Starting phenix.real_space_refine on Wed Aug 5 21:22:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hj4_34832/08_2026/8hj4_34832.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hj4_34832/08_2026/8hj4_34832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hj4_34832/08_2026/8hj4_34832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hj4_34832/08_2026/8hj4_34832.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hj4_34832/08_2026/8hj4_34832.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hj4_34832/08_2026/8hj4_34832.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hj4_34832/08_2026/8hj4_34832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hj4_34832/08_2026/8hj4_34832.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.023 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 P 113 5.49 5 S 30 5.16 5 C 6932 2.51 5 N 2080 2.21 5 O 2497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11652 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8187 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 43, 'TRANS': 989} Chain breaks: 3 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 5, 'ASN:plan1': 2, 'ASP:plan': 5, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 118 Chain: "B" Number of atoms: 2391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 2391 Classifications: {'RNAv2': 113} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 49, 'rna3p_pyr': 56} Link IDs: {'rna2p': 7, 'rna3p': 105} Chain breaks: 1 Chain: "C" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1074 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'TRANS': 129} Time building chain proxies: 2.16, per 1000 atoms: 0.19 Number of scatterers: 11652 At special positions: 0 Unit cell: (113.36, 110.24, 138.32, 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 30 16.00 P 113 15.00 O 2497 8.00 N 2080 7.00 C 6932 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 454.3 milliseconds 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2192 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 11 sheets defined 47.0% alpha, 8.9% beta 23 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 57 through 89 Processing helix chain 'A' and resid 109 through 117 Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 123 through 137 Processing helix chain 'A' and resid 154 through 172 Processing helix chain 'A' and resid 176 through 189 removed outlier: 3.545A pdb=" N LEU A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 removed outlier: 3.706A pdb=" N HIS A 201 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 202 " --> pdb=" O TYR A 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 202' Processing helix chain 'A' and resid 204 through 222 Processing helix chain 'A' and resid 230 through 241 removed outlier: 3.980A pdb=" N GLU A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 255 removed outlier: 3.893A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 285 Processing helix chain 'A' and resid 298 through 307 removed outlier: 4.231A pdb=" N ASP A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 350 through 363 Processing helix chain 'A' and resid 375 through 389 removed outlier: 3.807A pdb=" N PHE A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 399 removed outlier: 3.575A pdb=" N ILE A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 415 removed outlier: 4.127A pdb=" N HIS A 414 " --> pdb=" O ALA A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 436 Proline residue: A 433 - end of helix Processing helix chain 'A' and resid 474 through 496 Processing helix chain 'A' and resid 512 through 541 Processing helix chain 'A' and resid 549 through 562 removed outlier: 3.593A pdb=" N ILE A 553 " --> pdb=" O LYS A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 579 removed outlier: 4.048A pdb=" N ASN A 579 " --> pdb=" O GLY A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 596 Processing helix chain 'A' and resid 629 through 641 Processing helix chain 'A' and resid 645 through 653 removed outlier: 3.614A pdb=" N LEU A 653 " --> pdb=" O LYS A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 666 Processing helix chain 'A' and resid 671 through 684 Processing helix chain 'A' and resid 699 through 710 Processing helix chain 'A' and resid 721 through 732 Processing helix chain 'A' and resid 734 through 750 removed outlier: 4.189A pdb=" N MET A 750 " --> pdb=" O ARG A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 789 Processing helix chain 'A' and resid 802 through 814 Processing helix chain 'A' and resid 817 through 821 removed outlier: 3.648A pdb=" N VAL A 821 " --> pdb=" O PRO A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 868 removed outlier: 7.008A pdb=" N LYS A 868 " --> pdb=" O THR A 865 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 865 through 868' Processing helix chain 'A' and resid 869 through 874 removed outlier: 3.816A pdb=" N GLU A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS A 874 " --> pdb=" O LYS A 870 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 869 through 874' Processing helix chain 'A' and resid 875 through 879 removed outlier: 3.860A pdb=" N ARG A 878 " --> pdb=" O MET A 875 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU A 879 " --> pdb=" O VAL A 876 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 875 through 879' Processing helix chain 'A' and resid 881 through 895 removed outlier: 3.785A pdb=" N ARG A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 903 Processing helix chain 'A' and resid 966 through 971 Processing helix chain 'A' and resid 984 through 988 Processing helix chain 'C' and resid 21 through 38 Processing helix chain 'C' and resid 42 through 52 removed outlier: 4.178A pdb=" N GLU C 48 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 removed outlier: 3.625A pdb=" N LYS C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 102 removed outlier: 3.640A pdb=" N GLU C 100 " --> pdb=" O ASP C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 117 removed outlier: 3.671A pdb=" N PHE C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 Processing sheet with id=AA1, first strand: chain 'A' and resid 500 through 502 removed outlier: 7.311A pdb=" N TYR A 11 " --> pdb=" O ARG A 500 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N HIS A 502 " --> pdb=" O TYR A 11 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU A 13 " --> pdb=" O HIS A 502 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY A 23 " --> pdb=" O ASP A 16 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL A 22 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLY A 42 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N TRP A 24 " --> pdb=" O ASP A 40 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ASP A 40 " --> pdb=" O TRP A 24 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N MET A 26 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LEU A 38 " --> pdb=" O MET A 26 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU A 28 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N SER A 831 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 43 " --> pdb=" O SER A 831 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 287 through 290 Processing sheet with id=AA3, first strand: chain 'A' and resid 314 through 316 removed outlier: 7.188A pdb=" N LEU A 315 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 585 through 587 removed outlier: 3.796A pdb=" N VAL A 606 " --> pdb=" O GLU A 585 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 848 through 849 Processing sheet with id=AA6, first strand: chain 'A' and resid 860 through 863 Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 908 removed outlier: 4.117A pdb=" N PHE A 907 " --> pdb=" O VAL A 920 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 960 through 965 removed outlier: 4.533A pdb=" N PHE A 999 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1046 through 1050 removed outlier: 3.667A pdb=" N GLY A1049 " --> pdb=" O ILE A1030 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE A1030 " --> pdb=" O GLY A1049 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASN A1031 " --> pdb=" O ALA A1021 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP A1005 " --> pdb=" O PHE A1020 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU A1006 " --> pdb=" O TYR A1061 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.672A pdb=" N LYS C 89 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 14 through 15 391 hydrogen bonds defined for protein. 1125 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 0.98 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: 3280 1.34 - 1.46: 2661 1.46 - 1.58: 5893 1.58 - 1.70: 224 1.70 - 1.82: 49 Bond restraints: 12107 Sorted by residual: bond pdb=" N VAL A1007 " pdb=" CA VAL A1007 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.11e-02 8.12e+03 1.45e+01 bond pdb=" N VAL A1009 " pdb=" CA VAL A1009 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.19e-02 7.06e+03 9.76e+00 bond pdb=" N ILE A 423 " pdb=" CA ILE A 423 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.22e-02 6.72e+03 9.20e+00 bond pdb=" N VAL A 735 " pdb=" CA VAL A 735 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.62e+00 bond pdb=" N LYS A 266 " pdb=" CA LYS A 266 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.22e-02 6.72e+03 7.35e+00 ... (remaining 12102 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 16265 1.92 - 3.83: 542 3.83 - 5.75: 54 5.75 - 7.66: 6 7.66 - 9.58: 2 Bond angle restraints: 16869 Sorted by residual: angle pdb=" CA VAL A1007 " pdb=" C VAL A1007 " pdb=" O VAL A1007 " ideal model delta sigma weight residual 121.63 117.61 4.02 9.90e-01 1.02e+00 1.65e+01 angle pdb=" CA GLY A 840 " pdb=" C GLY A 840 " pdb=" O GLY A 840 " ideal model delta sigma weight residual 121.83 117.76 4.07 1.02e+00 9.61e-01 1.59e+01 angle pdb=" N ASN A 526 " pdb=" CA ASN A 526 " pdb=" C ASN A 526 " ideal model delta sigma weight residual 111.82 107.31 4.51 1.16e+00 7.43e-01 1.51e+01 angle pdb=" N GLN A 738 " pdb=" CA GLN A 738 " pdb=" C GLN A 738 " ideal model delta sigma weight residual 111.71 107.28 4.43 1.15e+00 7.56e-01 1.48e+01 angle pdb=" N ILE A 192 " pdb=" CA ILE A 192 " pdb=" C ILE A 192 " ideal model delta sigma weight residual 112.96 109.16 3.80 1.00e+00 1.00e+00 1.44e+01 ... (remaining 16864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.32: 6197 18.32 - 36.64: 660 36.64 - 54.96: 183 54.96 - 73.28: 65 73.28 - 91.60: 12 Dihedral angle restraints: 7117 sinusoidal: 3732 harmonic: 3385 Sorted by residual: dihedral pdb=" C4' G B 83 " pdb=" C3' G B 83 " pdb=" C2' G B 83 " pdb=" C1' G B 83 " ideal model delta sinusoidal sigma weight residual 36.35 -36.15 72.49 1 3.10e+00 1.04e-01 6.98e+02 dihedral pdb=" C4' A B 45 " pdb=" C3' A B 45 " pdb=" C2' A B 45 " pdb=" C1' A B 45 " ideal model delta sinusoidal sigma weight residual 36.34 -36.14 72.49 1 3.10e+00 1.04e-01 6.98e+02 dihedral pdb=" C4' A B 77 " pdb=" C3' A B 77 " pdb=" C2' A B 77 " pdb=" C1' A B 77 " ideal model delta sinusoidal sigma weight residual 36.34 -35.86 72.21 1 3.10e+00 1.04e-01 6.94e+02 ... (remaining 7114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1558 0.056 - 0.111: 217 0.111 - 0.167: 31 0.167 - 0.223: 32 0.223 - 0.278: 106 Chirality restraints: 1944 Sorted by residual: chirality pdb=" C2' C B 89 " pdb=" C3' C B 89 " pdb=" O2' C B 89 " pdb=" C1' C B 89 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C2' C B 94 " pdb=" C3' C B 94 " pdb=" O2' C B 94 " pdb=" C1' C B 94 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C2' U B 127 " pdb=" C3' U B 127 " pdb=" O2' U B 127 " pdb=" C1' U B 127 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 1941 not shown) Planarity restraints: 1776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 772 " -0.032 5.00e-02 4.00e+02 4.91e-02 3.87e+00 pdb=" N PRO A 773 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 773 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 773 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 974 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO A 975 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 955 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C LYS A 955 " 0.033 2.00e-02 2.50e+03 pdb=" O LYS A 955 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY A 956 " -0.011 2.00e-02 2.50e+03 ... (remaining 1773 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1448 2.75 - 3.29: 11677 3.29 - 3.82: 20860 3.82 - 4.36: 24968 4.36 - 4.90: 39166 Nonbonded interactions: 98119 Sorted by model distance: nonbonded pdb=" O ARG A 880 " pdb=" O2' C B 36 " model vdw 2.211 3.040 nonbonded pdb=" NH2 ARG A 138 " pdb=" OP1 U B 21 " model vdw 2.227 3.120 nonbonded pdb=" NE1 TRP A 111 " pdb=" OP1 A B 60 " model vdw 2.250 3.120 nonbonded pdb=" NH1 ARG A 721 " pdb=" OD2 ASP A1036 " model vdw 2.251 3.120 nonbonded pdb=" O ALA A 637 " pdb=" OG1 THR A 641 " model vdw 2.253 3.040 ... (remaining 98114 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.660 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 : 0.003 0.061 12107 Z= 0.195 Angle : 0.715 9.577 16869 Z= 0.367 Chirality : 0.073 0.278 1944 Planarity : 0.004 0.049 1776 Dihedral : 16.490 91.597 4925 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.85 % Favored : 92.89 % Rotamer: Outliers : 0.73 % Allowed : 0.62 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.25), residues: 1153 helix: 0.24 (0.24), residues: 488 sheet: -1.97 (0.53), residues: 99 loop : -1.37 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 638 TYR 0.009 0.001 TYR C 70 PHE 0.017 0.001 PHE A 797 TRP 0.009 0.001 TRP A 127 HIS 0.004 0.001 HIS A1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.20 (12107) covalent geometry : angle 0.71550 / 0.37 (16869) hydrogen bonds : bond 0.19664 / 13.31 ( 444) hydrogen bonds : angle 8.14703 / 6.07 ( 1227) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 258 CYS cc_start: 0.5549 (t) cc_final: 0.5306 (t) REVERT: A 728 VAL cc_start: 0.8095 (t) cc_final: 0.7718 (t) REVERT: A 748 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.6793 (pttt) REVERT: A 908 TYR cc_start: 0.7215 (m-80) cc_final: 0.6991 (m-80) outliers start: 7 outliers final: 2 residues processed: 113 average time/residue: 0.0998 time to fit residues: 15.9028 Evaluate side-chains 89 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 1012 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN C 101 ASN ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.180066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.140768 restraints weight = 18521.025| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 2.19 r_work: 0.3928 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 12107 Z= 0.263 Angle : 0.907 11.216 16869 Z= 0.402 Chirality : 0.064 0.600 1944 Planarity : 0.005 0.052 1776 Dihedral : 15.004 144.093 2639 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.37 % Favored : 92.54 % Rotamer: Outliers : 1.46 % Allowed : 10.61 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.25), residues: 1153 helix: 0.25 (0.23), residues: 502 sheet: -2.20 (0.51), residues: 102 loop : -1.39 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 651 TYR 0.019 0.002 TYR C 11 PHE 0.022 0.002 PHE C 124 TRP 0.009 0.002 TRP C 46 HIS 0.004 0.001 HIS A1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.26 (12107) covalent geometry : angle 0.90659 / 0.40 (16869) hydrogen bonds : bond 0.04887 / 3.33 ( 444) hydrogen bonds : angle 5.25442 / 3.92 ( 1227) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 748 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.6719 (pttt) REVERT: C 89 LYS cc_start: 0.7915 (tmtt) cc_final: 0.7202 (tmtt) outliers start: 14 outliers final: 8 residues processed: 96 average time/residue: 0.1070 time to fit residues: 14.4818 Evaluate side-chains 83 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1012 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 87 optimal weight: 0.1980 chunk 81 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 99 optimal weight: 0.1980 chunk 16 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** C 122 GLN ** 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 = 0.4888 r_free = 0.4888 target = 0.194481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.147561 restraints weight = 19102.531| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 2.16 r_work: 0.4265 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.4139 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12107 Z= 0.152 Angle : 0.746 10.516 16869 Z= 0.332 Chirality : 0.056 0.359 1944 Planarity : 0.004 0.047 1776 Dihedral : 14.900 150.797 2636 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.81 % Favored : 94.10 % Rotamer: Outliers : 2.08 % Allowed : 13.01 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.25), residues: 1153 helix: 0.61 (0.23), residues: 500 sheet: -1.84 (0.54), residues: 94 loop : -1.32 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 721 TYR 0.013 0.001 TYR C 11 PHE 0.019 0.001 PHE C 124 TRP 0.009 0.001 TRP A 127 HIS 0.003 0.001 HIS A1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (12107) covalent geometry : angle 0.74609 / 0.33 (16869) hydrogen bonds : bond 0.04150 / 2.82 ( 444) hydrogen bonds : angle 4.84845 / 3.62 ( 1227) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.6038 (tp) REVERT: A 632 TRP cc_start: 0.6987 (t-100) cc_final: 0.6035 (t-100) REVERT: A 706 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7718 (mt) REVERT: A 748 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.6638 (pttt) REVERT: A 812 GLU cc_start: 0.7326 (pp20) cc_final: 0.7104 (pt0) REVERT: C 11 TYR cc_start: 0.8147 (t80) cc_final: 0.7886 (t80) REVERT: C 89 LYS cc_start: 0.7753 (tmtt) cc_final: 0.7150 (tmtt) outliers start: 20 outliers final: 9 residues processed: 102 average time/residue: 0.1076 time to fit residues: 15.0831 Evaluate side-chains 90 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain C residue 101 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 112 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.183641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.138563 restraints weight = 18637.147| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 1.99 r_work: 0.4030 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3882 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12107 Z= 0.151 Angle : 0.740 11.091 16869 Z= 0.329 Chirality : 0.055 0.330 1944 Planarity : 0.004 0.049 1776 Dihedral : 14.691 153.762 2636 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.33 % Favored : 93.58 % Rotamer: Outliers : 2.08 % Allowed : 15.61 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.25), residues: 1153 helix: 0.81 (0.24), residues: 497 sheet: -1.77 (0.54), residues: 94 loop : -1.40 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 916 TYR 0.016 0.001 TYR C 70 PHE 0.020 0.001 PHE C 124 TRP 0.009 0.001 TRP A 127 HIS 0.003 0.001 HIS A1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (12107) covalent geometry : angle 0.74005 / 0.33 (16869) hydrogen bonds : bond 0.03910 / 2.66 ( 444) hydrogen bonds : angle 4.70276 / 3.51 ( 1227) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.6013 (tp) REVERT: A 185 PHE cc_start: 0.2465 (m-10) cc_final: 0.2230 (m-80) REVERT: A 632 TRP cc_start: 0.6983 (t-100) cc_final: 0.6011 (t-100) REVERT: A 706 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7704 (mt) REVERT: A 748 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.6633 (pttt) REVERT: A 812 GLU cc_start: 0.7310 (pp20) cc_final: 0.7052 (pt0) REVERT: A 908 TYR cc_start: 0.7723 (m-80) cc_final: 0.7025 (m-80) REVERT: A 1038 ASP cc_start: 0.8323 (t0) cc_final: 0.8074 (t0) REVERT: C 89 LYS cc_start: 0.7710 (tmtt) cc_final: 0.7181 (tmtt) outliers start: 20 outliers final: 10 residues processed: 96 average time/residue: 0.1055 time to fit residues: 14.0171 Evaluate side-chains 93 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1012 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 79 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 9 optimal weight: 0.0370 chunk 24 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 overall best weight: 2.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.181680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.143086 restraints weight = 18580.922| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 2.10 r_work: 0.3943 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12107 Z= 0.233 Angle : 0.804 11.130 16869 Z= 0.360 Chirality : 0.058 0.383 1944 Planarity : 0.005 0.051 1776 Dihedral : 14.759 161.304 2636 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.50 % Allowed : 17.07 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.25), residues: 1153 helix: 0.60 (0.23), residues: 496 sheet: -1.98 (0.53), residues: 94 loop : -1.50 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1015 TYR 0.018 0.002 TYR C 11 PHE 0.020 0.002 PHE C 124 TRP 0.008 0.001 TRP C 46 HIS 0.004 0.001 HIS A1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.23 (12107) covalent geometry : angle 0.80412 / 0.36 (16869) hydrogen bonds : bond 0.04233 / 2.87 ( 444) hydrogen bonds : angle 4.81744 / 3.58 ( 1227) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8191 (ptp) cc_final: 0.7983 (ptm) REVERT: A 706 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7684 (mt) REVERT: A 748 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.6837 (pttt) REVERT: A 812 GLU cc_start: 0.7253 (pp20) cc_final: 0.6941 (pt0) REVERT: C 48 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7822 (mm-30) REVERT: C 87 LEU cc_start: 0.8427 (tt) cc_final: 0.7474 (mt) REVERT: C 89 LYS cc_start: 0.7610 (tmtt) cc_final: 0.7128 (tmtt) outliers start: 24 outliers final: 16 residues processed: 98 average time/residue: 0.0931 time to fit residues: 12.8242 Evaluate side-chains 92 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 88 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 57 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 29 optimal weight: 0.0570 chunk 98 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.3500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.183527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.144044 restraints weight = 18616.153| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 2.06 r_work: 0.3993 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12107 Z= 0.168 Angle : 0.747 11.523 16869 Z= 0.333 Chirality : 0.055 0.356 1944 Planarity : 0.004 0.051 1776 Dihedral : 14.719 164.169 2636 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.91 % Allowed : 16.75 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.25), residues: 1153 helix: 0.72 (0.23), residues: 495 sheet: -2.24 (0.48), residues: 107 loop : -1.42 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 721 TYR 0.009 0.001 TYR C 70 PHE 0.019 0.001 PHE C 124 TRP 0.010 0.001 TRP A 127 HIS 0.003 0.001 HIS A1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (12107) covalent geometry : angle 0.74714 / 0.33 (16869) hydrogen bonds : bond 0.03934 / 2.67 ( 444) hydrogen bonds : angle 4.68265 / 3.49 ( 1227) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.7106 (mt) REVERT: A 185 PHE cc_start: 0.2769 (m-10) cc_final: 0.2558 (m-80) REVERT: A 632 TRP cc_start: 0.6898 (t-100) cc_final: 0.5983 (t-100) REVERT: A 706 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7666 (mt) REVERT: A 748 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.6832 (pttt) REVERT: A 812 GLU cc_start: 0.7215 (pp20) cc_final: 0.6985 (pt0) REVERT: A 886 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.5803 (mp0) REVERT: C 89 LYS cc_start: 0.7437 (tmtt) cc_final: 0.7099 (tmtt) outliers start: 28 outliers final: 18 residues processed: 107 average time/residue: 0.0986 time to fit residues: 14.5891 Evaluate side-chains 105 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain A residue 1016 MET Chi-restraints excluded: chain A residue 1027 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 46 optimal weight: 0.4980 chunk 74 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 121 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 82 optimal weight: 0.2980 chunk 6 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.185045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.146015 restraints weight = 18550.238| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 2.04 r_work: 0.4042 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12107 Z= 0.124 Angle : 0.713 11.665 16869 Z= 0.317 Chirality : 0.053 0.328 1944 Planarity : 0.004 0.054 1776 Dihedral : 14.578 164.992 2636 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.39 % Allowed : 17.79 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.25), residues: 1153 helix: 0.97 (0.24), residues: 495 sheet: -2.20 (0.46), residues: 117 loop : -1.35 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 916 TYR 0.008 0.001 TYR A 495 PHE 0.020 0.001 PHE C 124 TRP 0.010 0.001 TRP A 127 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (12107) covalent geometry : angle 0.71312 / 0.32 (16869) hydrogen bonds : bond 0.03631 / 2.46 ( 444) hydrogen bonds : angle 4.52063 / 3.38 ( 1227) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.6427 (tp) REVERT: A 552 ASP cc_start: 0.8520 (p0) cc_final: 0.8225 (p0) REVERT: A 632 TRP cc_start: 0.6815 (t-100) cc_final: 0.5908 (t-100) REVERT: A 669 ASP cc_start: 0.7608 (t0) cc_final: 0.7355 (t70) REVERT: A 706 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7602 (mt) REVERT: A 748 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.6824 (pttt) REVERT: A 812 GLU cc_start: 0.7272 (pp20) cc_final: 0.6983 (pt0) REVERT: A 886 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.5739 (mp0) REVERT: C 87 LEU cc_start: 0.8242 (tt) cc_final: 0.7310 (mt) REVERT: C 89 LYS cc_start: 0.7251 (tmtt) cc_final: 0.7047 (tmtt) outliers start: 23 outliers final: 16 residues processed: 109 average time/residue: 0.1006 time to fit residues: 15.1678 Evaluate side-chains 104 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 101 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 9 optimal weight: 1.9990 chunk 86 optimal weight: 0.0970 chunk 69 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.183499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.144550 restraints weight = 18472.263| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 2.00 r_work: 0.4007 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12107 Z= 0.145 Angle : 0.725 11.576 16869 Z= 0.323 Chirality : 0.053 0.339 1944 Planarity : 0.004 0.053 1776 Dihedral : 14.556 165.701 2636 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.60 % Allowed : 18.00 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.25), residues: 1153 helix: 0.96 (0.23), residues: 500 sheet: -2.04 (0.49), residues: 107 loop : -1.40 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 916 TYR 0.016 0.001 TYR C 103 PHE 0.031 0.001 PHE A 185 TRP 0.008 0.001 TRP A 127 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (12107) covalent geometry : angle 0.72485 / 0.32 (16869) hydrogen bonds : bond 0.03667 / 2.49 ( 444) hydrogen bonds : angle 4.53081 / 3.38 ( 1227) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.6037 (tp) REVERT: A 185 PHE cc_start: 0.3150 (m-80) cc_final: 0.2810 (m-10) REVERT: A 552 ASP cc_start: 0.8554 (p0) cc_final: 0.8279 (p0) REVERT: A 632 TRP cc_start: 0.6834 (t-100) cc_final: 0.5854 (t-100) REVERT: A 669 ASP cc_start: 0.7746 (t0) cc_final: 0.7523 (t70) REVERT: A 706 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7622 (mt) REVERT: A 748 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.6870 (pttt) REVERT: A 812 GLU cc_start: 0.7235 (pp20) cc_final: 0.6978 (pt0) REVERT: A 886 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.5780 (mp0) REVERT: C 89 LYS cc_start: 0.7270 (tmtt) cc_final: 0.7024 (tmtt) outliers start: 25 outliers final: 17 residues processed: 105 average time/residue: 0.0853 time to fit residues: 12.9102 Evaluate side-chains 104 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain C residue 101 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 35 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 ASN ** C 101 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 = 0.4634 r_free = 0.4634 target = 0.177031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.137520 restraints weight = 18625.587| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 2.15 r_work: 0.3902 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 12107 Z= 0.355 Angle : 0.933 11.722 16869 Z= 0.421 Chirality : 0.062 0.501 1944 Planarity : 0.006 0.051 1776 Dihedral : 14.774 166.962 2636 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 2.60 % Allowed : 18.31 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.24), residues: 1153 helix: 0.37 (0.23), residues: 494 sheet: -2.27 (0.51), residues: 102 loop : -1.67 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 832 TYR 0.021 0.002 TYR A 11 PHE 0.036 0.003 PHE A 185 TRP 0.010 0.002 TRP C 46 HIS 0.008 0.002 HIS A1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00813 / 0.36 (12107) covalent geometry : angle 0.93337 / 0.42 (16869) hydrogen bonds : bond 0.04804 / 3.25 ( 444) hydrogen bonds : angle 4.96168 / 3.68 ( 1227) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 669 ASP cc_start: 0.7873 (t0) cc_final: 0.7482 (t70) REVERT: A 706 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7751 (mt) REVERT: A 748 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.6929 (pttt) REVERT: A 812 GLU cc_start: 0.7442 (pp20) cc_final: 0.7146 (pt0) REVERT: A 886 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.5940 (mp0) REVERT: A 908 TYR cc_start: 0.7736 (m-80) cc_final: 0.7027 (m-80) outliers start: 25 outliers final: 20 residues processed: 106 average time/residue: 0.0883 time to fit residues: 13.3228 Evaluate side-chains 103 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain C residue 88 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 24 optimal weight: 0.0370 chunk 48 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.182415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.137354 restraints weight = 18717.432| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 2.07 r_work: 0.4023 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3877 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12107 Z= 0.136 Angle : 0.754 11.797 16869 Z= 0.338 Chirality : 0.054 0.365 1944 Planarity : 0.004 0.054 1776 Dihedral : 14.653 167.555 2636 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.16 % Favored : 93.76 % Rotamer: Outliers : 2.08 % Allowed : 19.04 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.25), residues: 1153 helix: 0.73 (0.23), residues: 502 sheet: -2.43 (0.46), residues: 117 loop : -1.45 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 916 TYR 0.010 0.001 TYR A 495 PHE 0.020 0.001 PHE C 124 TRP 0.012 0.001 TRP A 127 HIS 0.004 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (12107) covalent geometry : angle 0.75439 / 0.34 (16869) hydrogen bonds : bond 0.03800 / 2.59 ( 444) hydrogen bonds : angle 4.63827 / 3.46 ( 1227) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 632 TRP cc_start: 0.6907 (t-100) cc_final: 0.6048 (t-100) REVERT: A 706 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7751 (mt) REVERT: A 748 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.6861 (pttt) REVERT: A 812 GLU cc_start: 0.7466 (pp20) cc_final: 0.7114 (pt0) REVERT: A 886 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.5983 (mp0) REVERT: C 87 LEU cc_start: 0.8377 (tt) cc_final: 0.7316 (mt) outliers start: 20 outliers final: 17 residues processed: 101 average time/residue: 0.0951 time to fit residues: 13.4511 Evaluate side-chains 101 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain C residue 101 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 31 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.182238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.137172 restraints weight = 18702.594| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 2.05 r_work: 0.4020 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3875 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12107 Z= 0.167 Angle : 0.979 59.161 16869 Z= 0.509 Chirality : 0.054 0.365 1944 Planarity : 0.004 0.054 1776 Dihedral : 14.658 167.566 2636 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.07 % Favored : 93.84 % Rotamer: Outliers : 2.39 % Allowed : 19.25 % Favored : 78.36 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.25), residues: 1153 helix: 0.74 (0.23), residues: 502 sheet: -2.41 (0.46), residues: 117 loop : -1.45 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 916 TYR 0.009 0.001 TYR A 495 PHE 0.018 0.001 PHE C 124 TRP 0.011 0.001 TRP A 127 HIS 0.003 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (12107) covalent geometry : angle 0.97905 / 0.51 (16869) hydrogen bonds : bond 0.03840 / 2.61 ( 444) hydrogen bonds : angle 4.66787 / 3.47 ( 1227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2709.37 seconds wall clock time: 46 minutes 56.48 seconds (2816.48 seconds total)