Starting phenix.real_space_refine on Fri Dec 8 04:33:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gua_34271/12_2023/8gua_34271_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gua_34271/12_2023/8gua_34271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gua_34271/12_2023/8gua_34271.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gua_34271/12_2023/8gua_34271.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gua_34271/12_2023/8gua_34271_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gua_34271/12_2023/8gua_34271_updated.pdb" } resolution = 2.77 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= 0.055 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: 5 Type Number sf(0) Gaussians S 62 5.16 5 C 4481 2.51 5 N 1204 2.21 5 O 1267 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 127": "OE1" <-> "OE2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A PHE 937": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1034": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7017 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 856, 7017 Unusual residues: {'1LT': 1} Classifications: {'peptide': 855, 'undetermined': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 814, None: 1} Not linked: pdbres="GLY A1050 " pdbres="1LT A1101 " Chain breaks: 7 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ILE A 932 " occ=0.50 ... (6 atoms not shown) pdb=" CD1 ILE A 932 " occ=0.50 residue: pdb=" N ASP A 933 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP A 933 " occ=0.50 residue: pdb=" N PHE A 934 " occ=0.50 ... (9 atoms not shown) pdb=" CZ PHE A 934 " occ=0.50 residue: pdb=" N GLY A 935 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY A 935 " occ=0.50 Time building chain proxies: 3.91, per 1000 atoms: 0.56 Number of scatterers: 7017 At special positions: 0 Unit cell: (79.254, 95.319, 103.887, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 F 3 9.00 O 1267 8.00 N 1204 7.00 C 4481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.1 seconds 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1638 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 5 sheets defined 43.9% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 108 through 121 removed outlier: 3.792A pdb=" N ARG A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU A 116 " --> pdb=" O ILE A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 129 No H-bonds generated for 'chain 'A' and resid 126 through 129' Processing helix chain 'A' and resid 134 through 140 Processing helix chain 'A' and resid 145 through 154 Processing helix chain 'A' and resid 160 through 166 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 217 through 228 removed outlier: 4.110A pdb=" N ILE A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 223 " --> pdb=" O GLN A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'A' and resid 290 through 296 removed outlier: 3.630A pdb=" N GLN A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 393 through 395 No H-bonds generated for 'chain 'A' and resid 393 through 395' Processing helix chain 'A' and resid 489 through 499 removed outlier: 3.560A pdb=" N SER A 499 " --> pdb=" O HIS A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 535 removed outlier: 3.608A pdb=" N LYS A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 553 Processing helix chain 'A' and resid 555 through 558 No H-bonds generated for 'chain 'A' and resid 555 through 558' Processing helix chain 'A' and resid 562 through 571 Proline residue: A 566 - end of helix removed outlier: 3.743A pdb=" N LEU A 569 " --> pdb=" O PRO A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 588 removed outlier: 3.515A pdb=" N CYS A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 586 " --> pdb=" O GLN A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 602 removed outlier: 4.146A pdb=" N GLU A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A 601 " --> pdb=" O GLN A 597 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 622 removed outlier: 3.501A pdb=" N ALA A 615 " --> pdb=" O VAL A 611 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 616 " --> pdb=" O ARG A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 637 removed outlier: 4.942A pdb=" N ILE A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLN A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 657 Processing helix chain 'A' and resid 661 through 674 Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'A' and resid 696 through 721 removed outlier: 3.521A pdb=" N LYS A 700 " --> pdb=" O MET A 697 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 707 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU A 710 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 713 " --> pdb=" O GLU A 710 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 714 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 716 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 718 " --> pdb=" O LEU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 739 Processing helix chain 'A' and resid 742 through 748 removed outlier: 3.696A pdb=" N ALA A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 792 No H-bonds generated for 'chain 'A' and resid 790 through 792' Processing helix chain 'A' and resid 808 through 827 Processing helix chain 'A' and resid 857 through 860 No H-bonds generated for 'chain 'A' and resid 857 through 860' Processing helix chain 'A' and resid 876 through 883 removed outlier: 3.503A pdb=" N LEU A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 910 removed outlier: 3.735A pdb=" N PHE A 897 " --> pdb=" O ALA A 893 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 899 " --> pdb=" O ASP A 895 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 903 " --> pdb=" O ARG A 899 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR A 904 " --> pdb=" O SER A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 920 No H-bonds generated for 'chain 'A' and resid 918 through 920' Processing helix chain 'A' and resid 959 through 964 removed outlier: 3.939A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 1000 removed outlier: 3.745A pdb=" N ARG A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N CYS A 984 " --> pdb=" O PHE A 980 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR A 988 " --> pdb=" O CYS A 984 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU A 989 " --> pdb=" O TYR A 985 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 991 " --> pdb=" O ALA A 987 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ASN A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1008 Processing helix chain 'A' and resid 1011 through 1013 No H-bonds generated for 'chain 'A' and resid 1011 through 1013' Processing helix chain 'A' and resid 1016 through 1018 No H-bonds generated for 'chain 'A' and resid 1016 through 1018' Processing helix chain 'A' and resid 1020 through 1026 Processing helix chain 'A' and resid 1032 through 1046 removed outlier: 3.628A pdb=" N LEU A1036 " --> pdb=" O GLU A1032 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLU A1037 " --> pdb=" O GLN A1033 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR A1038 " --> pdb=" O GLU A1034 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE A1039 " --> pdb=" O ALA A1035 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A1045 " --> pdb=" O LYS A1041 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A1046 " --> pdb=" O GLN A1042 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 205 through 212 removed outlier: 3.555A pdb=" N ILE A 211 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TRP A 195 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU A 285 " --> pdb=" O TRP A 195 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 385 through 388 removed outlier: 7.147A pdb=" N GLU A 474 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA A 341 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N CYS A 472 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 354 through 361 removed outlier: 5.856A pdb=" N SER A 408 " --> pdb=" O PRO A 421 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 779 through 784 removed outlier: 3.514A pdb=" N GLY A 846 " --> pdb=" O LYS A 802 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 845 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU A 847 " --> pdb=" O SER A 840 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N SER A 840 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLU A 849 " --> pdb=" O CYS A 838 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N CYS A 838 " --> pdb=" O GLU A 849 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 854 through 856 removed outlier: 3.528A pdb=" N HIS A 855 " --> pdb=" O VAL A 923 " (cutoff:3.500A) 227 hydrogen bonds defined for protein. 588 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1160 1.30 - 1.43: 1820 1.43 - 1.56: 4092 1.56 - 1.68: 7 1.68 - 1.81: 94 Bond restraints: 7173 Sorted by residual: bond pdb=" C9 1LT A1101 " pdb=" S 1LT A1101 " ideal model delta sigma weight residual 1.738 1.530 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C2 1LT A1101 " pdb=" S 1LT A1101 " ideal model delta sigma weight residual 1.734 1.533 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" N 1LT A1101 " pdb=" C1 1LT A1101 " ideal model delta sigma weight residual 1.368 1.568 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C5 1LT A1101 " pdb=" C6 1LT A1101 " ideal model delta sigma weight residual 1.525 1.350 0.175 2.00e-02 2.50e+03 7.62e+01 bond pdb=" N 1LT A1101 " pdb=" C2 1LT A1101 " ideal model delta sigma weight residual 1.291 1.415 -0.124 2.00e-02 2.50e+03 3.84e+01 ... (remaining 7168 not shown) Histogram of bond angle deviations from ideal: 97.98 - 105.92: 170 105.92 - 113.85: 4051 113.85 - 121.78: 3927 121.78 - 129.71: 1489 129.71 - 137.64: 59 Bond angle restraints: 9696 Sorted by residual: angle pdb=" N1 1LT A1101 " pdb=" C2 1LT A1101 " pdb=" S 1LT A1101 " ideal model delta sigma weight residual 118.47 137.64 -19.17 3.00e+00 1.11e-01 4.09e+01 angle pdb=" C TRP A 446 " pdb=" N PRO A 447 " pdb=" CA PRO A 447 " ideal model delta sigma weight residual 120.03 113.74 6.29 9.90e-01 1.02e+00 4.04e+01 angle pdb=" C2 1LT A1101 " pdb=" S 1LT A1101 " pdb=" C9 1LT A1101 " ideal model delta sigma weight residual 88.90 107.66 -18.76 3.00e+00 1.11e-01 3.91e+01 angle pdb=" N 1LT A1101 " pdb=" C2 1LT A1101 " pdb=" N1 1LT A1101 " ideal model delta sigma weight residual 126.74 114.29 12.45 3.00e+00 1.11e-01 1.72e+01 angle pdb=" N PRO A 449 " pdb=" CA PRO A 449 " pdb=" C PRO A 449 " ideal model delta sigma weight residual 112.47 120.27 -7.80 2.06e+00 2.36e-01 1.43e+01 ... (remaining 9691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 3868 17.85 - 35.69: 408 35.69 - 53.54: 71 53.54 - 71.39: 15 71.39 - 89.24: 7 Dihedral angle restraints: 4369 sinusoidal: 1851 harmonic: 2518 Sorted by residual: dihedral pdb=" C PHE A 937 " pdb=" N PHE A 937 " pdb=" CA PHE A 937 " pdb=" CB PHE A 937 " ideal model delta harmonic sigma weight residual -122.60 -131.55 8.95 0 2.50e+00 1.60e-01 1.28e+01 dihedral pdb=" N PHE A 937 " pdb=" C PHE A 937 " pdb=" CA PHE A 937 " pdb=" CB PHE A 937 " ideal model delta harmonic sigma weight residual 122.80 130.99 -8.19 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" CA PRO A 539 " pdb=" C PRO A 539 " pdb=" N LEU A 540 " pdb=" CA LEU A 540 " ideal model delta harmonic sigma weight residual 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 4366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 966 0.069 - 0.139: 82 0.139 - 0.208: 2 0.208 - 0.278: 2 0.278 - 0.347: 2 Chirality restraints: 1054 Sorted by residual: chirality pdb=" CA PRO A 449 " pdb=" N PRO A 449 " pdb=" C PRO A 449 " pdb=" CB PRO A 449 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA PHE A 937 " pdb=" N PHE A 937 " pdb=" C PHE A 937 " pdb=" CB PHE A 937 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CA LEU A 938 " pdb=" N LEU A 938 " pdb=" C LEU A 938 " pdb=" CB LEU A 938 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1051 not shown) Planarity restraints: 1238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 448 " -0.069 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO A 449 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO A 449 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 449 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 159 " 0.017 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C PRO A 159 " -0.063 2.00e-02 2.50e+03 pdb=" O PRO A 159 " 0.025 2.00e-02 2.50e+03 pdb=" N HIS A 160 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 858 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.60e+00 pdb=" C MET A 858 " 0.037 2.00e-02 2.50e+03 pdb=" O MET A 858 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN A 859 " -0.013 2.00e-02 2.50e+03 ... (remaining 1235 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1094 2.76 - 3.29: 6918 3.29 - 3.83: 11653 3.83 - 4.36: 14615 4.36 - 4.90: 23821 Nonbonded interactions: 58101 Sorted by model distance: nonbonded pdb=" OG SER A 900 " pdb=" O LEU A 929 " model vdw 2.224 2.440 nonbonded pdb=" OH TYR A 584 " pdb=" OD1 ASP A 608 " model vdw 2.235 2.440 nonbonded pdb=" O GLU A 722 " pdb=" NE2 GLN A 731 " model vdw 2.245 2.520 nonbonded pdb=" NH1 ARG A 808 " pdb=" O SER A1008 " model vdw 2.248 2.520 nonbonded pdb=" NE2 GLN A 825 " pdb=" O LEU A 831 " model vdw 2.251 2.520 ... (remaining 58096 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=0.50 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.850 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 21.110 Find NCS groups from input model: 0.180 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:10.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5968 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 : 0.007 0.208 7173 Z= 0.485 Angle : 0.695 19.175 9696 Z= 0.345 Chirality : 0.044 0.347 1054 Planarity : 0.005 0.103 1238 Dihedral : 15.036 89.236 2731 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.81 % Favored : 95.95 % Rotamer: Outliers : 0.13 % Allowed : 0.77 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.29), residues: 839 helix: -0.84 (0.27), residues: 363 sheet: 0.24 (0.51), residues: 98 loop : -0.20 (0.35), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 783 HIS 0.003 0.001 HIS A 160 PHE 0.012 0.001 PHE A 960 TYR 0.024 0.001 TYR A 392 ARG 0.005 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.700 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 103 average time/residue: 1.2223 time to fit residues: 133.0482 Evaluate side-chains 78 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.765 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 22 optimal weight: 0.0270 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 GLN ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6016 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7173 Z= 0.219 Angle : 0.587 6.243 9696 Z= 0.303 Chirality : 0.042 0.224 1054 Planarity : 0.006 0.100 1238 Dihedral : 5.272 35.062 943 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.81 % Favored : 96.07 % Rotamer: Outliers : 1.28 % Allowed : 11.48 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.77 (0.28), residues: 839 helix: -0.67 (0.25), residues: 381 sheet: 0.41 (0.49), residues: 99 loop : -0.38 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.004 0.001 HIS A 936 PHE 0.012 0.001 PHE A 937 TYR 0.019 0.002 TYR A 392 ARG 0.007 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.733 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 97 average time/residue: 1.1237 time to fit residues: 115.9114 Evaluate side-chains 84 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.762 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0671 time to fit residues: 1.2417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 52 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 76 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7173 Z= 0.181 Angle : 0.543 6.696 9696 Z= 0.277 Chirality : 0.041 0.219 1054 Planarity : 0.005 0.096 1238 Dihedral : 4.985 34.446 943 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.69 % Favored : 96.19 % Rotamer: Outliers : 1.91 % Allowed : 15.82 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.52 (0.29), residues: 839 helix: -0.42 (0.25), residues: 378 sheet: 0.43 (0.49), residues: 98 loop : -0.28 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.003 0.001 HIS A 665 PHE 0.011 0.001 PHE A 937 TYR 0.015 0.001 TYR A 392 ARG 0.009 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 0.856 Fit side-chains outliers start: 15 outliers final: 4 residues processed: 101 average time/residue: 1.0475 time to fit residues: 113.0408 Evaluate side-chains 89 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.736 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.0607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 73 optimal weight: 0.0980 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 GLN ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6069 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7173 Z= 0.240 Angle : 0.588 6.764 9696 Z= 0.298 Chirality : 0.043 0.219 1054 Planarity : 0.005 0.093 1238 Dihedral : 5.162 34.661 943 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.65 % Favored : 95.23 % Rotamer: Outliers : 3.19 % Allowed : 17.35 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.51 (0.29), residues: 839 helix: -0.40 (0.26), residues: 375 sheet: 0.19 (0.48), residues: 96 loop : -0.21 (0.35), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 386 HIS 0.003 0.001 HIS A 180 PHE 0.017 0.002 PHE A 666 TYR 0.015 0.002 TYR A 392 ARG 0.009 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 0.811 Fit side-chains outliers start: 25 outliers final: 7 residues processed: 105 average time/residue: 1.0862 time to fit residues: 121.5156 Evaluate side-chains 94 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.767 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.1131 time to fit residues: 1.3050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 GLN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN A 917 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7173 Z= 0.284 Angle : 0.631 7.233 9696 Z= 0.323 Chirality : 0.044 0.219 1054 Planarity : 0.006 0.092 1238 Dihedral : 5.394 34.864 943 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.41 % Favored : 95.47 % Rotamer: Outliers : 3.57 % Allowed : 18.49 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.69 (0.29), residues: 839 helix: -0.53 (0.25), residues: 376 sheet: -0.07 (0.48), residues: 96 loop : -0.26 (0.35), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 386 HIS 0.005 0.001 HIS A 665 PHE 0.017 0.002 PHE A 666 TYR 0.018 0.002 TYR A 691 ARG 0.006 0.001 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 91 time to evaluate : 0.800 Fit side-chains outliers start: 28 outliers final: 9 residues processed: 108 average time/residue: 1.0766 time to fit residues: 124.0446 Evaluate side-chains 95 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.821 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.6433 time to fit residues: 2.5823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 68 optimal weight: 0.1980 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 HIS A 575 ASN A 637 GLN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN A 917 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6075 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7173 Z= 0.209 Angle : 0.567 6.349 9696 Z= 0.291 Chirality : 0.042 0.218 1054 Planarity : 0.006 0.090 1238 Dihedral : 5.207 34.134 943 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.05 % Favored : 95.83 % Rotamer: Outliers : 3.06 % Allowed : 19.52 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.48 (0.29), residues: 839 helix: -0.35 (0.26), residues: 379 sheet: -0.04 (0.48), residues: 96 loop : -0.14 (0.36), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.004 0.001 HIS A 665 PHE 0.014 0.002 PHE A 960 TYR 0.013 0.002 TYR A 432 ARG 0.009 0.000 ARG A 777 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 93 time to evaluate : 0.811 Fit side-chains outliers start: 24 outliers final: 9 residues processed: 109 average time/residue: 1.0394 time to fit residues: 121.1143 Evaluate side-chains 95 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.789 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.1268 time to fit residues: 1.4080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 HIS A 637 GLN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7173 Z= 0.210 Angle : 0.569 6.438 9696 Z= 0.291 Chirality : 0.042 0.220 1054 Planarity : 0.006 0.088 1238 Dihedral : 5.198 34.343 943 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.41 % Favored : 95.47 % Rotamer: Outliers : 2.81 % Allowed : 20.03 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.41 (0.29), residues: 839 helix: -0.30 (0.26), residues: 380 sheet: 0.02 (0.48), residues: 96 loop : -0.10 (0.36), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.004 0.001 HIS A 665 PHE 0.015 0.002 PHE A 794 TYR 0.014 0.002 TYR A 432 ARG 0.012 0.001 ARG A 777 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 0.787 Fit side-chains outliers start: 22 outliers final: 9 residues processed: 103 average time/residue: 0.9826 time to fit residues: 108.4765 Evaluate side-chains 93 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.819 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.1200 time to fit residues: 1.3902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 HIS A 637 GLN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6071 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7173 Z= 0.209 Angle : 0.565 6.791 9696 Z= 0.288 Chirality : 0.042 0.232 1054 Planarity : 0.006 0.084 1238 Dihedral : 5.186 34.125 943 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.05 % Favored : 95.83 % Rotamer: Outliers : 2.55 % Allowed : 21.30 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.29), residues: 839 helix: -0.28 (0.26), residues: 381 sheet: 0.10 (0.48), residues: 96 loop : -0.12 (0.36), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.004 0.001 HIS A 665 PHE 0.015 0.002 PHE A 960 TYR 0.014 0.002 TYR A 432 ARG 0.013 0.001 ARG A 777 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.820 Fit side-chains outliers start: 20 outliers final: 11 residues processed: 102 average time/residue: 1.0156 time to fit residues: 110.7327 Evaluate side-chains 97 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.1138 time to fit residues: 1.4847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 59 optimal weight: 0.0010 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 HIS A 637 GLN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7173 Z= 0.218 Angle : 0.590 7.706 9696 Z= 0.299 Chirality : 0.043 0.234 1054 Planarity : 0.006 0.082 1238 Dihedral : 5.214 34.102 943 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.53 % Favored : 95.35 % Rotamer: Outliers : 2.17 % Allowed : 22.07 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.29), residues: 839 helix: -0.25 (0.26), residues: 380 sheet: 0.10 (0.49), residues: 96 loop : -0.15 (0.36), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.004 0.001 HIS A 665 PHE 0.015 0.002 PHE A 794 TYR 0.014 0.002 TYR A 432 ARG 0.014 0.001 ARG A 777 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.765 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 99 average time/residue: 1.0192 time to fit residues: 107.7967 Evaluate side-chains 94 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.757 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.1147 time to fit residues: 1.2984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 67 optimal weight: 0.0980 chunk 7 optimal weight: 0.0040 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 53 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 HIS A 637 GLN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 ASN ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7173 Z= 0.173 Angle : 0.565 10.095 9696 Z= 0.284 Chirality : 0.041 0.233 1054 Planarity : 0.005 0.080 1238 Dihedral : 4.998 33.243 943 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.58 % Favored : 96.31 % Rotamer: Outliers : 1.53 % Allowed : 23.21 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.28 (0.30), residues: 839 helix: -0.11 (0.26), residues: 386 sheet: 0.20 (0.49), residues: 96 loop : -0.17 (0.36), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 669 HIS 0.003 0.000 HIS A 665 PHE 0.016 0.002 PHE A 960 TYR 0.015 0.001 TYR A 432 ARG 0.014 0.001 ARG A 777 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.698 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 103 average time/residue: 0.9392 time to fit residues: 104.0072 Evaluate side-chains 99 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.812 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.1218 time to fit residues: 1.3952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 9 optimal weight: 0.0170 chunk 18 optimal weight: 0.0370 chunk 67 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 0.0030 chunk 3 optimal weight: 1.9990 overall best weight: 0.3706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 HIS ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.228519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.203222 restraints weight = 6427.841| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 1.21 r_work: 0.4148 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4019 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3999 r_free = 0.3999 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3996 r_free = 0.3996 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7173 Z= 0.176 Angle : 0.565 9.744 9696 Z= 0.282 Chirality : 0.042 0.232 1054 Planarity : 0.005 0.078 1238 Dihedral : 4.961 33.619 943 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.69 % Favored : 96.19 % Rotamer: Outliers : 1.40 % Allowed : 23.72 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.22 (0.30), residues: 839 helix: -0.05 (0.27), residues: 386 sheet: 0.26 (0.49), residues: 96 loop : -0.17 (0.36), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 669 HIS 0.003 0.001 HIS A 665 PHE 0.015 0.001 PHE A 794 TYR 0.014 0.001 TYR A 432 ARG 0.014 0.001 ARG A 777 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2746.90 seconds wall clock time: 49 minutes 43.12 seconds (2983.12 seconds total)