Starting phenix.real_space_refine on Wed Feb 14 18:29:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x23_32956/02_2024/7x23_32956_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x23_32956/02_2024/7x23_32956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x23_32956/02_2024/7x23_32956.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x23_32956/02_2024/7x23_32956.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x23_32956/02_2024/7x23_32956_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x23_32956/02_2024/7x23_32956_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 P 3 5.49 5 S 50 5.16 5 Na 3 4.78 5 C 6395 2.51 5 N 1650 2.21 5 O 1875 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9976 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7666 Classifications: {'peptide': 985} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 948} Chain: "B" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2255 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 257} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' NA': 3, 'ACP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 6.04, per 1000 atoms: 0.61 Number of scatterers: 9976 At special positions: 0 Unit cell: (122.84, 93.79, 160.19, 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) S 50 16.00 P 3 15.00 Na 3 11.00 O 1875 8.00 N 1650 7.00 C 6395 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 277 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied NAG-ASN " NAG B 401 " - " ASN B 158 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.40 Conformation dependent library (CDL) restraints added in 1.9 seconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 10 sheets defined 42.4% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 62 through 68 removed outlier: 3.976A pdb=" N GLN A 66 " --> pdb=" O THR A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 88 removed outlier: 3.594A pdb=" N ALA A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 114 through 134 removed outlier: 3.719A pdb=" N ASN A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 175 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 278 through 281 No H-bonds generated for 'chain 'A' and resid 278 through 281' Processing helix chain 'A' and resid 295 through 324 Processing helix chain 'A' and resid 329 through 343 Processing helix chain 'A' and resid 348 through 365 removed outlier: 3.758A pdb=" N LYS A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 381 Processing helix chain 'A' and resid 428 through 440 Processing helix chain 'A' and resid 463 through 475 Processing helix chain 'A' and resid 479 through 485 Processing helix chain 'A' and resid 523 through 528 Processing helix chain 'A' and resid 544 through 560 removed outlier: 3.993A pdb=" N LEU A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 620 Processing helix chain 'A' and resid 633 through 643 Processing helix chain 'A' and resid 653 through 660 Processing helix chain 'A' and resid 679 through 683 Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 707 through 719 Processing helix chain 'A' and resid 731 through 739 Proline residue: A 735 - end of helix Processing helix chain 'A' and resid 752 through 757 Processing helix chain 'A' and resid 767 through 807 removed outlier: 3.569A pdb=" N LEU A 792 " --> pdb=" O ALA A 789 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 794 " --> pdb=" O THR A 791 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A 795 " --> pdb=" O LEU A 792 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE A 796 " --> pdb=" O THR A 793 " (cutoff:3.500A) Proline residue: A 797 - end of helix removed outlier: 4.641A pdb=" N CYS A 800 " --> pdb=" O PRO A 797 " (cutoff:3.500A) Proline residue: A 801 - end of helix Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 829 through 836 removed outlier: 3.770A pdb=" N ALA A 835 " --> pdb=" O SER A 831 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR A 836 " --> pdb=" O ILE A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 845 No H-bonds generated for 'chain 'A' and resid 843 through 845' Processing helix chain 'A' and resid 859 through 867 Processing helix chain 'A' and resid 869 through 888 Processing helix chain 'A' and resid 899 through 902 No H-bonds generated for 'chain 'A' and resid 899 through 902' Processing helix chain 'A' and resid 920 through 950 removed outlier: 3.650A pdb=" N LYS A 950 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 959 No H-bonds generated for 'chain 'A' and resid 956 through 959' Processing helix chain 'A' and resid 965 through 983 Processing helix chain 'A' and resid 998 through 1001 Processing helix chain 'A' and resid 1005 through 1024 Processing helix chain 'A' and resid 1029 through 1033 Processing helix chain 'B' and resid 29 through 60 removed outlier: 3.787A pdb=" N LYS B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 112 removed outlier: 4.514A pdb=" N ALA B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N TYR B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LYS B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N TYR B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing sheet with id= A, first strand: chain 'A' and resid 180 through 185 removed outlier: 3.709A pdb=" N VAL A 183 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 202 through 206 removed outlier: 4.307A pdb=" N THR A 265 " --> pdb=" O GLN A 221 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 254 through 256 removed outlier: 3.548A pdb=" N ASN A 272 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ARG A 216 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL A 270 " --> pdb=" O ARG A 216 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 368 through 370 removed outlier: 3.940A pdb=" N MET A 746 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A 384 " --> pdb=" O ALA A 725 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N THR A 727 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N CYS A 386 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LYS A 624 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N SER A 387 " --> pdb=" O LYS A 624 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE A 626 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE A 700 " --> pdb=" O MET A 627 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 409 through 411 removed outlier: 3.664A pdb=" N THR A 399 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 401 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N SER A 602 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU A 403 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU A 600 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N PHE A 405 " --> pdb=" O VAL A 598 " (cutoff:3.500A) removed outlier: 9.744A pdb=" N VAL A 598 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N CYS A 596 " --> pdb=" O HIS A 569 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS A 569 " --> pdb=" O CYS A 596 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 598 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N PHE A 567 " --> pdb=" O VAL A 598 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU A 600 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU A 565 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER A 602 " --> pdb=" O ARG A 563 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ARG A 563 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS A 505 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 518 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 503 " --> pdb=" O VAL A 518 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 520 " --> pdb=" O GLN A 501 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A 490 " --> pdb=" O ILE A 504 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 538 through 541 removed outlier: 6.991A pdb=" N PHE A 595 " --> pdb=" O SER A 531 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ILE A 533 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N PHE A 597 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ILE A 535 " --> pdb=" O PHE A 597 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 224 through 226 removed outlier: 6.336A pdb=" N ASP A 226 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N CYS A 261 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 77 through 79 Processing sheet with id= I, first strand: chain 'B' and resid 87 through 91 removed outlier: 8.201A pdb=" N ILE B 88 " --> pdb=" O ASP B 297 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LYS B 299 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N PHE B 90 " --> pdb=" O LYS B 299 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU B 301 " --> pdb=" O PHE B 90 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 209 through 211 410 hydrogen bonds defined for protein. 1104 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: 3.37 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3174 1.34 - 1.46: 1499 1.46 - 1.58: 5412 1.58 - 1.69: 6 1.69 - 1.81: 81 Bond restraints: 10172 Sorted by residual: bond pdb=" O2B ACP A1101 " pdb=" PB ACP A1101 " ideal model delta sigma weight residual 1.507 1.610 -0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" O3A ACP A1101 " pdb=" PB ACP A1101 " ideal model delta sigma weight residual 1.698 1.609 0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C4 ACP A1101 " pdb=" C5 ACP A1101 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" CG PRO A 612 " pdb=" CD PRO A 612 " ideal model delta sigma weight residual 1.503 1.370 0.133 3.40e-02 8.65e+02 1.54e+01 bond pdb=" O3G ACP A1101 " pdb=" PG ACP A1101 " ideal model delta sigma weight residual 1.532 1.610 -0.078 2.00e-02 2.50e+03 1.53e+01 ... (remaining 10167 not shown) Histogram of bond angle deviations from ideal: 93.40 - 101.94: 33 101.94 - 110.49: 2544 110.49 - 119.04: 5837 119.04 - 127.58: 5298 127.58 - 136.13: 89 Bond angle restraints: 13801 Sorted by residual: angle pdb=" N PRO A 612 " pdb=" CD PRO A 612 " pdb=" CG PRO A 612 " ideal model delta sigma weight residual 103.20 93.40 9.80 1.50e+00 4.44e-01 4.27e+01 angle pdb=" C3B ACP A1101 " pdb=" PB ACP A1101 " pdb=" O3A ACP A1101 " ideal model delta sigma weight residual 98.05 110.00 -11.95 3.00e+00 1.11e-01 1.59e+01 angle pdb=" N ASN B 206 " pdb=" CA ASN B 206 " pdb=" C ASN B 206 " ideal model delta sigma weight residual 109.81 117.62 -7.81 2.21e+00 2.05e-01 1.25e+01 angle pdb=" O1B ACP A1101 " pdb=" PB ACP A1101 " pdb=" O2B ACP A1101 " ideal model delta sigma weight residual 119.60 109.41 10.19 3.00e+00 1.11e-01 1.15e+01 angle pdb=" C LEU A 867 " pdb=" N HIS A 868 " pdb=" CA HIS A 868 " ideal model delta sigma weight residual 122.56 117.50 5.06 1.50e+00 4.44e-01 1.14e+01 ... (remaining 13796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 5533 16.05 - 32.10: 470 32.10 - 48.15: 121 48.15 - 64.21: 25 64.21 - 80.26: 9 Dihedral angle restraints: 6158 sinusoidal: 2499 harmonic: 3659 Sorted by residual: dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 148.58 -55.58 1 1.00e+01 1.00e-02 4.17e+01 dihedral pdb=" CA TYR B 247 " pdb=" C TYR B 247 " pdb=" N GLY B 248 " pdb=" CA GLY B 248 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA TYR A 983 " pdb=" C TYR A 983 " pdb=" N GLY A 984 " pdb=" CA GLY A 984 " ideal model delta harmonic sigma weight residual 180.00 162.76 17.24 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 6155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1256 0.049 - 0.098: 258 0.098 - 0.147: 64 0.147 - 0.196: 2 0.196 - 0.246: 2 Chirality restraints: 1582 Sorted by residual: chirality pdb=" C1 NAG B 401 " pdb=" ND2 ASN B 158 " pdb=" C2 NAG B 401 " pdb=" O5 NAG B 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ASN B 206 " pdb=" N ASN B 206 " pdb=" C ASN B 206 " pdb=" CB ASN B 206 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.90e-01 chirality pdb=" CB VAL A 110 " pdb=" CA VAL A 110 " pdb=" CG1 VAL A 110 " pdb=" CG2 VAL A 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 1579 not shown) Planarity restraints: 1752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 401 " -0.055 2.00e-02 2.50e+03 4.49e-02 2.52e+01 pdb=" C7 NAG B 401 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG B 401 " -0.042 2.00e-02 2.50e+03 pdb=" N2 NAG B 401 " 0.071 2.00e-02 2.50e+03 pdb=" O7 NAG B 401 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 686 " -0.043 5.00e-02 4.00e+02 6.62e-02 7.01e+00 pdb=" N PRO A 687 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 687 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 687 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 632 " -0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO A 633 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 633 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 633 " -0.029 5.00e-02 4.00e+02 ... (remaining 1749 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1658 2.77 - 3.30: 9981 3.30 - 3.83: 16871 3.83 - 4.37: 19630 4.37 - 4.90: 33821 Nonbonded interactions: 81961 Sorted by model distance: nonbonded pdb=" OG1 THR A 793 " pdb="NA NA A1104 " model vdw 2.232 2.470 nonbonded pdb=" OG1 THR A 390 " pdb=" O3G ACP A1101 " model vdw 2.254 2.440 nonbonded pdb=" OE2 GLU A 692 " pdb=" ND2 ASN A 696 " model vdw 2.256 2.520 nonbonded pdb=" OD1 ASP A 782 " pdb=" NH1 ARG A 952 " model vdw 2.261 2.520 nonbonded pdb=" OH TYR A 914 " pdb=" O SER B 62 " model vdw 2.262 2.440 ... (remaining 81956 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.850 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: 3.950 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.470 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 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 0.133 10172 Z= 0.218 Angle : 0.589 11.954 13801 Z= 0.296 Chirality : 0.042 0.246 1582 Planarity : 0.004 0.066 1751 Dihedral : 13.252 80.256 3797 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.24), residues: 1258 helix: 2.19 (0.23), residues: 543 sheet: 0.28 (0.41), residues: 158 loop : -0.30 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 32 HIS 0.003 0.001 HIS A 632 PHE 0.019 0.001 PHE A 318 TYR 0.014 0.001 TYR A 881 ARG 0.003 0.000 ARG B 295 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.1780 (mtt) cc_final: 0.0394 (ptm) REVERT: A 107 LYS cc_start: 0.5045 (tttt) cc_final: 0.4718 (ttmm) REVERT: A 176 MET cc_start: 0.1800 (pmm) cc_final: 0.0525 (ptm) REVERT: A 392 THR cc_start: 0.4596 (m) cc_final: 0.4267 (m) REVERT: A 455 MET cc_start: 0.1475 (ptp) cc_final: 0.1148 (ptm) REVERT: A 613 ASP cc_start: 0.5106 (t70) cc_final: 0.4740 (t70) REVERT: A 746 MET cc_start: 0.5926 (mpp) cc_final: 0.5385 (mmp) REVERT: A 842 ASP cc_start: 0.5850 (t70) cc_final: 0.5535 (t0) REVERT: A 976 ILE cc_start: 0.7888 (mm) cc_final: 0.7466 (mt) REVERT: A 995 MET cc_start: 0.7137 (mtp) cc_final: 0.6895 (mtm) REVERT: A 1017 MET cc_start: 0.6661 (mmp) cc_final: 0.6420 (mmt) REVERT: B 91 ARG cc_start: 0.5144 (ttm-80) cc_final: 0.4833 (ttp-110) REVERT: B 274 ARG cc_start: 0.6115 (mtt180) cc_final: 0.5850 (mtp85) REVERT: B 297 ASP cc_start: 0.7134 (m-30) cc_final: 0.6844 (m-30) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2747 time to fit residues: 74.7729 Evaluate side-chains 118 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 8.9990 chunk 97 optimal weight: 0.0870 chunk 37 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 overall best weight: 1.2760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 396 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN A 958 GLN B 213 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10172 Z= 0.221 Angle : 0.562 7.502 13801 Z= 0.292 Chirality : 0.043 0.194 1582 Planarity : 0.005 0.064 1751 Dihedral : 5.440 48.011 1412 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.38 % Allowed : 7.16 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.94 (0.23), residues: 1258 helix: 1.76 (0.23), residues: 548 sheet: -0.03 (0.40), residues: 152 loop : -0.27 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 968 HIS 0.005 0.001 HIS A 632 PHE 0.014 0.002 PHE A 318 TYR 0.016 0.002 TYR A 881 ARG 0.003 0.000 ARG B 295 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.212 Fit side-chains REVERT: A 52 MET cc_start: 0.2220 (mtt) cc_final: 0.0634 (ptm) REVERT: A 176 MET cc_start: 0.1809 (pmm) cc_final: 0.1189 (mtm) REVERT: A 392 THR cc_start: 0.4666 (m) cc_final: 0.4434 (m) REVERT: A 455 MET cc_start: 0.1563 (ptp) cc_final: 0.1194 (ptm) REVERT: A 613 ASP cc_start: 0.5046 (t70) cc_final: 0.4717 (t70) REVERT: A 746 MET cc_start: 0.6104 (mpp) cc_final: 0.5769 (mmm) REVERT: A 843 ILE cc_start: 0.8249 (tp) cc_final: 0.7946 (tp) REVERT: A 906 ASP cc_start: 0.6233 (m-30) cc_final: 0.5963 (m-30) REVERT: A 976 ILE cc_start: 0.7919 (mm) cc_final: 0.7443 (mt) REVERT: A 995 MET cc_start: 0.7208 (mtp) cc_final: 0.6940 (mtm) REVERT: A 1025 TYR cc_start: 0.7699 (m-80) cc_final: 0.7468 (m-10) REVERT: B 39 TYR cc_start: 0.7046 (m-10) cc_final: 0.6718 (m-10) REVERT: B 91 ARG cc_start: 0.5295 (ttm-80) cc_final: 0.5024 (ttp-110) REVERT: B 179 LYS cc_start: 0.8453 (pttt) cc_final: 0.8232 (pttt) outliers start: 15 outliers final: 10 residues processed: 138 average time/residue: 0.2286 time to fit residues: 44.3552 Evaluate side-chains 117 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 267 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 101 optimal weight: 0.0040 chunk 112 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 168 ASN A 396 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10172 Z= 0.152 Angle : 0.485 7.641 13801 Z= 0.253 Chirality : 0.041 0.176 1582 Planarity : 0.004 0.062 1751 Dihedral : 5.174 43.042 1412 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.92 % Allowed : 10.00 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.98 (0.24), residues: 1258 helix: 1.75 (0.23), residues: 548 sheet: -0.04 (0.40), residues: 152 loop : -0.20 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 902 HIS 0.004 0.001 HIS A 632 PHE 0.009 0.001 PHE A 935 TYR 0.016 0.001 TYR A 881 ARG 0.003 0.000 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 1.088 Fit side-chains REVERT: A 52 MET cc_start: 0.2378 (mtt) cc_final: 0.0728 (ptm) REVERT: A 176 MET cc_start: 0.1850 (pmm) cc_final: 0.1332 (mtm) REVERT: A 392 THR cc_start: 0.4649 (m) cc_final: 0.4369 (m) REVERT: A 455 MET cc_start: 0.1604 (ptp) cc_final: 0.1165 (ptm) REVERT: A 746 MET cc_start: 0.6040 (mpp) cc_final: 0.5766 (mmm) REVERT: A 843 ILE cc_start: 0.8318 (tp) cc_final: 0.8117 (tp) REVERT: A 906 ASP cc_start: 0.6195 (m-30) cc_final: 0.5849 (m-30) REVERT: A 976 ILE cc_start: 0.7890 (mm) cc_final: 0.7443 (mt) REVERT: A 995 MET cc_start: 0.7090 (mtp) cc_final: 0.6887 (mtm) REVERT: B 39 TYR cc_start: 0.6986 (m-10) cc_final: 0.6546 (m-80) REVERT: B 91 ARG cc_start: 0.5290 (ttm-80) cc_final: 0.5012 (ttp-110) REVERT: B 129 MET cc_start: 0.5177 (mmm) cc_final: 0.4806 (tpt) REVERT: B 179 LYS cc_start: 0.8475 (pttt) cc_final: 0.8242 (pttt) outliers start: 10 outliers final: 10 residues processed: 124 average time/residue: 0.2244 time to fit residues: 39.7894 Evaluate side-chains 120 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 987 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 268 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 114 optimal weight: 0.0050 chunk 120 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 168 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10172 Z= 0.156 Angle : 0.488 8.740 13801 Z= 0.251 Chirality : 0.041 0.161 1582 Planarity : 0.004 0.061 1751 Dihedral : 5.117 40.482 1412 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.28 % Allowed : 10.83 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.97 (0.24), residues: 1258 helix: 1.76 (0.23), residues: 547 sheet: -0.06 (0.40), residues: 152 loop : -0.22 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 902 HIS 0.006 0.001 HIS A 632 PHE 0.009 0.001 PHE A 935 TYR 0.016 0.001 TYR A 881 ARG 0.003 0.000 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 1.178 Fit side-chains REVERT: A 176 MET cc_start: 0.2083 (pmm) cc_final: 0.1457 (mtm) REVERT: A 392 THR cc_start: 0.4779 (m) cc_final: 0.4484 (m) REVERT: A 455 MET cc_start: 0.1685 (ptp) cc_final: 0.1136 (ptm) REVERT: A 534 MET cc_start: 0.2030 (ptt) cc_final: 0.1828 (ptt) REVERT: A 641 LYS cc_start: 0.6713 (ttmt) cc_final: 0.6506 (ttmt) REVERT: A 746 MET cc_start: 0.6015 (mpp) cc_final: 0.5589 (mmp) REVERT: A 821 PHE cc_start: 0.7592 (m-80) cc_final: 0.7283 (m-80) REVERT: A 906 ASP cc_start: 0.6265 (m-30) cc_final: 0.5941 (m-30) REVERT: A 976 ILE cc_start: 0.7939 (mm) cc_final: 0.7438 (mt) REVERT: A 995 MET cc_start: 0.7084 (mtp) cc_final: 0.6879 (mtm) REVERT: B 39 TYR cc_start: 0.6890 (m-10) cc_final: 0.6640 (m-10) REVERT: B 91 ARG cc_start: 0.5295 (ttm-80) cc_final: 0.5030 (ttp-110) REVERT: B 129 MET cc_start: 0.5193 (mmm) cc_final: 0.4784 (tpt) REVERT: B 179 LYS cc_start: 0.8524 (pttt) cc_final: 0.8259 (pttt) outliers start: 14 outliers final: 13 residues processed: 132 average time/residue: 0.2291 time to fit residues: 43.2453 Evaluate side-chains 124 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 987 SER Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 268 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 61 optimal weight: 0.0370 chunk 108 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 168 ASN A 396 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN A1033 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10172 Z= 0.182 Angle : 0.498 6.705 13801 Z= 0.257 Chirality : 0.041 0.153 1582 Planarity : 0.004 0.061 1751 Dihedral : 5.131 45.705 1412 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.02 % Allowed : 11.38 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.88 (0.24), residues: 1258 helix: 1.66 (0.23), residues: 552 sheet: -0.15 (0.40), residues: 152 loop : -0.23 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 968 HIS 0.005 0.001 HIS A 632 PHE 0.010 0.001 PHE A 935 TYR 0.017 0.001 TYR A 881 ARG 0.006 0.000 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.2139 (pmm) cc_final: 0.1539 (mtm) REVERT: A 392 THR cc_start: 0.4840 (m) cc_final: 0.4538 (m) REVERT: A 455 MET cc_start: 0.1735 (ptp) cc_final: 0.1166 (ptm) REVERT: A 641 LYS cc_start: 0.6758 (ttmt) cc_final: 0.6517 (ttmt) REVERT: A 746 MET cc_start: 0.5979 (mpp) cc_final: 0.5678 (mmm) REVERT: A 821 PHE cc_start: 0.7632 (m-80) cc_final: 0.7321 (m-80) REVERT: A 976 ILE cc_start: 0.7953 (mm) cc_final: 0.7358 (mt) REVERT: B 39 TYR cc_start: 0.6812 (m-10) cc_final: 0.6610 (m-10) REVERT: B 91 ARG cc_start: 0.5326 (ttm-80) cc_final: 0.5072 (ttp-110) REVERT: B 129 MET cc_start: 0.5108 (mmm) cc_final: 0.4838 (tpt) REVERT: B 179 LYS cc_start: 0.8534 (pttt) cc_final: 0.8232 (pttt) outliers start: 22 outliers final: 19 residues processed: 133 average time/residue: 0.2217 time to fit residues: 42.9956 Evaluate side-chains 130 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 987 SER Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 283 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 55 optimal weight: 0.0570 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 overall best weight: 1.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 168 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10172 Z= 0.210 Angle : 0.526 10.107 13801 Z= 0.270 Chirality : 0.042 0.164 1582 Planarity : 0.004 0.061 1751 Dihedral : 5.336 46.966 1412 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.20 % Allowed : 11.93 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.75 (0.24), residues: 1258 helix: 1.53 (0.23), residues: 552 sheet: -0.23 (0.40), residues: 152 loop : -0.28 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1029 HIS 0.008 0.001 HIS A 632 PHE 0.013 0.001 PHE A 935 TYR 0.017 0.001 TYR A 881 ARG 0.014 0.001 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 1.162 Fit side-chains REVERT: A 176 MET cc_start: 0.2104 (pmm) cc_final: 0.1595 (mtm) REVERT: A 455 MET cc_start: 0.1748 (ptp) cc_final: 0.1049 (mtt) REVERT: A 746 MET cc_start: 0.5957 (mpp) cc_final: 0.5719 (mmm) REVERT: A 821 PHE cc_start: 0.7684 (m-80) cc_final: 0.7417 (m-80) REVERT: A 906 ASP cc_start: 0.6249 (m-30) cc_final: 0.6011 (m-30) REVERT: A 976 ILE cc_start: 0.7955 (mm) cc_final: 0.7299 (mt) REVERT: B 91 ARG cc_start: 0.5345 (ttm-80) cc_final: 0.5083 (ttp-110) outliers start: 24 outliers final: 21 residues processed: 133 average time/residue: 0.2146 time to fit residues: 41.5090 Evaluate side-chains 131 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 987 SER Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 283 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 168 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 HIS A 718 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10172 Z= 0.162 Angle : 0.494 9.352 13801 Z= 0.255 Chirality : 0.041 0.172 1582 Planarity : 0.004 0.061 1751 Dihedral : 5.250 49.412 1412 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.11 % Allowed : 11.65 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.81 (0.24), residues: 1258 helix: 1.58 (0.23), residues: 554 sheet: -0.19 (0.41), residues: 152 loop : -0.24 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 902 HIS 0.007 0.001 HIS A 632 PHE 0.011 0.001 PHE A 935 TYR 0.017 0.001 TYR A 805 ARG 0.010 0.000 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 1.143 Fit side-chains REVERT: A 176 MET cc_start: 0.2237 (pmm) cc_final: 0.1713 (mtm) REVERT: A 455 MET cc_start: 0.1750 (ptp) cc_final: 0.1186 (ptm) REVERT: A 746 MET cc_start: 0.5969 (mpp) cc_final: 0.5638 (mmm) REVERT: A 776 GLU cc_start: 0.6356 (mm-30) cc_final: 0.5819 (mm-30) REVERT: A 821 PHE cc_start: 0.7603 (m-80) cc_final: 0.7356 (m-80) REVERT: A 906 ASP cc_start: 0.6149 (m-30) cc_final: 0.5938 (m-30) REVERT: A 976 ILE cc_start: 0.7940 (mm) cc_final: 0.7286 (mt) REVERT: B 91 ARG cc_start: 0.5375 (ttm-80) cc_final: 0.5109 (ttp-110) REVERT: B 129 MET cc_start: 0.5156 (mmm) cc_final: 0.4939 (tpt) outliers start: 23 outliers final: 21 residues processed: 136 average time/residue: 0.1995 time to fit residues: 39.8703 Evaluate side-chains 135 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 987 SER Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 283 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 76 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 168 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10172 Z= 0.180 Angle : 0.515 9.605 13801 Z= 0.264 Chirality : 0.041 0.172 1582 Planarity : 0.004 0.061 1751 Dihedral : 5.334 53.652 1412 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.39 % Allowed : 11.93 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.79 (0.24), residues: 1258 helix: 1.55 (0.23), residues: 555 sheet: -0.18 (0.41), residues: 152 loop : -0.24 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 902 HIS 0.002 0.001 HIS A 868 PHE 0.011 0.001 PHE A 935 TYR 0.018 0.001 TYR A 805 ARG 0.010 0.000 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 1.107 Fit side-chains REVERT: A 135 ASN cc_start: 0.5331 (m-40) cc_final: 0.4795 (m110) REVERT: A 176 MET cc_start: 0.2246 (pmm) cc_final: 0.1482 (mtm) REVERT: A 455 MET cc_start: 0.1891 (ptp) cc_final: 0.1284 (ptm) REVERT: A 746 MET cc_start: 0.5821 (mpp) cc_final: 0.5461 (mmm) REVERT: A 821 PHE cc_start: 0.7633 (m-80) cc_final: 0.7404 (m-80) REVERT: A 906 ASP cc_start: 0.6131 (m-30) cc_final: 0.5886 (m-30) REVERT: A 976 ILE cc_start: 0.7949 (mm) cc_final: 0.7291 (mt) REVERT: B 91 ARG cc_start: 0.5387 (ttm-80) cc_final: 0.5136 (ttp-110) REVERT: B 129 MET cc_start: 0.5236 (mmm) cc_final: 0.4834 (tpt) outliers start: 26 outliers final: 23 residues processed: 139 average time/residue: 0.2074 time to fit residues: 41.9159 Evaluate side-chains 138 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 987 SER Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 283 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.7980 chunk 115 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 101 optimal weight: 0.1980 chunk 106 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10172 Z= 0.144 Angle : 0.485 9.442 13801 Z= 0.251 Chirality : 0.040 0.178 1582 Planarity : 0.004 0.061 1751 Dihedral : 5.235 54.101 1412 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.02 % Allowed : 12.48 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.86 (0.24), residues: 1258 helix: 1.63 (0.23), residues: 555 sheet: -0.18 (0.41), residues: 152 loop : -0.23 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 902 HIS 0.001 0.000 HIS A 868 PHE 0.009 0.001 PHE A 935 TYR 0.018 0.001 TYR A 805 ARG 0.018 0.001 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.2374 (pmm) cc_final: 0.1670 (mtm) REVERT: A 455 MET cc_start: 0.1898 (ptp) cc_final: 0.1107 (mtp) REVERT: A 746 MET cc_start: 0.5740 (mpp) cc_final: 0.5372 (mmm) REVERT: A 821 PHE cc_start: 0.7519 (m-80) cc_final: 0.7317 (m-80) REVERT: A 906 ASP cc_start: 0.6026 (m-30) cc_final: 0.5824 (m-30) REVERT: B 91 ARG cc_start: 0.5380 (ttm-80) cc_final: 0.5128 (ttp-110) outliers start: 22 outliers final: 20 residues processed: 138 average time/residue: 0.1942 time to fit residues: 39.7361 Evaluate side-chains 139 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 987 SER Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 283 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 0.2980 chunk 56 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 114 optimal weight: 0.0870 chunk 99 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 78 optimal weight: 0.0050 chunk 105 optimal weight: 0.8980 overall best weight: 0.3372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 168 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10172 Z= 0.130 Angle : 0.481 9.568 13801 Z= 0.246 Chirality : 0.040 0.165 1582 Planarity : 0.004 0.060 1751 Dihedral : 5.042 53.848 1412 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.47 % Allowed : 13.12 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.94 (0.24), residues: 1258 helix: 1.70 (0.23), residues: 556 sheet: -0.18 (0.40), residues: 155 loop : -0.19 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 155 HIS 0.002 0.000 HIS A 868 PHE 0.007 0.001 PHE B 264 TYR 0.020 0.001 TYR B 205 ARG 0.017 0.000 ARG A 704 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 135 ASN cc_start: 0.5372 (m-40) cc_final: 0.4832 (m110) REVERT: A 176 MET cc_start: 0.2298 (pmm) cc_final: 0.1629 (mtm) REVERT: A 455 MET cc_start: 0.1850 (ptp) cc_final: 0.1220 (mtp) REVERT: A 641 LYS cc_start: 0.6532 (ttmt) cc_final: 0.6188 (ttmm) REVERT: A 746 MET cc_start: 0.5659 (mpp) cc_final: 0.5332 (mmm) REVERT: A 906 ASP cc_start: 0.6034 (m-30) cc_final: 0.5774 (m-30) REVERT: B 91 ARG cc_start: 0.5357 (ttm-80) cc_final: 0.5134 (ttp-110) outliers start: 16 outliers final: 15 residues processed: 135 average time/residue: 0.1951 time to fit residues: 39.1283 Evaluate side-chains 130 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 987 SER Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 283 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 41 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 87 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 536 ASN A 569 HIS A 718 GLN B 208 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.221131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.170795 restraints weight = 12162.327| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 1.98 r_work: 0.3452 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10172 Z= 0.169 Angle : 0.495 9.204 13801 Z= 0.258 Chirality : 0.041 0.185 1582 Planarity : 0.004 0.060 1751 Dihedral : 5.142 54.172 1412 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.56 % Allowed : 13.03 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.91 (0.24), residues: 1258 helix: 1.64 (0.23), residues: 555 sheet: -0.14 (0.40), residues: 154 loop : -0.17 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 968 HIS 0.002 0.000 HIS A 868 PHE 0.009 0.001 PHE A 935 TYR 0.018 0.001 TYR A 805 ARG 0.012 0.000 ARG A 704 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2558.40 seconds wall clock time: 46 minutes 51.64 seconds (2811.64 seconds total)