Starting phenix.real_space_refine on Tue Feb 20 01:46:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smp_25204/02_2024/7smp_25204_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smp_25204/02_2024/7smp_25204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smp_25204/02_2024/7smp_25204.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smp_25204/02_2024/7smp_25204.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smp_25204/02_2024/7smp_25204_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smp_25204/02_2024/7smp_25204_trim_updated.pdb" } resolution = 3.28 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= 0.042 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 K 2 8.98 5 S 83 5.16 5 C 8573 2.51 5 N 2148 2.21 5 O 2318 1.98 5 H 13353 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 924": "OE1" <-> "OE2" Residue "A GLU 1158": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26477 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 13184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 13184 Classifications: {'peptide': 833} Link IDs: {'PTRANS': 29, 'TRANS': 803} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 13216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 13216 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 29, 'TRANS': 805} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' K': 1, '82U': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' K': 1, '82U': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.73, per 1000 atoms: 0.44 Number of scatterers: 26477 At special positions: 0 Unit cell: (84.53, 151.94, 124.12, 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) K 2 19.00 S 83 16.00 O 2318 8.00 N 2148 7.00 C 8573 6.00 H 13353 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 577 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 568 " distance=2.04 Simple disulfide: pdb=" SG CYS A 577 " - pdb=" SG CYS A 582 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 22.83 Conformation dependent library (CDL) restraints added in 2.5 seconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3098 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 3 sheets defined 57.7% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.87 Creating SS restraints... Processing helix chain 'B' and resid 287 through 290 No H-bonds generated for 'chain 'B' and resid 287 through 290' Processing helix chain 'B' and resid 292 through 299 Processing helix chain 'B' and resid 302 through 305 No H-bonds generated for 'chain 'B' and resid 302 through 305' Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'B' and resid 317 through 342 Processing helix chain 'B' and resid 352 through 359 Processing helix chain 'B' and resid 362 through 397 removed outlier: 3.619A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 425 Processing helix chain 'B' and resid 428 through 454 Processing helix chain 'B' and resid 458 through 460 No H-bonds generated for 'chain 'B' and resid 458 through 460' Processing helix chain 'B' and resid 470 through 476 Processing helix chain 'B' and resid 487 through 497 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 501 through 503 No H-bonds generated for 'chain 'B' and resid 501 through 503' Processing helix chain 'B' and resid 514 through 543 Proline residue: B 519 - end of helix Processing helix chain 'B' and resid 552 through 554 No H-bonds generated for 'chain 'B' and resid 552 through 554' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 576 through 578 No H-bonds generated for 'chain 'B' and resid 576 through 578' Processing helix chain 'B' and resid 592 through 596 Processing helix chain 'B' and resid 600 through 632 Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 640 through 642 No H-bonds generated for 'chain 'B' and resid 640 through 642' Processing helix chain 'B' and resid 652 through 668 Processing helix chain 'B' and resid 675 through 698 Processing helix chain 'B' and resid 713 through 730 Processing helix chain 'B' and resid 732 through 751 removed outlier: 3.625A pdb=" N LEU B 736 " --> pdb=" O TRP B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 779 Processing helix chain 'B' and resid 798 through 810 removed outlier: 3.605A pdb=" N ARG B 801 " --> pdb=" O PRO B 798 " (cutoff:3.500A) Proline residue: B 802 - end of helix Processing helix chain 'B' and resid 828 through 848 removed outlier: 4.239A pdb=" N MET B 832 " --> pdb=" O ARG B 828 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LYS B 833 " --> pdb=" O ARG B 829 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU B 834 " --> pdb=" O GLN B 830 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 843 " --> pdb=" O GLN B 839 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 844 " --> pdb=" O ALA B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 873 Processing helix chain 'B' and resid 897 through 912 Processing helix chain 'B' and resid 1035 through 1044 Proline residue: B1040 - end of helix Processing helix chain 'B' and resid 1047 through 1049 No H-bonds generated for 'chain 'B' and resid 1047 through 1049' Processing helix chain 'B' and resid 1065 through 1078 Processing helix chain 'B' and resid 1098 through 1111 Proline residue: B1110 - end of helix Processing helix chain 'B' and resid 1120 through 1128 Processing helix chain 'B' and resid 1136 through 1159 removed outlier: 5.682A pdb=" N THR B1144 " --> pdb=" O GLU B1140 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LYS B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1190 Processing helix chain 'A' and resid 292 through 299 Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 317 through 342 Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 362 through 397 removed outlier: 3.648A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 426 removed outlier: 3.659A pdb=" N ALA A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 453 removed outlier: 4.056A pdb=" N ALA A 434 " --> pdb=" O TRP A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 475 Processing helix chain 'A' and resid 487 through 497 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 514 through 542 Proline residue: A 519 - end of helix removed outlier: 3.526A pdb=" N SER A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 569 Processing helix chain 'A' and resid 592 through 596 Processing helix chain 'A' and resid 600 through 631 Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 652 through 668 Processing helix chain 'A' and resid 672 through 698 Proline residue: A 676 - end of helix Processing helix chain 'A' and resid 713 through 730 Processing helix chain 'A' and resid 732 through 751 Processing helix chain 'A' and resid 761 through 779 Processing helix chain 'A' and resid 798 through 810 Proline residue: A 802 - end of helix Processing helix chain 'A' and resid 831 through 848 Processing helix chain 'A' and resid 863 through 873 Processing helix chain 'A' and resid 897 through 912 Processing helix chain 'A' and resid 1035 through 1044 Proline residue: A1040 - end of helix Processing helix chain 'A' and resid 1062 through 1078 removed outlier: 5.795A pdb=" N ASP A1066 " --> pdb=" O ASN A1063 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS A1067 " --> pdb=" O ARG A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1111 Proline residue: A1110 - end of helix Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1136 through 1159 removed outlier: 5.776A pdb=" N THR A1144 " --> pdb=" O GLU A1140 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LYS A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1190 Processing sheet with id= A, first strand: chain 'B' and resid 791 through 793 removed outlier: 6.658A pdb=" N PHE B 854 " --> pdb=" O CYS B 820 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N HIS B 822 " --> pdb=" O PHE B 854 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA B 856 " --> pdb=" O HIS B 822 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N HIS B 824 " --> pdb=" O ALA B 856 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 858 " --> pdb=" O HIS B 824 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 883 through 887 removed outlier: 6.222A pdb=" N GLY B 916 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU B 886 " --> pdb=" O GLY B 916 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL B 918 " --> pdb=" O LEU B 886 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE B1166 " --> pdb=" O LEU B1198 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL B1200 " --> pdb=" O ILE B1166 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N MET B1168 " --> pdb=" O VAL B1200 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER B1169 " --> pdb=" O TRP B1027 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASP B1085 " --> pdb=" O VAL B1056 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ILE B1058 " --> pdb=" O ASP B1085 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N MET B1087 " --> pdb=" O ILE B1058 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1086 through 1089 removed outlier: 6.386A pdb=" N VAL A1056 " --> pdb=" O MET A1087 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU A1089 " --> pdb=" O VAL A1056 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A1058 " --> pdb=" O LEU A1089 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER A1169 " --> pdb=" O TRP A1027 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N MET A1168 " --> pdb=" O PRO A1196 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU A1198 " --> pdb=" O MET A1168 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLY A 887 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N PHE A 854 " --> pdb=" O CYS A 820 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N HIS A 822 " --> pdb=" O PHE A 854 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA A 856 " --> pdb=" O HIS A 822 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N HIS A 824 " --> pdb=" O ALA A 856 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL A 858 " --> pdb=" O HIS A 824 " (cutoff:3.500A) 683 hydrogen bonds defined for protein. 1965 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: 10.78 Time building geometry restraints manager: 23.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13337 1.03 - 1.23: 55 1.23 - 1.42: 5511 1.42 - 1.62: 7728 1.62 - 1.82: 142 Bond restraints: 26773 Sorted by residual: bond pdb=" N 82U B1302 " pdb=" CA 82U B1302 " ideal model delta sigma weight residual 1.366 1.433 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" N 82U A1301 " pdb=" CA 82U A1301 " ideal model delta sigma weight residual 1.366 1.433 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" N 82U B1301 " pdb=" CA 82U B1301 " ideal model delta sigma weight residual 1.366 1.432 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" NE1 82U A1301 " pdb=" S1 82U A1301 " ideal model delta sigma weight residual 1.647 1.705 -0.058 2.00e-02 2.50e+03 8.39e+00 bond pdb=" NE1 82U B1302 " pdb=" S1 82U B1302 " ideal model delta sigma weight residual 1.647 1.705 -0.058 2.00e-02 2.50e+03 8.34e+00 ... (remaining 26768 not shown) Histogram of bond angle deviations from ideal: 99.10 - 107.00: 583 107.00 - 114.89: 33450 114.89 - 122.79: 11726 122.79 - 130.69: 2695 130.69 - 138.59: 63 Bond angle restraints: 48517 Sorted by residual: angle pdb=" C 82U B1301 " pdb=" C1 82U B1301 " pdb=" S1 82U B1301 " ideal model delta sigma weight residual 120.11 138.59 -18.48 3.00e+00 1.11e-01 3.79e+01 angle pdb=" O1 82U B1302 " pdb=" S1 82U B1302 " pdb=" O2 82U B1302 " ideal model delta sigma weight residual 118.12 100.23 17.89 3.00e+00 1.11e-01 3.56e+01 angle pdb=" O1 82U A1301 " pdb=" S1 82U A1301 " pdb=" O2 82U A1301 " ideal model delta sigma weight residual 118.12 100.59 17.53 3.00e+00 1.11e-01 3.42e+01 angle pdb=" CD2 82U B1301 " pdb=" C1 82U B1301 " pdb=" S1 82U B1301 " ideal model delta sigma weight residual 118.42 101.58 16.84 3.00e+00 1.11e-01 3.15e+01 angle pdb=" C 82U B1302 " pdb=" C1 82U B1302 " pdb=" S1 82U B1302 " ideal model delta sigma weight residual 120.11 136.89 -16.78 3.00e+00 1.11e-01 3.13e+01 ... (remaining 48512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 11118 17.47 - 34.94: 1028 34.94 - 52.41: 262 52.41 - 69.88: 108 69.88 - 87.36: 25 Dihedral angle restraints: 12541 sinusoidal: 6757 harmonic: 5784 Sorted by residual: dihedral pdb=" CB CYS A 577 " pdb=" SG CYS A 577 " pdb=" SG CYS A 582 " pdb=" CB CYS A 582 " ideal model delta sinusoidal sigma weight residual 93.00 34.97 58.03 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" C 82U A1301 " pdb=" N 82U A1301 " pdb=" CA 82U A1301 " pdb=" CB 82U A1301 " ideal model delta harmonic sigma weight residual -122.60 -137.94 15.34 0 2.50e+00 1.60e-01 3.77e+01 dihedral pdb=" C 82U B1301 " pdb=" N 82U B1301 " pdb=" CA 82U B1301 " pdb=" CB 82U B1301 " ideal model delta harmonic sigma weight residual -122.60 -137.90 15.30 0 2.50e+00 1.60e-01 3.75e+01 ... (remaining 12538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1387 0.034 - 0.067: 512 0.067 - 0.101: 142 0.101 - 0.134: 49 0.134 - 0.168: 2 Chirality restraints: 2092 Sorted by residual: chirality pdb=" CG LEU B 683 " pdb=" CB LEU B 683 " pdb=" CD1 LEU B 683 " pdb=" CD2 LEU B 683 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA GLN A1149 " pdb=" N GLN A1149 " pdb=" C GLN A1149 " pdb=" CB GLN A1149 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA ILE A1086 " pdb=" N ILE A1086 " pdb=" C ILE A1086 " pdb=" CB ILE A1086 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 2089 not shown) Planarity restraints: 3862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N 82U B1302 " 0.073 2.00e-02 2.50e+03 8.17e-02 1.67e+02 pdb=" CA 82U B1302 " -0.224 2.00e-02 2.50e+03 pdb=" C 82U B1302 " 0.080 2.00e-02 2.50e+03 pdb=" O 82U B1302 " 0.002 2.00e-02 2.50e+03 pdb=" CB 82U B1302 " 0.070 2.00e-02 2.50e+03 pdb=" CG 82U B1302 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 82U B1302 " -0.000 2.00e-02 2.50e+03 pdb=" C1 82U B1302 " 0.001 2.00e-02 2.50e+03 pdb=" C17 82U B1302 " -0.001 2.00e-02 2.50e+03 pdb=" S1 82U B1302 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 82U B1301 " 0.073 2.00e-02 2.50e+03 8.15e-02 1.66e+02 pdb=" CA 82U B1301 " -0.224 2.00e-02 2.50e+03 pdb=" C 82U B1301 " 0.080 2.00e-02 2.50e+03 pdb=" O 82U B1301 " 0.002 2.00e-02 2.50e+03 pdb=" CB 82U B1301 " 0.068 2.00e-02 2.50e+03 pdb=" CG 82U B1301 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 82U B1301 " -0.000 2.00e-02 2.50e+03 pdb=" C1 82U B1301 " 0.001 2.00e-02 2.50e+03 pdb=" C17 82U B1301 " 0.000 2.00e-02 2.50e+03 pdb=" S1 82U B1301 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 82U A1301 " 0.072 2.00e-02 2.50e+03 8.13e-02 1.65e+02 pdb=" CA 82U A1301 " -0.224 2.00e-02 2.50e+03 pdb=" C 82U A1301 " 0.079 2.00e-02 2.50e+03 pdb=" O 82U A1301 " 0.006 2.00e-02 2.50e+03 pdb=" CB 82U A1301 " 0.068 2.00e-02 2.50e+03 pdb=" CG 82U A1301 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 82U A1301 " 0.002 2.00e-02 2.50e+03 pdb=" C1 82U A1301 " -0.001 2.00e-02 2.50e+03 pdb=" C17 82U A1301 " 0.002 2.00e-02 2.50e+03 pdb=" S1 82U A1301 " -0.003 2.00e-02 2.50e+03 ... (remaining 3859 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.27: 4003 2.27 - 2.98: 73560 2.98 - 3.70: 100079 3.70 - 4.42: 151609 4.42 - 5.14: 239702 Nonbonded interactions: 568953 Sorted by model distance: nonbonded pdb=" H MET B 303 " pdb=" O4 82U B1302 " model vdw 1.548 1.850 nonbonded pdb=" O ASP A 404 " pdb=" H ASP A 408 " model vdw 1.624 1.850 nonbonded pdb=" O ILE B1054 " pdb=" H SER B1084 " model vdw 1.628 1.850 nonbonded pdb=" O TRP B1132 " pdb=" HG SER B1179 " model vdw 1.629 1.850 nonbonded pdb="HD22 ASN B 506 " pdb=" OG SER B 621 " model vdw 1.645 1.850 ... (remaining 568948 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 283 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 284 through 907 or (resi \ d 908 and (name N or name CA or name C or name O or name CB or name CG or name N \ D1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name \ HB3 or name HD2 or name HE1 or name HE2)) or resid 909 through 1210 or resid 130 \ 1 through 1302)) selection = (chain 'B' and (resid 283 through 1210 or resid 1302 through 1303)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 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: 0.390 Extract box with map and model: 14.590 Check model and map are aligned: 0.360 Set scattering table: 0.250 Process input model: 91.600 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.120 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: 0.020 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 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 0.067 13420 Z= 0.271 Angle : 0.763 18.480 18203 Z= 0.371 Chirality : 0.039 0.168 2092 Planarity : 0.006 0.082 2256 Dihedral : 14.908 87.355 4836 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1660 helix: 1.17 (0.16), residues: 1017 sheet: -1.66 (0.49), residues: 114 loop : -1.84 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 758 HIS 0.009 0.001 HIS A 398 PHE 0.021 0.001 PHE B 495 TYR 0.022 0.001 TYR A 353 ARG 0.010 0.000 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1072 MET cc_start: 0.7696 (tpt) cc_final: 0.7463 (tpt) REVERT: B 1125 LYS cc_start: 0.7395 (tptt) cc_final: 0.7170 (tppt) REVERT: A 429 GLU cc_start: 0.7425 (tm-30) cc_final: 0.7173 (tm-30) REVERT: A 697 SER cc_start: 0.8837 (t) cc_final: 0.8255 (t) REVERT: A 713 MET cc_start: 0.7833 (ttp) cc_final: 0.7334 (ttp) REVERT: A 725 ILE cc_start: 0.8108 (mm) cc_final: 0.7888 (mm) REVERT: A 1072 MET cc_start: 0.7456 (tpt) cc_final: 0.7179 (tpt) REVERT: A 1077 SER cc_start: 0.8855 (m) cc_final: 0.8613 (m) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.5148 time to fit residues: 203.1595 Evaluate side-chains 225 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 GLN A1137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13420 Z= 0.299 Angle : 0.580 11.202 18203 Z= 0.301 Chirality : 0.039 0.136 2092 Planarity : 0.005 0.081 2256 Dihedral : 8.530 89.821 1830 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.78 % Allowed : 6.70 % Favored : 92.52 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.21), residues: 1660 helix: 1.18 (0.16), residues: 1012 sheet: -1.87 (0.49), residues: 114 loop : -1.90 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 732 HIS 0.006 0.001 HIS B1159 PHE 0.014 0.001 PHE A1210 TYR 0.014 0.001 TYR A 903 ARG 0.003 0.000 ARG B1201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 224 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 MET cc_start: 0.7177 (tpp) cc_final: 0.6959 (tpp) REVERT: A 429 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7282 (tm-30) REVERT: A 697 SER cc_start: 0.8780 (t) cc_final: 0.8081 (t) REVERT: A 713 MET cc_start: 0.7836 (ttp) cc_final: 0.7353 (ttp) REVERT: A 725 ILE cc_start: 0.8205 (mm) cc_final: 0.7956 (mm) REVERT: A 1072 MET cc_start: 0.7362 (tpt) cc_final: 0.7123 (tpt) REVERT: A 1077 SER cc_start: 0.8935 (m) cc_final: 0.8717 (m) outliers start: 11 outliers final: 11 residues processed: 232 average time/residue: 0.5670 time to fit residues: 199.2301 Evaluate side-chains 223 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 212 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1206 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13420 Z= 0.266 Angle : 0.561 12.088 18203 Z= 0.291 Chirality : 0.039 0.169 2092 Planarity : 0.005 0.080 2256 Dihedral : 8.078 86.966 1830 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.50 % Allowed : 8.91 % Favored : 89.59 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 1660 helix: 1.15 (0.16), residues: 1011 sheet: -1.75 (0.51), residues: 108 loop : -1.95 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 732 HIS 0.006 0.001 HIS B1159 PHE 0.017 0.001 PHE A1210 TYR 0.013 0.001 TYR A 903 ARG 0.002 0.000 ARG B1201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 219 time to evaluate : 2.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 468 TYR cc_start: 0.6998 (m-80) cc_final: 0.6545 (m-80) REVERT: B 1072 MET cc_start: 0.7735 (tpt) cc_final: 0.7448 (tpt) REVERT: A 428 MET cc_start: 0.7257 (tpp) cc_final: 0.7052 (tpp) REVERT: A 429 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7312 (tm-30) REVERT: A 697 SER cc_start: 0.8794 (t) cc_final: 0.7990 (t) REVERT: A 713 MET cc_start: 0.7823 (ttp) cc_final: 0.7317 (ttp) REVERT: A 725 ILE cc_start: 0.8223 (mm) cc_final: 0.7975 (mm) REVERT: A 1072 MET cc_start: 0.7356 (tpt) cc_final: 0.7129 (tpt) REVERT: A 1077 SER cc_start: 0.8901 (m) cc_final: 0.8672 (m) outliers start: 21 outliers final: 18 residues processed: 234 average time/residue: 0.5400 time to fit residues: 190.0001 Evaluate side-chains 228 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 210 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1206 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 0.5980 chunk 113 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13420 Z= 0.201 Angle : 0.530 11.123 18203 Z= 0.273 Chirality : 0.037 0.123 2092 Planarity : 0.005 0.081 2256 Dihedral : 7.522 82.391 1830 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.28 % Allowed : 9.62 % Favored : 89.09 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.21), residues: 1660 helix: 1.28 (0.16), residues: 1009 sheet: -1.70 (0.51), residues: 108 loop : -1.93 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 732 HIS 0.005 0.001 HIS B1159 PHE 0.012 0.001 PHE B 811 TYR 0.013 0.001 TYR A1147 ARG 0.002 0.000 ARG A1201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 242 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 224 time to evaluate : 2.158 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 468 TYR cc_start: 0.6983 (m-80) cc_final: 0.6495 (m-80) REVERT: B 1072 MET cc_start: 0.7750 (tpt) cc_final: 0.7403 (tpt) REVERT: A 428 MET cc_start: 0.7231 (tpp) cc_final: 0.7013 (tpp) REVERT: A 429 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7352 (tm-30) REVERT: A 697 SER cc_start: 0.8802 (t) cc_final: 0.8011 (t) REVERT: A 713 MET cc_start: 0.7790 (ttp) cc_final: 0.7282 (ttp) REVERT: A 725 ILE cc_start: 0.8192 (mm) cc_final: 0.7941 (mm) REVERT: A 1072 MET cc_start: 0.7293 (tpt) cc_final: 0.7070 (tpt) REVERT: A 1077 SER cc_start: 0.8873 (m) cc_final: 0.8638 (m) outliers start: 18 outliers final: 18 residues processed: 234 average time/residue: 0.5230 time to fit residues: 184.4430 Evaluate side-chains 232 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 214 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1128 GLU Chi-restraints excluded: chain A residue 1206 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 0.0980 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 66 optimal weight: 0.0980 chunk 136 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13420 Z= 0.200 Angle : 0.527 11.250 18203 Z= 0.270 Chirality : 0.038 0.124 2092 Planarity : 0.005 0.080 2256 Dihedral : 6.925 76.414 1830 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.35 % Allowed : 10.55 % Favored : 88.10 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1660 helix: 1.34 (0.16), residues: 1009 sheet: -1.70 (0.51), residues: 108 loop : -1.90 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 732 HIS 0.005 0.001 HIS A 398 PHE 0.012 0.001 PHE B 811 TYR 0.012 0.001 TYR A 903 ARG 0.002 0.000 ARG A1201 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 242 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 223 time to evaluate : 2.253 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: symmetry clash REVERT: B 468 TYR cc_start: 0.7078 (m-80) cc_final: 0.6565 (m-80) REVERT: B 1072 MET cc_start: 0.7720 (tpt) cc_final: 0.7352 (tpt) REVERT: A 429 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7411 (tm-30) REVERT: A 697 SER cc_start: 0.8800 (t) cc_final: 0.8018 (t) REVERT: A 713 MET cc_start: 0.7779 (ttp) cc_final: 0.7271 (ttp) REVERT: A 725 ILE cc_start: 0.8215 (mm) cc_final: 0.7962 (mm) REVERT: A 1072 MET cc_start: 0.7295 (tpt) cc_final: 0.7075 (tpt) REVERT: A 1077 SER cc_start: 0.8851 (m) cc_final: 0.8620 (m) outliers start: 19 outliers final: 18 residues processed: 234 average time/residue: 0.5603 time to fit residues: 194.5588 Evaluate side-chains 239 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 221 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1206 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 94 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 133 optimal weight: 0.0060 chunk 74 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13420 Z= 0.146 Angle : 0.505 10.948 18203 Z= 0.256 Chirality : 0.037 0.139 2092 Planarity : 0.005 0.081 2256 Dihedral : 5.986 64.380 1830 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.50 % Allowed : 10.91 % Favored : 87.60 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1660 helix: 1.51 (0.16), residues: 1011 sheet: -1.50 (0.52), residues: 106 loop : -1.81 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 732 HIS 0.005 0.001 HIS A 398 PHE 0.010 0.001 PHE B 811 TYR 0.011 0.001 TYR A 903 ARG 0.001 0.000 ARG A1201 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 256 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 235 time to evaluate : 2.181 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 589 ASN cc_start: 0.7456 (t0) cc_final: 0.7087 (t0) REVERT: B 1072 MET cc_start: 0.7725 (tpt) cc_final: 0.7330 (tpt) REVERT: A 429 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7386 (tm-30) REVERT: A 725 ILE cc_start: 0.8217 (mm) cc_final: 0.7955 (mm) REVERT: A 1072 MET cc_start: 0.7298 (tpt) cc_final: 0.7093 (tpt) REVERT: A 1077 SER cc_start: 0.8820 (m) cc_final: 0.8585 (m) outliers start: 21 outliers final: 17 residues processed: 248 average time/residue: 0.5436 time to fit residues: 202.7623 Evaluate side-chains 238 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 221 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 1091 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 73 optimal weight: 0.0980 chunk 98 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13420 Z= 0.168 Angle : 0.510 10.937 18203 Z= 0.259 Chirality : 0.037 0.144 2092 Planarity : 0.005 0.081 2256 Dihedral : 5.372 62.902 1830 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.35 % Allowed : 11.90 % Favored : 86.74 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.21), residues: 1660 helix: 1.56 (0.16), residues: 1009 sheet: -1.48 (0.52), residues: 106 loop : -1.77 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 732 HIS 0.005 0.001 HIS A 398 PHE 0.014 0.001 PHE B 465 TYR 0.012 0.001 TYR A 903 ARG 0.002 0.000 ARG A1201 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 246 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 227 time to evaluate : 1.980 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: symmetry clash revert: symmetry clash REVERT: B 468 TYR cc_start: 0.6921 (m-80) cc_final: 0.6566 (m-80) REVERT: B 589 ASN cc_start: 0.7461 (t0) cc_final: 0.7091 (t0) REVERT: B 1072 MET cc_start: 0.7699 (tpt) cc_final: 0.7300 (tpt) REVERT: A 429 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7376 (tm-30) REVERT: A 725 ILE cc_start: 0.8077 (mm) cc_final: 0.7829 (mm) REVERT: A 1077 SER cc_start: 0.8849 (m) cc_final: 0.8614 (m) outliers start: 19 outliers final: 19 residues processed: 237 average time/residue: 0.5288 time to fit residues: 189.5923 Evaluate side-chains 243 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 224 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1206 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 0.4980 chunk 95 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 125 optimal weight: 0.0770 chunk 145 optimal weight: 1.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13420 Z= 0.186 Angle : 0.517 11.117 18203 Z= 0.263 Chirality : 0.037 0.124 2092 Planarity : 0.005 0.081 2256 Dihedral : 4.857 62.017 1830 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.50 % Allowed : 12.33 % Favored : 86.17 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.21), residues: 1660 helix: 1.56 (0.16), residues: 1009 sheet: -1.51 (0.52), residues: 106 loop : -1.75 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 732 HIS 0.006 0.001 HIS A 398 PHE 0.011 0.001 PHE B 811 TYR 0.012 0.001 TYR A 903 ARG 0.002 0.000 ARG A1201 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 248 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 227 time to evaluate : 2.108 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: symmetry clash REVERT: B 468 TYR cc_start: 0.6954 (m-80) cc_final: 0.6662 (m-80) REVERT: B 589 ASN cc_start: 0.7483 (t0) cc_final: 0.7099 (t0) REVERT: B 1072 MET cc_start: 0.7708 (tpt) cc_final: 0.7328 (tpt) REVERT: A 725 ILE cc_start: 0.8093 (mm) cc_final: 0.7854 (mm) REVERT: A 1077 SER cc_start: 0.8846 (m) cc_final: 0.8611 (m) outliers start: 21 outliers final: 21 residues processed: 239 average time/residue: 0.5258 time to fit residues: 189.1939 Evaluate side-chains 246 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 225 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1128 GLU Chi-restraints excluded: chain A residue 1206 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 149 optimal weight: 0.3980 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 134 optimal weight: 0.2980 chunk 141 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13420 Z= 0.157 Angle : 0.510 11.015 18203 Z= 0.258 Chirality : 0.037 0.127 2092 Planarity : 0.005 0.081 2256 Dihedral : 4.550 61.790 1830 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.57 % Allowed : 12.62 % Favored : 85.82 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.21), residues: 1660 helix: 1.60 (0.17), residues: 1011 sheet: -1.44 (0.52), residues: 106 loop : -1.71 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 732 HIS 0.006 0.001 HIS A 398 PHE 0.010 0.001 PHE B 473 TYR 0.012 0.001 TYR A 903 ARG 0.002 0.000 ARG A1201 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 228 time to evaluate : 2.220 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: symmetry clash revert: symmetry clash REVERT: B 468 TYR cc_start: 0.7004 (m-80) cc_final: 0.6703 (m-80) REVERT: B 589 ASN cc_start: 0.7468 (t0) cc_final: 0.7101 (t0) REVERT: B 1072 MET cc_start: 0.7680 (tpt) cc_final: 0.7307 (tpt) REVERT: A 697 SER cc_start: 0.8824 (t) cc_final: 0.8523 (t) REVERT: A 725 ILE cc_start: 0.8080 (mm) cc_final: 0.7838 (mm) REVERT: A 1077 SER cc_start: 0.8813 (m) cc_final: 0.8575 (m) outliers start: 22 outliers final: 21 residues processed: 240 average time/residue: 0.5796 time to fit residues: 212.3598 Evaluate side-chains 246 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 225 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1206 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 chunk 165 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13420 Z= 0.213 Angle : 0.537 11.351 18203 Z= 0.275 Chirality : 0.038 0.125 2092 Planarity : 0.005 0.081 2256 Dihedral : 4.542 61.292 1830 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.57 % Allowed : 12.83 % Favored : 85.60 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.21), residues: 1660 helix: 1.51 (0.16), residues: 1009 sheet: -1.50 (0.52), residues: 106 loop : -1.73 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 732 HIS 0.006 0.001 HIS A 398 PHE 0.011 0.001 PHE A1210 TYR 0.012 0.001 TYR A 903 ARG 0.002 0.000 ARG A1201 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 247 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 225 time to evaluate : 2.182 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: symmetry clash revert: symmetry clash REVERT: B 326 MET cc_start: 0.7657 (mtt) cc_final: 0.7291 (mtm) REVERT: B 468 TYR cc_start: 0.7118 (m-80) cc_final: 0.6871 (m-80) REVERT: B 589 ASN cc_start: 0.7478 (t0) cc_final: 0.7090 (t0) REVERT: B 1072 MET cc_start: 0.7715 (tpt) cc_final: 0.7327 (tpt) REVERT: A 429 GLU cc_start: 0.7359 (tm-30) cc_final: 0.7099 (tp30) REVERT: A 725 ILE cc_start: 0.8082 (mm) cc_final: 0.7857 (mm) REVERT: A 1077 SER cc_start: 0.8845 (m) cc_final: 0.8609 (m) outliers start: 22 outliers final: 22 residues processed: 237 average time/residue: 0.5293 time to fit residues: 188.4963 Evaluate side-chains 244 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 222 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 731 ASN Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1206 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.155920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.127068 restraints weight = 56109.781| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.36 r_work: 0.3453 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.223 13420 Z= 0.278 Angle : 0.793 59.197 18203 Z= 0.466 Chirality : 0.038 0.153 2092 Planarity : 0.005 0.081 2256 Dihedral : 4.544 61.293 1830 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.50 % Allowed : 13.19 % Favored : 85.32 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.21), residues: 1660 helix: 1.51 (0.16), residues: 1009 sheet: -1.51 (0.52), residues: 106 loop : -1.73 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 732 HIS 0.005 0.001 HIS A 398 PHE 0.011 0.001 PHE A1210 TYR 0.012 0.001 TYR A 903 ARG 0.002 0.000 ARG A1201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6343.35 seconds wall clock time: 113 minutes 14.68 seconds (6794.68 seconds total)