Starting phenix.real_space_refine on Fri Jul 3 03:21:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hj4_34832/07_2026/8hj4_34832.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hj4_34832/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hj4_34832/07_2026/8hj4_34832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hj4_34832/07_2026/8hj4_34832.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8hj4_34832/07_2026/8hj4_34832.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hj4_34832/07_2026/8hj4_34832.cif" model { file = "/net/cci-nas-00/data/ceres_data/8hj4_34832/07_2026/8hj4_34832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hj4_34832/07_2026/8hj4_34832.cif" } 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-dev-6108/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: {'RNA': 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: 2.39, per 1000 atoms: 0.21 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: 0.88 Conformation dependent library (CDL) restraints added in 404.8 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: 1.65 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: 3.22 Time building geometry restraints manager: 1.13 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: 16530 1.92 - 3.83: 295 3.83 - 5.75: 37 5.75 - 7.66: 5 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 - 20.17: 6447 20.17 - 40.34: 546 40.34 - 60.52: 87 60.52 - 80.69: 18 80.69 - 100.86: 19 Dihedral angle restraints: 7117 sinusoidal: 3732 harmonic: 3385 Sorted by residual: dihedral pdb=" CA VAL A 91 " pdb=" C VAL A 91 " pdb=" N LEU A 92 " pdb=" CA LEU A 92 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ARG A 402 " pdb=" C ARG A 402 " pdb=" N ILE A 403 " pdb=" CA ILE A 403 " ideal model delta harmonic sigma weight residual 180.00 -160.44 -19.56 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ASP A 683 " pdb=" C ASP A 683 " pdb=" N ARG A 684 " pdb=" CA ARG A 684 " ideal model delta harmonic sigma weight residual 180.00 -161.40 -18.60 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 7114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1485 0.038 - 0.076: 323 0.076 - 0.114: 95 0.114 - 0.153: 28 0.153 - 0.191: 13 Chirality restraints: 1944 Sorted by residual: chirality pdb=" CA VAL A1007 " pdb=" N VAL A1007 " pdb=" C VAL A1007 " pdb=" CB VAL A1007 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.10e-01 chirality pdb=" CA LYS A 528 " pdb=" N LYS A 528 " pdb=" C LYS A 528 " pdb=" CB LYS A 528 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.38e-01 chirality pdb=" CA LEU A 231 " pdb=" N LEU A 231 " pdb=" C LEU A 231 " pdb=" CB LEU A 231 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.30e-01 ... (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: 1.060 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.290 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.710 ------------------------------------------------------------------------------- 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= 0.191 Angle : 0.600 9.577 16869 Z= 0.345 Chirality : 0.040 0.191 1944 Planarity : 0.004 0.049 1776 Dihedral : 15.158 100.859 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 0.00331 / 0.19 (12107) covalent geometry : angle 0.60039 / 0.35 (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 : 0.418 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: 0.1159 time to fit residues: 18.4512 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 : 0.363 ------------------------------------------------------------------------------- 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: 6.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 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 = 0.4656 r_free = 0.4656 target = 0.178421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.138779 restraints weight = 18367.984| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 2.13 r_work: 0.3930 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 12107 Z= 0.247 Angle : 0.681 9.169 16869 Z= 0.348 Chirality : 0.043 0.167 1944 Planarity : 0.005 0.052 1776 Dihedral : 12.711 101.787 2639 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.46 % Favored : 92.45 % Rotamer: Outliers : 1.46 % Allowed : 10.09 % Favored : 88.45 % 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: 0.28 (0.23), residues: 500 sheet: -2.18 (0.51), residues: 102 loop : -1.39 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 721 TYR 0.018 0.002 TYR C 11 PHE 0.019 0.002 PHE A 709 TRP 0.009 0.002 TRP A 127 HIS 0.005 0.001 HIS A1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.25 (12107) covalent geometry : angle 0.68093 / 0.35 (16869) hydrogen bonds : bond 0.05147 / 3.53 ( 444) hydrogen bonds : angle 5.28420 / 3.94 ( 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 99 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 748 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.6737 (pttt) REVERT: C 89 LYS cc_start: 0.7938 (tmtt) cc_final: 0.7209 (tmtt) outliers start: 14 outliers final: 8 residues processed: 97 average time/residue: 0.1182 time to fit residues: 16.1359 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 : 0.365 ------------------------------------------------------------------------------- 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: 4.9990 chunk 74 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 87 optimal weight: 0.0170 chunk 81 optimal weight: 0.6980 chunk 122 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.7424 ------------------------------------------------------------------------------- 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 191 HIS ** A 611 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.180517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.135405 restraints weight = 18628.099| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.06 r_work: 0.3973 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3826 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12107 Z= 0.192 Angle : 0.616 9.050 16869 Z= 0.316 Chirality : 0.040 0.183 1944 Planarity : 0.005 0.051 1776 Dihedral : 12.729 110.601 2636 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.42 % Favored : 93.50 % Rotamer: Outliers : 2.50 % Allowed : 13.53 % Favored : 83.98 % 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: -0.96 (0.25), residues: 1153 helix: 0.46 (0.23), residues: 499 sheet: -1.97 (0.53), residues: 94 loop : -1.39 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 429 TYR 0.016 0.001 TYR C 11 PHE 0.019 0.002 PHE C 124 TRP 0.012 0.002 TRP A 24 HIS 0.004 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (12107) covalent geometry : angle 0.61634 / 0.32 (16869) hydrogen bonds : bond 0.04341 / 2.96 ( 444) hydrogen bonds : angle 4.92158 / 3.67 ( 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 113 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7385 (mt) REVERT: A 632 TRP cc_start: 0.7033 (t-100) cc_final: 0.6063 (t-100) REVERT: A 706 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7723 (mt) REVERT: A 748 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.6685 (pttt) REVERT: A 812 GLU cc_start: 0.7414 (pp20) cc_final: 0.7141 (pt0) REVERT: A 1038 ASP cc_start: 0.8341 (t0) cc_final: 0.8106 (t0) REVERT: C 50 LEU cc_start: 0.8458 (mt) cc_final: 0.8186 (mt) REVERT: C 89 LYS cc_start: 0.7762 (tmtt) cc_final: 0.7123 (tmtt) outliers start: 24 outliers final: 9 residues processed: 104 average time/residue: 0.1175 time to fit residues: 17.1243 Evaluate side-chains 91 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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: 0.9990 chunk 89 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 ** 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 = 0.4677 r_free = 0.4677 target = 0.180265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.135499 restraints weight = 18725.732| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 1.98 r_work: 0.3983 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3842 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12107 Z= 0.192 Angle : 0.618 8.835 16869 Z= 0.317 Chirality : 0.040 0.188 1944 Planarity : 0.005 0.052 1776 Dihedral : 12.696 111.966 2636 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.63 % Favored : 92.28 % Rotamer: Outliers : 2.50 % Allowed : 16.13 % Favored : 81.37 % 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: -0.96 (0.25), residues: 1153 helix: 0.56 (0.23), residues: 495 sheet: -1.99 (0.53), residues: 94 loop : -1.49 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 721 TYR 0.015 0.001 TYR C 11 PHE 0.019 0.002 PHE C 124 TRP 0.010 0.001 TRP A 127 HIS 0.004 0.001 HIS A1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (12107) covalent geometry : angle 0.61784 / 0.32 (16869) hydrogen bonds : bond 0.04203 / 2.86 ( 444) hydrogen bonds : angle 4.83807 / 3.60 ( 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 104 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 706 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7729 (mt) REVERT: A 748 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.6770 (pttt) REVERT: A 812 GLU cc_start: 0.7350 (pp20) cc_final: 0.7056 (pt0) REVERT: A 1038 ASP cc_start: 0.8385 (t0) cc_final: 0.8141 (t0) REVERT: C 89 LYS cc_start: 0.7644 (tmtt) cc_final: 0.7082 (tmtt) outliers start: 24 outliers final: 15 residues processed: 97 average time/residue: 0.1215 time to fit residues: 16.4590 Evaluate side-chains 93 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 1009 VAL Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain C residue 88 VAL 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: 0.7980 chunk 63 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 81 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 ** 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 = 0.4694 r_free = 0.4694 target = 0.181596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.139342 restraints weight = 18684.374| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 2.09 r_work: 0.3981 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12107 Z= 0.176 Angle : 0.597 8.788 16869 Z= 0.306 Chirality : 0.039 0.190 1944 Planarity : 0.005 0.051 1776 Dihedral : 12.648 112.703 2636 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.81 % Allowed : 16.34 % Favored : 80.85 % 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: -0.94 (0.25), residues: 1153 helix: 0.62 (0.23), residues: 497 sheet: -1.98 (0.53), residues: 94 loop : -1.53 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 721 TYR 0.014 0.001 TYR C 11 PHE 0.018 0.002 PHE C 124 TRP 0.010 0.001 TRP A 127 HIS 0.004 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (12107) covalent geometry : angle 0.59715 / 0.31 (16869) hydrogen bonds : bond 0.04034 / 2.74 ( 444) hydrogen bonds : angle 4.74860 / 3.54 ( 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 117 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7168 (mt) REVERT: A 632 TRP cc_start: 0.6912 (t-100) cc_final: 0.6021 (t-100) REVERT: A 706 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7681 (mt) REVERT: A 748 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.6867 (pttt) REVERT: A 812 GLU cc_start: 0.7318 (pp20) cc_final: 0.6995 (pt0) REVERT: A 886 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.5795 (mp0) REVERT: C 87 LEU cc_start: 0.8400 (tt) cc_final: 0.7535 (mt) REVERT: C 89 LYS cc_start: 0.7242 (tmtt) cc_final: 0.6906 (tmtt) outliers start: 27 outliers final: 20 residues processed: 112 average time/residue: 0.1161 time to fit residues: 18.1484 Evaluate side-chains 107 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 952 VAL Chi-restraints excluded: chain A residue 1009 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 57 optimal weight: 0.6980 chunk 25 optimal weight: 8.9990 chunk 29 optimal weight: 0.0970 chunk 98 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** 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 = 0.4725 r_free = 0.4725 target = 0.184729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.140303 restraints weight = 18735.164| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 2.05 r_work: 0.4049 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3908 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2416 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= 0.118 Angle : 0.562 8.539 16869 Z= 0.288 Chirality : 0.037 0.189 1944 Planarity : 0.004 0.053 1776 Dihedral : 12.524 111.816 2636 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.50 % Allowed : 17.48 % Favored : 80.02 % 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: -0.80 (0.25), residues: 1153 helix: 0.82 (0.24), residues: 500 sheet: -2.23 (0.47), residues: 117 loop : -1.42 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 916 TYR 0.010 0.001 TYR C 11 PHE 0.020 0.001 PHE C 124 TRP 0.010 0.001 TRP A 127 HIS 0.006 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (12107) covalent geometry : angle 0.56238 / 0.29 (16869) hydrogen bonds : bond 0.03676 / 2.50 ( 444) hydrogen bonds : angle 4.56405 / 3.41 ( 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 114 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.7466 (OUTLIER) cc_final: 0.6493 (tp) REVERT: A 552 ASP cc_start: 0.8527 (p0) cc_final: 0.8235 (p0) REVERT: A 632 TRP cc_start: 0.6939 (t-100) cc_final: 0.5985 (t-100) REVERT: A 669 ASP cc_start: 0.7888 (t0) cc_final: 0.7601 (t70) REVERT: A 706 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7650 (mt) REVERT: A 748 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.6859 (pttt) REVERT: A 812 GLU cc_start: 0.7371 (pp20) cc_final: 0.7029 (pt0) REVERT: A 886 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.5992 (mp0) REVERT: C 89 LYS cc_start: 0.7407 (tmtt) cc_final: 0.7072 (tmtt) outliers start: 24 outliers final: 15 residues processed: 109 average time/residue: 0.1051 time to fit residues: 16.2176 Evaluate side-chains 105 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 126 GLU 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 0.3980 chunk 18 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 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 = 0.183466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.139740 restraints weight = 18657.004| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 2.25 r_work: 0.4002 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12107 Z= 0.135 Angle : 0.566 8.569 16869 Z= 0.289 Chirality : 0.037 0.187 1944 Planarity : 0.004 0.054 1776 Dihedral : 12.448 111.076 2636 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.50 % Allowed : 18.00 % Favored : 79.50 % 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: -0.71 (0.25), residues: 1153 helix: 0.91 (0.24), residues: 500 sheet: -2.02 (0.49), residues: 107 loop : -1.46 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1015 TYR 0.009 0.001 TYR A 495 PHE 0.019 0.001 PHE C 124 TRP 0.009 0.001 TRP A 127 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (12107) covalent geometry : angle 0.56627 / 0.29 (16869) hydrogen bonds : bond 0.03655 / 2.50 ( 444) hydrogen bonds : angle 4.54015 / 3.39 ( 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 113 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.5894 (tp) REVERT: A 706 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7576 (mt) REVERT: A 748 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.6843 (pttt) REVERT: A 812 GLU cc_start: 0.7193 (pp20) cc_final: 0.6878 (pt0) REVERT: A 886 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.5846 (mp0) REVERT: A 908 TYR cc_start: 0.7634 (m-80) cc_final: 0.6957 (m-80) REVERT: C 87 LEU cc_start: 0.8223 (tt) cc_final: 0.7262 (mt) REVERT: C 89 LYS cc_start: 0.7395 (tmtt) cc_final: 0.7083 (tmtt) outliers start: 24 outliers final: 19 residues processed: 109 average time/residue: 0.1170 time to fit residues: 17.8785 Evaluate side-chains 104 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 126 GLU 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 1027 THR 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: 0.8980 chunk 86 optimal weight: 0.0570 chunk 69 optimal weight: 2.9990 chunk 10 optimal weight: 0.0070 chunk 47 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- 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 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 = 0.4734 r_free = 0.4734 target = 0.185362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.146543 restraints weight = 18551.285| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 2.04 r_work: 0.4057 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12107 Z= 0.107 Angle : 0.547 9.253 16869 Z= 0.279 Chirality : 0.036 0.185 1944 Planarity : 0.004 0.055 1776 Dihedral : 12.357 110.169 2636 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.50 % Allowed : 18.83 % Favored : 78.67 % 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: -0.59 (0.25), residues: 1153 helix: 1.08 (0.24), residues: 500 sheet: -2.21 (0.47), residues: 115 loop : -1.39 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 594 TYR 0.015 0.001 TYR C 103 PHE 0.028 0.001 PHE A 185 TRP 0.010 0.001 TRP A 127 HIS 0.008 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (12107) covalent geometry : angle 0.54728 / 0.28 (16869) hydrogen bonds : bond 0.03485 / 2.37 ( 444) hydrogen bonds : angle 4.46285 / 3.35 ( 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 118 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.7159 (OUTLIER) cc_final: 0.6322 (tp) REVERT: A 185 PHE cc_start: 0.2744 (m-80) cc_final: 0.2537 (m-10) REVERT: A 552 ASP cc_start: 0.8539 (p0) cc_final: 0.8328 (p0) REVERT: A 632 TRP cc_start: 0.6793 (t-100) cc_final: 0.6001 (t-100) REVERT: A 706 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7543 (mt) REVERT: A 748 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.6830 (pttt) REVERT: A 812 GLU cc_start: 0.7267 (pp20) cc_final: 0.7013 (pt0) REVERT: A 886 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.5684 (mp0) outliers start: 24 outliers final: 17 residues processed: 113 average time/residue: 0.1088 time to fit residues: 17.3635 Evaluate side-chains 110 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 26 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 30.0000 chunk 57 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 58 optimal weight: 0.0170 chunk 124 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 overall best weight: 1.1220 ------------------------------------------------------------------------------- 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 ** 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 = 0.4710 r_free = 0.4710 target = 0.183033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.138406 restraints weight = 18450.667| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 2.08 r_work: 0.4032 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3884 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12107 Z= 0.142 Angle : 0.576 9.379 16869 Z= 0.292 Chirality : 0.037 0.184 1944 Planarity : 0.004 0.055 1776 Dihedral : 12.290 110.024 2636 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.98 % Favored : 93.93 % Rotamer: Outliers : 2.19 % Allowed : 18.83 % Favored : 78.98 % 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: -0.56 (0.25), residues: 1153 helix: 1.09 (0.24), residues: 500 sheet: -2.03 (0.49), residues: 107 loop : -1.41 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 916 TYR 0.008 0.001 TYR A 11 PHE 0.024 0.001 PHE A 185 TRP 0.007 0.001 TRP C 46 HIS 0.005 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (12107) covalent geometry : angle 0.57639 / 0.29 (16869) hydrogen bonds : bond 0.03601 / 2.47 ( 444) hydrogen bonds : angle 4.49270 / 3.37 ( 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 107 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.6050 (tp) REVERT: A 632 TRP cc_start: 0.6892 (t-100) cc_final: 0.5938 (t-100) REVERT: A 706 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7670 (mt) REVERT: A 748 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.6827 (pttt) REVERT: A 812 GLU cc_start: 0.7345 (pp20) cc_final: 0.6991 (pt0) REVERT: A 886 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6073 (mp0) REVERT: C 87 LEU cc_start: 0.8306 (tt) cc_final: 0.7290 (mt) outliers start: 21 outliers final: 17 residues processed: 104 average time/residue: 0.1163 time to fit residues: 17.2583 Evaluate side-chains 103 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 126 GLU 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 ** 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 = 0.4702 r_free = 0.4702 target = 0.182591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.137553 restraints weight = 18745.563| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 2.05 r_work: 0.4012 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3873 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12107 Z= 0.158 Angle : 0.598 9.349 16869 Z= 0.302 Chirality : 0.038 0.182 1944 Planarity : 0.004 0.055 1776 Dihedral : 12.265 109.517 2636 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.90 % Favored : 94.02 % Rotamer: Outliers : 2.39 % Allowed : 19.25 % Favored : 78.36 % 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: -0.63 (0.25), residues: 1153 helix: 1.00 (0.23), residues: 497 sheet: -2.06 (0.50), residues: 107 loop : -1.41 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 916 TYR 0.010 0.001 TYR C 66 PHE 0.019 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 0.00353 / 0.16 (12107) covalent geometry : angle 0.59778 / 0.30 (16869) hydrogen bonds : bond 0.03725 / 2.56 ( 444) hydrogen bonds : angle 4.54774 / 3.40 ( 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 107 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.6198 (tp) REVERT: A 632 TRP cc_start: 0.6893 (t-100) cc_final: 0.6008 (t-100) REVERT: A 706 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7720 (mt) REVERT: A 748 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.6948 (pttt) REVERT: A 812 GLU cc_start: 0.7391 (pp20) cc_final: 0.7033 (pt0) REVERT: A 886 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6023 (mp0) REVERT: C 87 LEU cc_start: 0.8341 (tt) cc_final: 0.7320 (mt) outliers start: 23 outliers final: 18 residues processed: 102 average time/residue: 0.1183 time to fit residues: 17.0646 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 : 0.354 ------------------------------------------------------------------------------- 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 126 GLU 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 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 1011 THR Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain A residue 1027 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 31 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 9 optimal weight: 0.0770 chunk 67 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 overall best weight: 1.0144 ------------------------------------------------------------------------------- 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 ** 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 = 0.4706 r_free = 0.4706 target = 0.183462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.137311 restraints weight = 18805.223| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 2.18 r_work: 0.4019 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2809 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= 0.135 Angle : 0.572 9.411 16869 Z= 0.290 Chirality : 0.037 0.181 1944 Planarity : 0.004 0.055 1776 Dihedral : 12.162 108.988 2636 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.55 % Favored : 94.36 % Rotamer: Outliers : 2.50 % Allowed : 19.15 % Favored : 78.36 % 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: -0.53 (0.25), residues: 1153 helix: 1.06 (0.24), residues: 498 sheet: -1.99 (0.50), residues: 107 loop : -1.33 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 916 TYR 0.011 0.001 TYR C 11 PHE 0.019 0.001 PHE C 124 TRP 0.008 0.001 TRP A 127 HIS 0.003 0.001 HIS A1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (12107) covalent geometry : angle 0.57165 / 0.29 (16869) hydrogen bonds : bond 0.03616 / 2.48 ( 444) hydrogen bonds : angle 4.49313 / 3.37 ( 1227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3312.56 seconds wall clock time: 57 minutes 25.73 seconds (3445.73 seconds total)