Starting phenix.real_space_refine on Thu Mar 13 16:36:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8snm_40629/03_2025/8snm_40629.cif Found real_map, /net/cci-nas-00/data/ceres_data/8snm_40629/03_2025/8snm_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/cci-nas-00/data/ceres_data/8snm_40629/03_2025/8snm_40629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8snm_40629/03_2025/8snm_40629.map" model { file = "/net/cci-nas-00/data/ceres_data/8snm_40629/03_2025/8snm_40629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8snm_40629/03_2025/8snm_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.90, per 1000 atoms: 0.66 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: 2.36 Conformation dependent library (CDL) restraints added in 1.0 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: 0.88 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: 2.58 Time building geometry restraints manager: 2.81 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: 5.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.340 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.980 ------------------------------------------------------------------------------- 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 : 0.938 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: 0.2587 time to fit residues: 88.2425 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 : 1.010 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.118437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.096494 restraints weight = 18043.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.099652 restraints weight = 10171.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.101859 restraints weight = 7116.718| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 : 0.941 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: 0.8759 (mmm-85) cc_final: 0.7943 (mmm-85) REVERT: C 515 THR cc_start: 0.8290 (p) cc_final: 0.7932 (t) REVERT: C 529 GLU cc_start: 0.7587 (tt0) cc_final: 0.7141 (tt0) REVERT: C 555 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.7949 (t0) REVERT: C 618 ASN cc_start: 0.8722 (t0) cc_final: 0.8387 (t0) REVERT: C 694 SER cc_start: 0.8816 (m) cc_final: 0.8431 (p) REVERT: C 740 ASP cc_start: 0.6076 (p0) cc_final: 0.5545 (p0) REVERT: A 61 GLN cc_start: 0.8326 (tt0) cc_final: 0.7990 (tm-30) REVERT: B 267 TRP cc_start: 0.7629 (m100) cc_final: 0.7255 (m100) REVERT: B 345 MET cc_start: 0.7874 (mmp) cc_final: 0.7581 (mmm) REVERT: B 564 ASP cc_start: 0.6424 (m-30) cc_final: 0.5392 (t0) REVERT: B 693 CYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7744 (t) outliers start: 18 outliers final: 8 residues processed: 142 average time/residue: 0.2186 time to fit residues: 42.7656 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 : 0.954 ------------------------------------------------------------------------------- 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 107 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 GLN 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.109704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.087669 restraints weight = 18837.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.090575 restraints weight = 10799.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.092552 restraints weight = 7590.045| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9199 Z= 0.315 Angle : 0.642 9.419 12463 Z= 0.335 Chirality : 0.044 0.167 1366 Planarity : 0.005 0.065 1602 Dihedral : 4.672 27.483 1221 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.63 % Allowed : 12.93 % Favored : 84.44 % 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: 1.71 (0.27), residues: 357 sheet: -0.19 (0.46), residues: 124 loop : -1.33 (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 0.004 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 134 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.971 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: 0.8163 (t0) cc_final: 0.7104 (p0) REVERT: C 480 ILE cc_start: 0.8645 (tp) cc_final: 0.8185 (tt) REVERT: C 515 THR cc_start: 0.8269 (p) cc_final: 0.7962 (t) REVERT: C 562 MET cc_start: 0.8466 (mmm) cc_final: 0.8211 (ttm) REVERT: C 618 ASN cc_start: 0.8650 (t0) cc_final: 0.8441 (t0) REVERT: C 694 SER cc_start: 0.8989 (m) cc_final: 0.8615 (p) REVERT: B 387 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8992 (p) REVERT: B 435 MET cc_start: 0.8987 (mmm) cc_final: 0.8277 (mmm) REVERT: B 693 CYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7787 (t) outliers start: 26 outliers final: 8 residues processed: 122 average time/residue: 0.2094 time to fit residues: 36.5036 Evaluate side-chains 97 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 69 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 387 THR 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 4 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 94 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 C 800 ASN A 92 GLN B 497 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.110757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.088888 restraints weight = 18462.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.091867 restraints weight = 10481.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.093899 restraints weight = 7321.210| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4398 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= 0.204 Angle : 0.563 7.708 12463 Z= 0.293 Chirality : 0.042 0.170 1366 Planarity : 0.004 0.060 1602 Dihedral : 4.454 23.583 1221 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.02 % Allowed : 15.25 % Favored : 82.73 % 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: -0.11 (0.24), residues: 1126 helix: 1.87 (0.28), residues: 360 sheet: 0.04 (0.49), residues: 108 loop : -1.27 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 267 HIS 0.005 0.001 HIS C 635 PHE 0.021 0.001 PHE B 655 TYR 0.010 0.001 TYR C 685 ARG 0.006 0.000 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 125 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.955 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: 0.8150 (t0) cc_final: 0.7369 (p0) REVERT: C 515 THR cc_start: 0.8199 (p) cc_final: 0.7874 (t) REVERT: C 562 MET cc_start: 0.8458 (mmm) cc_final: 0.8200 (ttm) REVERT: C 694 SER cc_start: 0.8908 (m) cc_final: 0.8460 (p) REVERT: A 61 GLN cc_start: 0.8358 (tt0) cc_final: 0.7896 (tm-30) REVERT: B 435 MET cc_start: 0.8949 (mmm) cc_final: 0.8168 (mmm) REVERT: B 693 CYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7668 (t) outliers start: 20 outliers final: 11 residues processed: 118 average time/residue: 0.1964 time to fit residues: 33.4338 Evaluate side-chains 98 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Chi-restraints excluded: chain B residue 693 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 58 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 800 ASN A 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.111829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.089207 restraints weight = 18631.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.092104 restraints weight = 10877.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.094060 restraints weight = 7804.127| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4690 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= 0.196 Angle : 0.578 13.574 12463 Z= 0.291 Chirality : 0.042 0.132 1366 Planarity : 0.004 0.055 1602 Dihedral : 4.353 23.509 1221 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.42 % Allowed : 15.45 % Favored : 82.12 % 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: -0.03 (0.24), residues: 1126 helix: 1.91 (0.28), residues: 359 sheet: 0.07 (0.48), residues: 108 loop : -1.20 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 267 HIS 0.014 0.001 HIS C 556 PHE 0.022 0.001 PHE C 812 TYR 0.010 0.001 TYR B 304 ARG 0.009 0.000 ARG A 31 *********************** 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 125 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 1.013 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: 0.8168 (t0) cc_final: 0.7557 (p0) REVERT: C 515 THR cc_start: 0.8156 (p) cc_final: 0.7814 (t) REVERT: C 555 ASN cc_start: 0.8240 (t0) cc_final: 0.8033 (t0) REVERT: C 562 MET cc_start: 0.8488 (mmm) cc_final: 0.7881 (ttt) REVERT: C 694 SER cc_start: 0.8891 (m) cc_final: 0.8445 (p) REVERT: C 736 LEU cc_start: 0.8369 (tt) cc_final: 0.7843 (pp) REVERT: B 693 CYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7649 (t) outliers start: 24 outliers final: 14 residues processed: 117 average time/residue: 0.2475 time to fit residues: 41.9922 Evaluate side-chains 104 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 490 THR 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 762 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 0.0670 chunk 4 optimal weight: 0.5980 chunk 43 optimal weight: 7.9990 chunk 3 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 800 ASN ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.116048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.093485 restraints weight = 18495.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.096355 restraints weight = 11038.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.098246 restraints weight = 7972.401| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9199 Z= 0.194 Angle : 0.562 10.811 12463 Z= 0.285 Chirality : 0.042 0.148 1366 Planarity : 0.004 0.052 1602 Dihedral : 4.279 23.446 1221 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.32 % Allowed : 16.97 % 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: 0.08 (0.24), residues: 1126 helix: 2.05 (0.28), residues: 356 sheet: 0.04 (0.48), residues: 108 loop : -1.13 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 153 HIS 0.005 0.001 HIS C 635 PHE 0.012 0.001 PHE C 668 TYR 0.007 0.001 TYR B 298 ARG 0.010 0.000 ARG A 31 *********************** 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: 23 poor density : 100 time to evaluate : 1.000 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: 0.8214 (t0) cc_final: 0.7736 (p0) REVERT: C 515 THR cc_start: 0.8062 (p) cc_final: 0.7723 (t) REVERT: C 562 MET cc_start: 0.8447 (mmm) cc_final: 0.7818 (ttt) REVERT: C 694 SER cc_start: 0.8862 (m) cc_final: 0.8403 (p) REVERT: B 435 MET cc_start: 0.8720 (mmm) cc_final: 0.8161 (mmm) outliers start: 23 outliers final: 16 residues processed: 115 average time/residue: 0.2031 time to fit residues: 33.3172 Evaluate side-chains 107 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 781 LEU 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 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 602 VAL Chi-restraints excluded: chain B residue 641 CYS Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 chunk 104 optimal weight: 0.0970 chunk 53 optimal weight: 0.0470 chunk 8 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 overall best weight: 0.5676 ------------------------------------------------------------------------------- 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** A 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.111776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.089185 restraints weight = 18901.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.092074 restraints weight = 11015.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.094042 restraints weight = 7872.063| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.5187 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= 0.181 Angle : 0.557 10.254 12463 Z= 0.282 Chirality : 0.042 0.151 1366 Planarity : 0.004 0.050 1602 Dihedral : 4.197 23.242 1221 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.22 % Allowed : 17.88 % Favored : 79.90 % 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: 0.12 (0.24), residues: 1126 helix: 2.08 (0.28), residues: 357 sheet: 0.05 (0.48), residues: 108 loop : -1.11 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 153 HIS 0.004 0.001 HIS C 635 PHE 0.024 0.001 PHE B 652 TYR 0.008 0.001 TYR B 298 ARG 0.006 0.000 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 115 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8186 (t0) cc_final: 0.7740 (p0) REVERT: C 515 THR cc_start: 0.8126 (p) cc_final: 0.7779 (t) REVERT: C 650 THR cc_start: 0.8755 (m) cc_final: 0.8491 (m) REVERT: C 694 SER cc_start: 0.8879 (m) cc_final: 0.8419 (p) REVERT: A 153 TRP cc_start: 0.8529 (p-90) cc_final: 0.7673 (p-90) REVERT: B 435 MET cc_start: 0.8779 (mmm) cc_final: 0.8113 (mmm) REVERT: B 588 LEU cc_start: 0.8261 (mt) cc_final: 0.7607 (mt) outliers start: 22 outliers final: 18 residues processed: 110 average time/residue: 0.2242 time to fit residues: 35.6912 Evaluate side-chains 107 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 555 ASN Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 689 VAL 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 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 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 641 CYS Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 95 optimal weight: 0.3980 chunk 23 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 555 ASN C 556 HIS ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.110852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.088164 restraints weight = 19083.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.091002 restraints weight = 11218.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.092890 restraints weight = 8030.554| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5364 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 : 0.567 11.107 12463 Z= 0.288 Chirality : 0.042 0.137 1366 Planarity : 0.004 0.050 1602 Dihedral : 4.204 23.228 1221 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.32 % Allowed : 18.08 % 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: 2.04 (0.28), residues: 358 sheet: 0.04 (0.48), residues: 108 loop : -1.08 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 153 HIS 0.004 0.001 HIS C 635 PHE 0.012 0.001 PHE C 668 TYR 0.026 0.001 TYR B 340 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 116 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8242 (t0) cc_final: 0.7806 (p0) REVERT: C 515 THR cc_start: 0.8087 (p) cc_final: 0.7748 (t) REVERT: C 650 THR cc_start: 0.8588 (m) cc_final: 0.8360 (m) REVERT: C 694 SER cc_start: 0.8907 (m) cc_final: 0.8452 (p) REVERT: A 30 GLN cc_start: 0.6537 (mm110) cc_final: 0.5997 (mp10) REVERT: B 435 MET cc_start: 0.8808 (mmm) cc_final: 0.8166 (mmm) REVERT: B 588 LEU cc_start: 0.8331 (mt) cc_final: 0.7667 (mt) outliers start: 23 outliers final: 19 residues processed: 109 average time/residue: 0.2308 time to fit residues: 35.4141 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 : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 749 LEU 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 B residue 265 THR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 95 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 chunk 3 optimal weight: 0.8980 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.110653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.088104 restraints weight = 18893.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.090883 restraints weight = 11154.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.092557 restraints weight = 8047.293| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.5440 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= 0.198 Angle : 0.569 11.591 12463 Z= 0.287 Chirality : 0.042 0.141 1366 Planarity : 0.004 0.049 1602 Dihedral : 4.196 23.453 1221 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.22 % Allowed : 18.48 % Favored : 79.29 % 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: 0.14 (0.25), residues: 1126 helix: 2.07 (0.28), residues: 358 sheet: 0.05 (0.49), residues: 108 loop : -1.08 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 153 HIS 0.004 0.001 HIS C 439 PHE 0.025 0.001 PHE B 652 TYR 0.020 0.001 TYR B 340 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 114 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8229 (t0) cc_final: 0.7868 (p0) REVERT: C 515 THR cc_start: 0.8143 (p) cc_final: 0.7816 (t) REVERT: C 650 THR cc_start: 0.8298 (m) cc_final: 0.8012 (m) REVERT: C 694 SER cc_start: 0.8853 (m) cc_final: 0.8385 (p) REVERT: A 30 GLN cc_start: 0.6474 (mm110) cc_final: 0.5956 (mp10) REVERT: A 153 TRP cc_start: 0.8560 (p-90) cc_final: 0.7690 (p-90) REVERT: B 435 MET cc_start: 0.8808 (mmm) cc_final: 0.8142 (mmm) REVERT: B 588 LEU cc_start: 0.8344 (mt) cc_final: 0.7739 (mt) outliers start: 22 outliers final: 21 residues processed: 107 average time/residue: 0.2389 time to fit residues: 36.8176 Evaluate side-chains 109 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 749 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 100 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** A 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.111387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.089261 restraints weight = 19005.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.092045 restraints weight = 10965.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.093959 restraints weight = 7830.241| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5589 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= 0.186 Angle : 0.569 11.907 12463 Z= 0.286 Chirality : 0.042 0.143 1366 Planarity : 0.004 0.049 1602 Dihedral : 4.149 23.445 1221 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.22 % Allowed : 18.59 % Favored : 79.19 % 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: 0.16 (0.25), residues: 1126 helix: 2.10 (0.28), residues: 358 sheet: 0.03 (0.49), residues: 108 loop : -1.07 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 348 HIS 0.006 0.001 HIS C 556 PHE 0.012 0.001 PHE C 668 TYR 0.033 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 117 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 1.280 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: 0.8222 (t0) cc_final: 0.7955 (p0) REVERT: C 515 THR cc_start: 0.8052 (p) cc_final: 0.7739 (t) REVERT: C 650 THR cc_start: 0.8143 (m) cc_final: 0.7922 (m) REVERT: C 694 SER cc_start: 0.8832 (m) cc_final: 0.8375 (p) REVERT: A 30 GLN cc_start: 0.6784 (mm110) cc_final: 0.6297 (mt0) REVERT: A 153 TRP cc_start: 0.8585 (p-90) cc_final: 0.7735 (p-90) REVERT: B 389 ASN cc_start: 0.8346 (t0) cc_final: 0.7922 (t0) REVERT: B 435 MET cc_start: 0.8809 (mmm) cc_final: 0.8073 (mmm) REVERT: B 588 LEU cc_start: 0.8346 (mt) cc_final: 0.7764 (mt) outliers start: 22 outliers final: 19 residues processed: 110 average time/residue: 0.2049 time to fit residues: 32.5253 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 : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 749 LEU 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 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 668 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 0.0870 chunk 20 optimal weight: 0.0000 chunk 64 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 overall best weight: 0.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 350 ASN ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.111793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.089599 restraints weight = 18979.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.092437 restraints weight = 10989.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.094365 restraints weight = 7827.655| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5649 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= 0.169 Angle : 0.563 11.821 12463 Z= 0.282 Chirality : 0.041 0.141 1366 Planarity : 0.004 0.049 1602 Dihedral : 4.083 23.585 1221 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.92 % Allowed : 18.69 % Favored : 79.39 % 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: 0.23 (0.25), residues: 1126 helix: 2.13 (0.28), residues: 361 sheet: -0.01 (0.49), residues: 110 loop : -1.00 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 348 HIS 0.004 0.001 HIS C 635 PHE 0.034 0.001 PHE C 812 TYR 0.025 0.001 TYR B 340 ARG 0.006 0.000 ARG C 412 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2763.00 seconds wall clock time: 50 minutes 10.45 seconds (3010.45 seconds total)