 (p0) REVERT: C 515 THR cc_start: 0.8147 (p) cc_final: 0.7821 (t) REVERT: C 562 MET cc_start: 0.8507 (mmm) cc_final: 0.8159 (ttm) REVERT: C 694 SER cc_start: 0.8904 (m) cc_final: 0.8459 (p) outliers start: 21 outliers final: 13 residues processed: 115 average time/residue: 0.2167 time to fit residues: 35.0584 Evaluate side-chains 98 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 790 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 108 optimal weight: 0.0470 chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 104 optimal weight: 0.0000 overall best weight: 0.7084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 556 HIS ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9199 Z= 0.202 Angle : 0.582 12.357 12463 Z= 0.295 Chirality : 0.042 0.143 1366 Planarity : 0.004 0.052 1602 Dihedral : 4.362 23.656 1221 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.22 % Allowed : 17.07 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.04 (0.24), residues: 1126 helix: 2.00 (0.28), residues: 359 sheet: 0.07 (0.50), residues: 108 loop : -1.18 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 267 HIS 0.015 0.001 HIS C 556 PHE 0.012 0.001 PHE C 668 TYR 0.009 0.001 TYR B 298 ARG 0.006 0.000 ARG C 412 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8318 (t0) cc_final: 0.7753 (p0) REVERT: C 515 THR cc_start: 0.8130 (p) cc_final: 0.7780 (t) REVERT: C 555 ASN cc_start: 0.7997 (t0) cc_final: 0.7742 (t0) REVERT: C 562 MET cc_start: 0.8548 (mmm) cc_final: 0.8215 (ttm) REVERT: C 694 SER cc_start: 0.8906 (m) cc_final: 0.8460 (p) REVERT: A 61 GLN cc_start: 0.8136 (tt0) cc_final: 0.7856 (tm-30) outliers start: 22 outliers final: 19 residues processed: 117 average time/residue: 0.2169 time to fit residues: 35.6047 Evaluate side-chains 110 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 790 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 641 CYS Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 693 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 107 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9199 Z= 0.334 Angle : 0.644 11.346 12463 Z= 0.328 Chirality : 0.044 0.175 1366 Planarity : 0.004 0.049 1602 Dihedral : 4.572 23.874 1221 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.93 % Allowed : 17.47 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.13 (0.24), residues: 1126 helix: 1.86 (0.28), residues: 358 sheet: -0.09 (0.47), residues: 112 loop : -1.27 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 153 HIS 0.005 0.001 HIS B 415 PHE 0.023 0.002 PHE B 652 TYR 0.013 0.001 TYR B 298 ARG 0.006 0.001 ARG C 412 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8451 (t0) cc_final: 0.7836 (p0) REVERT: C 515 THR cc_start: 0.8209 (p) cc_final: 0.7899 (t) REVERT: C 562 MET cc_start: 0.8622 (mmm) cc_final: 0.8298 (ttm) REVERT: C 694 SER cc_start: 0.9056 (m) cc_final: 0.8648 (p) REVERT: A 170 GLU cc_start: 0.8160 (mp0) cc_final: 0.7947 (mp0) outliers start: 29 outliers final: 22 residues processed: 110 average time/residue: 0.2371 time to fit residues: 35.8098 Evaluate side-chains 106 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 790 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 641 CYS Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 693 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 7.9990 chunk 32 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 68 optimal weight: 0.0670 chunk 73 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 98 optimal weight: 0.0770 chunk 103 optimal weight: 3.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 555 ASN ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.5476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9199 Z= 0.173 Angle : 0.595 11.685 12463 Z= 0.300 Chirality : 0.042 0.204 1366 Planarity : 0.004 0.050 1602 Dihedral : 4.319 23.358 1221 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.12 % Allowed : 18.99 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.10 (0.25), residues: 1126 helix: 2.14 (0.28), residues: 356 sheet: -0.02 (0.49), residues: 106 loop : -1.15 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 153 HIS 0.004 0.001 HIS C 635 PHE 0.012 0.001 PHE C 668 TYR 0.009 0.001 TYR C 626 ARG 0.007 0.000 ARG C 412 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8320 (t0) cc_final: 0.7970 (p0) REVERT: C 515 THR cc_start: 0.8080 (p) cc_final: 0.7738 (t) REVERT: C 562 MET cc_start: 0.8541 (mmm) cc_final: 0.8216 (ttm) REVERT: C 650 THR cc_start: 0.8433 (m) cc_final: 0.8130 (m) REVERT: C 694 SER cc_start: 0.8885 (m) cc_final: 0.8450 (p) REVERT: C 736 LEU cc_start: 0.8586 (tt) cc_final: 0.8198 (pp) REVERT: A 61 GLN cc_start: 0.8152 (tt0) cc_final: 0.7814 (tm-30) REVERT: A 153 TRP cc_start: 0.8574 (p-90) cc_final: 0.7743 (p-90) REVERT: B 588 LEU cc_start: 0.8091 (mt) cc_final: 0.7385 (mt) outliers start: 21 outliers final: 16 residues processed: 117 average time/residue: 0.2225 time to fit residues: 36.4346 Evaluate side-chains 104 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain C residue 555 ASN Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 693 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 103 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 555 ASN ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9199 Z= 0.200 Angle : 0.595 11.724 12463 Z= 0.299 Chirality : 0.042 0.174 1366 Planarity : 0.004 0.049 1602 Dihedral : 4.270 23.272 1221 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.12 % Allowed : 19.09 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.08 (0.25), residues: 1126 helix: 2.13 (0.28), residues: 357 sheet: -0.10 (0.48), residues: 108 loop : -1.17 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 348 HIS 0.005 0.001 HIS C 635 PHE 0.029 0.001 PHE B 652 TYR 0.009 0.001 TYR B 298 ARG 0.007 0.000 ARG C 412 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8350 (t0) cc_final: 0.8030 (p0) REVERT: C 515 THR cc_start: 0.8089 (p) cc_final: 0.7757 (t) REVERT: C 562 MET cc_start: 0.8554 (mmm) cc_final: 0.8258 (ttm) REVERT: C 650 THR cc_start: 0.8308 (m) cc_final: 0.8017 (m) REVERT: C 694 SER cc_start: 0.8915 (m) cc_final: 0.8496 (p) REVERT: C 736 LEU cc_start: 0.8606 (tt) cc_final: 0.8250 (pp) REVERT: A 30 GLN cc_start: 0.6813 (mm110) cc_final: 0.6492 (mt0) REVERT: A 61 GLN cc_start: 0.8192 (tt0) cc_final: 0.7816 (tm-30) REVERT: B 583 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7516 (mm-30) REVERT: B 588 LEU cc_start: 0.8229 (mt) cc_final: 0.7480 (mt) outliers start: 21 outliers final: 16 residues processed: 112 average time/residue: 0.2249 time to fit residues: 35.1677 Evaluate side-chains 103 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain C residue 555 ASN Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 693 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 350 ASN C 555 ASN ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 HIS C 648 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9199 Z= 0.204 Angle : 0.603 11.949 12463 Z= 0.302 Chirality : 0.042 0.167 1366 Planarity : 0.004 0.049 1602 Dihedral : 4.260 23.049 1221 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.82 % Allowed : 19.09 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.09 (0.25), residues: 1126 helix: 2.13 (0.28), residues: 357 sheet: -0.09 (0.49), residues: 108 loop : -1.15 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 153 HIS 0.008 0.001 HIS C 556 PHE 0.032 0.001 PHE B 652 TYR 0.030 0.001 TYR B 340 ARG 0.007 0.000 ARG C 412 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8335 (t0) cc_final: 0.8059 (p0) REVERT: C 515 THR cc_start: 0.8070 (p) cc_final: 0.7758 (t) REVERT: C 562 MET cc_start: 0.8583 (mmm) cc_final: 0.8264 (ttm) REVERT: C 650 THR cc_start: 0.8184 (m) cc_final: 0.7914 (m) REVERT: C 694 SER cc_start: 0.8913 (m) cc_final: 0.8483 (p) REVERT: A 30 GLN cc_start: 0.6801 (mm110) cc_final: 0.6537 (mt0) REVERT: A 61 GLN cc_start: 0.8178 (tt0) cc_final: 0.7867 (tm-30) REVERT: A 153 TRP cc_start: 0.8554 (p-90) cc_final: 0.7673 (p-90) REVERT: B 583 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7534 (mm-30) REVERT: B 588 LEU cc_start: 0.8251 (mt) cc_final: 0.7540 (mt) outliers start: 18 outliers final: 15 residues processed: 105 average time/residue: 0.2219 time to fit residues: 32.9199 Evaluate side-chains 104 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 693 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 555 ASN ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.113793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.091338 restraints weight = 18628.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.094106 restraints weight = 11134.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.095844 restraints weight = 8052.180| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.5813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9199 Z= 0.218 Angle : 0.603 11.754 12463 Z= 0.302 Chirality : 0.042 0.150 1366 Planarity : 0.004 0.049 1602 Dihedral : 4.246 22.651 1221 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.92 % Allowed : 19.70 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.10 (0.25), residues: 1126 helix: 2.12 (0.28), residues: 356 sheet: 0.01 (0.49), residues: 108 loop : -1.14 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 153 HIS 0.003 0.001 HIS C 439 PHE 0.034 0.001 PHE C 812 TYR 0.023 0.001 TYR B 340 ARG 0.008 0.000 ARG A 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2027.03 seconds wall clock time: 38 minutes 11.46 seconds (2291.46 seconds total)