Starting phenix.real_space_refine on Sat Aug 23 11:44:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hj4_34832/08_2025/8hj4_34832.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hj4_34832/08_2025/8hj4_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_34832/08_2025/8hj4_34832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hj4_34832/08_2025/8hj4_34832.map" model { file = "/net/cci-nas-00/data/ceres_data/8hj4_34832/08_2025/8hj4_34832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hj4_34832/08_2025/8hj4_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-2.0-5787/lib/python3.9/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: 2.94, per 1000 atoms: 0.25 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: 0.69 Conformation dependent library (CDL) restraints added in 568.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.83 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: 3.05 Time building geometry restraints manager: 0.95 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: 6573 20.17 - 40.34: 606 40.34 - 60.52: 212 60.52 - 80.69: 97 80.69 - 100.86: 19 Dihedral angle restraints: 7507 sinusoidal: 4122 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 7504 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: 1.650 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 14.620 Find NCS groups from input model: 0.060 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 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 : 18.932 100.859 5315 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 aren 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 covalent geometry : bond 0.00331 (12107) covalent geometry : angle 0.60039 (16869) hydrogen bonds : bond 0.19664 ( 444) hydrogen bonds : angle 8.14703 ( 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 : 0.333 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: 0.7596 (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: 0.1328 time to fit residues: 20.8347 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 : 0.408 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4842 r_free = 0.4842 target = 0.189814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.150228 restraints weight = 19096.935| |-----------------------------------------------------------------------------| r_work (start): 0.4386 rms_B_bonded: 2.16 r_work: 0.4130 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1430 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 : 0.683 9.142 16869 Z= 0.349 Chirality : 0.043 0.171 1944 Planarity : 0.005 0.052 1776 Dihedral : 19.583 102.064 3029 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.55 % Favored : 92.37 % Rotamer: Outliers : 1.35 % Allowed : 10.61 % Favored : 88.03 % 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 aren not related in a simple way. whole: -1.13 (0.25), residues: 1153 helix: 0.27 (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 0.017 0.002 TYR C 11 PHE 0.020 0.002 PHE A 709 TRP 0.009 0.002 TRP C 46 HIS 0.005 0.001 HIS A1024 Details of bonding type rmsd covalent geometry : bond 0.00558 (12107) covalent geometry : angle 0.68303 (16869) hydrogen bonds : bond 0.05168 ( 444) hydrogen bonds : angle 5.29588 ( 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 96 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 748 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.6710 (pttt) REVERT: C 89 LYS cc_start: 0.7952 (tmtt) cc_final: 0.7198 (tmtt) outliers start: 13 outliers final: 6 residues processed: 94 average time/residue: 0.1361 time to fit residues: 17.8272 Evaluate side-chains 81 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR 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: 6.9990 chunk 107 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 87 optimal weight: 0.2980 chunk 81 optimal weight: 0.5980 chunk 122 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.192564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.152661 restraints weight = 19155.083| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 2.13 r_work: 0.4228 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.4094 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1715 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= 0.161 Angle : 0.594 9.052 16869 Z= 0.304 Chirality : 0.039 0.178 1944 Planarity : 0.005 0.049 1776 Dihedral : 19.469 108.740 3026 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.33 % Favored : 93.58 % Rotamer: Outliers : 2.29 % Allowed : 13.11 % Favored : 84.60 % 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 aren not related in a simple way. whole: -0.83 (0.25), residues: 1153 helix: 0.61 (0.23), residues: 494 sheet: -1.89 (0.53), residues: 94 loop : -1.36 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 429 TYR 0.014 0.001 TYR C 11 PHE 0.019 0.002 PHE C 124 TRP 0.009 0.001 TRP A 127 HIS 0.004 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00359 (12107) covalent geometry : angle 0.59368 (16869) hydrogen bonds : bond 0.04255 ( 444) hydrogen bonds : angle 4.89519 ( 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 111 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.6060 (tp) REVERT: A 632 TRP cc_start: 0.7022 (t-100) cc_final: 0.6044 (t-100) REVERT: A 706 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7746 (mt) REVERT: A 748 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.6621 (pttt) REVERT: A 812 GLU cc_start: 0.7351 (pp20) cc_final: 0.7122 (pt0) REVERT: C 89 LYS cc_start: 0.7778 (tmtt) cc_final: 0.7154 (tmtt) outliers start: 22 outliers final: 10 residues processed: 103 average time/residue: 0.1412 time to fit residues: 20.0516 Evaluate side-chains 92 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 254 MET 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: 30.0000 chunk 111 optimal weight: 5.9990 chunk 56 optimal weight: 0.0970 chunk 77 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** 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 = 0.4709 r_free = 0.4709 target = 0.183115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.144411 restraints weight = 18619.215| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 2.06 r_work: 0.4014 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1976 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= 0.125 Angle : 0.567 8.693 16869 Z= 0.290 Chirality : 0.038 0.184 1944 Planarity : 0.004 0.050 1776 Dihedral : 19.405 110.242 3026 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.07 % Favored : 93.84 % Rotamer: Outliers : 2.08 % Allowed : 15.92 % Favored : 82.00 % 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 aren not related in a simple way. whole: -0.69 (0.25), residues: 1153 helix: 0.81 (0.24), residues: 497 sheet: -1.72 (0.54), residues: 94 loop : -1.41 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 721 TYR 0.018 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 covalent geometry : bond 0.00270 (12107) covalent geometry : angle 0.56701 (16869) hydrogen bonds : bond 0.03818 ( 444) hydrogen bonds : angle 4.67271 ( 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 108 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.7310 (OUTLIER) cc_final: 0.6413 (tp) REVERT: A 185 PHE cc_start: 0.2546 (m-10) cc_final: 0.2321 (m-80) REVERT: A 632 TRP cc_start: 0.6917 (t-100) cc_final: 0.6014 (t-100) REVERT: A 706 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7630 (mt) REVERT: A 748 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.6652 (pttt) REVERT: A 812 GLU cc_start: 0.7263 (pp20) cc_final: 0.7024 (pt0) REVERT: A 908 TYR cc_start: 0.7436 (m-80) cc_final: 0.6899 (m-80) REVERT: C 11 TYR cc_start: 0.8043 (t80) cc_final: 0.7741 (t80) REVERT: C 89 LYS cc_start: 0.7519 (tmtt) cc_final: 0.7110 (tmtt) outliers start: 20 outliers final: 10 residues processed: 101 average time/residue: 0.1483 time to fit residues: 20.4393 Evaluate side-chains 94 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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: 0.7980 chunk 63 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** A1029 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 = 0.4658 r_free = 0.4658 target = 0.178498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.139226 restraints weight = 18472.964| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 2.20 r_work: 0.3932 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2149 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= 0.223 Angle : 0.640 8.617 16869 Z= 0.327 Chirality : 0.041 0.185 1944 Planarity : 0.005 0.050 1776 Dihedral : 19.400 111.219 3026 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.81 % Allowed : 16.96 % Favored : 80.23 % 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 aren not related in a simple way. whole: -0.94 (0.25), residues: 1153 helix: 0.59 (0.23), residues: 495 sheet: -1.93 (0.53), residues: 94 loop : -1.50 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 721 TYR 0.014 0.002 TYR A 11 PHE 0.019 0.002 PHE C 124 TRP 0.008 0.001 TRP C 46 HIS 0.004 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00498 (12107) covalent geometry : angle 0.63957 (16869) hydrogen bonds : bond 0.04261 ( 444) hydrogen bonds : angle 4.81200 ( 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 110 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8203 (ptp) cc_final: 0.7985 (ptm) REVERT: A 706 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7695 (mt) REVERT: A 748 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.6847 (pttt) REVERT: A 812 GLU cc_start: 0.7276 (pp20) cc_final: 0.6958 (pt0) REVERT: C 48 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7828 (mm-30) REVERT: C 87 LEU cc_start: 0.8417 (tt) cc_final: 0.7473 (mt) REVERT: C 89 LYS cc_start: 0.7612 (tmtt) cc_final: 0.7171 (tmtt) outliers start: 27 outliers final: 17 residues processed: 103 average time/residue: 0.1465 time to fit residues: 20.7369 Evaluate side-chains 95 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 845 GLU 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: 6.9990 chunk 25 optimal weight: 20.0000 chunk 29 optimal weight: 0.3980 chunk 98 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4671 r_free = 0.4671 target = 0.179628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.140141 restraints weight = 18587.814| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.10 r_work: 0.3947 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12107 Z= 0.182 Angle : 0.609 8.611 16869 Z= 0.311 Chirality : 0.039 0.184 1944 Planarity : 0.004 0.052 1776 Dihedral : 19.417 110.715 3026 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.81 % Allowed : 17.27 % Favored : 79.92 % 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 aren not related in a simple way. whole: -0.93 (0.25), residues: 1153 helix: 0.64 (0.23), residues: 492 sheet: -2.17 (0.51), residues: 97 loop : -1.47 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 721 TYR 0.019 0.001 TYR C 11 PHE 0.021 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 covalent geometry : bond 0.00408 (12107) covalent geometry : angle 0.60878 (16869) hydrogen bonds : bond 0.04039 ( 444) hydrogen bonds : angle 4.72861 ( 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 116 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7272 (mt) REVERT: A 185 PHE cc_start: 0.2949 (m-10) cc_final: 0.2684 (m-80) REVERT: A 632 TRP cc_start: 0.6930 (t-100) cc_final: 0.5983 (t-100) REVERT: A 706 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7697 (mt) REVERT: A 748 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.6843 (pttt) REVERT: A 812 GLU cc_start: 0.7288 (pp20) cc_final: 0.7041 (pt0) REVERT: A 886 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.5818 (mp0) REVERT: C 89 LYS cc_start: 0.7423 (tmtt) cc_final: 0.7075 (tmtt) outliers start: 27 outliers final: 17 residues processed: 109 average time/residue: 0.1383 time to fit residues: 20.9825 Evaluate side-chains 106 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 1027 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 0.0770 chunk 18 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** 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 = 0.4705 r_free = 0.4705 target = 0.182773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.139665 restraints weight = 18692.505| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.19 r_work: 0.3999 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12107 Z= 0.144 Angle : 0.587 8.645 16869 Z= 0.299 Chirality : 0.038 0.182 1944 Planarity : 0.004 0.054 1776 Dihedral : 19.369 109.892 3026 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.60 % Allowed : 17.27 % Favored : 80.12 % 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 aren not related in a simple way. whole: -0.81 (0.25), residues: 1153 helix: 0.79 (0.24), residues: 494 sheet: -2.13 (0.49), residues: 107 loop : -1.43 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 916 TYR 0.010 0.001 TYR A 495 PHE 0.022 0.001 PHE A 797 TRP 0.010 0.001 TRP A 127 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00320 (12107) covalent geometry : angle 0.58722 (16869) hydrogen bonds : bond 0.03757 ( 444) hydrogen bonds : angle 4.63353 ( 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 112 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.7344 (OUTLIER) cc_final: 0.5966 (tp) REVERT: A 185 PHE cc_start: 0.2857 (m-10) cc_final: 0.2595 (m-80) REVERT: A 552 ASP cc_start: 0.8570 (p0) cc_final: 0.8294 (p0) REVERT: A 632 TRP cc_start: 0.6881 (t-100) cc_final: 0.5904 (t-100) REVERT: A 706 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7632 (mt) REVERT: A 748 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.6844 (pttt) REVERT: A 812 GLU cc_start: 0.7224 (pp20) cc_final: 0.6955 (pt0) REVERT: A 886 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.5779 (mp0) REVERT: C 89 LYS cc_start: 0.7281 (tmtt) cc_final: 0.6991 (tmtt) outliers start: 25 outliers final: 17 residues processed: 106 average time/residue: 0.1407 time to fit residues: 20.7162 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 : 0.406 ------------------------------------------------------------------------------- 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 88 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 9 optimal weight: 0.0870 chunk 86 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 overall best weight: 1.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4705 r_free = 0.4705 target = 0.182694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.137902 restraints weight = 18607.996| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 2.02 r_work: 0.4020 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3875 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12107 Z= 0.146 Angle : 0.590 9.149 16869 Z= 0.299 Chirality : 0.038 0.180 1944 Planarity : 0.004 0.053 1776 Dihedral : 19.312 109.135 3026 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.81 % Allowed : 18.00 % Favored : 79.19 % 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 aren not related in a simple way. whole: -0.80 (0.25), residues: 1153 helix: 0.79 (0.23), residues: 501 sheet: -2.12 (0.49), residues: 107 loop : -1.45 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1015 TYR 0.010 0.001 TYR C 41 PHE 0.024 0.001 PHE A 797 TRP 0.010 0.001 TRP A 127 HIS 0.003 0.001 HIS A1024 Details of bonding type rmsd covalent geometry : bond 0.00326 (12107) covalent geometry : angle 0.59049 (16869) hydrogen bonds : bond 0.03712 ( 444) hydrogen bonds : angle 4.60998 ( 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 114 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 PHE cc_start: 0.2866 (m-10) cc_final: 0.2575 (m-80) REVERT: A 552 ASP cc_start: 0.8541 (p0) cc_final: 0.8249 (p0) REVERT: A 632 TRP cc_start: 0.6942 (t-100) cc_final: 0.5922 (t-100) REVERT: A 706 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7710 (mt) REVERT: A 748 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.6868 (pttt) REVERT: A 812 GLU cc_start: 0.7358 (pp20) cc_final: 0.7047 (pt0) REVERT: A 886 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.5988 (mp0) REVERT: C 89 LYS cc_start: 0.7463 (tmtt) cc_final: 0.7112 (tmtt) outliers start: 27 outliers final: 18 residues processed: 107 average time/residue: 0.1347 time to fit residues: 20.1205 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 : 0.506 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 35 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 124 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4685 r_free = 0.4685 target = 0.180797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.135985 restraints weight = 18633.873| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 2.07 r_work: 0.3975 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3826 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12107 Z= 0.220 Angle : 0.648 9.085 16869 Z= 0.330 Chirality : 0.040 0.178 1944 Planarity : 0.005 0.053 1776 Dihedral : 19.323 109.013 3026 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.71 % Allowed : 18.31 % 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 aren not related in a simple way. whole: -0.98 (0.25), residues: 1153 helix: 0.64 (0.23), residues: 501 sheet: -2.18 (0.49), residues: 104 loop : -1.56 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 721 TYR 0.013 0.002 TYR A 11 PHE 0.025 0.002 PHE A 797 TRP 0.008 0.002 TRP C 46 HIS 0.005 0.001 HIS A1024 Details of bonding type rmsd covalent geometry : bond 0.00498 (12107) covalent geometry : angle 0.64759 (16869) hydrogen bonds : bond 0.04098 ( 444) hydrogen bonds : angle 4.75814 ( 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: 26 poor density : 86 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 706 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7786 (mt) REVERT: A 748 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.6879 (pttt) REVERT: A 812 GLU cc_start: 0.7540 (pp20) cc_final: 0.7202 (pt0) REVERT: A 886 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6058 (mp0) REVERT: C 89 LYS cc_start: 0.7558 (tmtt) cc_final: 0.7190 (tmtt) outliers start: 26 outliers final: 21 residues processed: 107 average time/residue: 0.1346 time to fit residues: 20.1133 Evaluate side-chains 105 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 48 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 21 optimal weight: 0.5980 chunk 109 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 71 optimal weight: 0.0770 chunk 93 optimal weight: 1.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4709 r_free = 0.4709 target = 0.182721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.144333 restraints weight = 18725.908| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.06 r_work: 0.4006 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12107 Z= 0.135 Angle : 0.592 9.653 16869 Z= 0.300 Chirality : 0.038 0.176 1944 Planarity : 0.004 0.055 1776 Dihedral : 19.278 108.108 3026 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.60 % Allowed : 19.15 % Favored : 78.25 % 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 aren not related in a simple way. whole: -0.85 (0.25), residues: 1153 helix: 0.76 (0.23), residues: 506 sheet: -2.33 (0.46), residues: 117 loop : -1.44 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 916 TYR 0.011 0.001 TYR C 41 PHE 0.028 0.001 PHE A 797 TRP 0.013 0.001 TRP A 127 HIS 0.005 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00298 (12107) covalent geometry : angle 0.59211 (16869) hydrogen bonds : bond 0.03707 ( 444) hydrogen bonds : angle 4.59305 ( 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 116 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 632 TRP cc_start: 0.6858 (t-100) cc_final: 0.6037 (t-100) REVERT: A 669 ASP cc_start: 0.7810 (t70) cc_final: 0.7182 (t70) REVERT: A 706 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7666 (mt) REVERT: A 748 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.6897 (pttt) REVERT: A 812 GLU cc_start: 0.7236 (pp20) cc_final: 0.6977 (pt0) REVERT: A 886 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.5758 (mp0) outliers start: 25 outliers final: 20 residues processed: 110 average time/residue: 0.1472 time to fit residues: 22.5797 Evaluate side-chains 102 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 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 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 31 optimal weight: 5.9990 chunk 92 optimal weight: 0.3980 chunk 69 optimal weight: 0.0070 chunk 124 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 73 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4719 r_free = 0.4719 target = 0.184074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.139048 restraints weight = 18737.503| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 2.11 r_work: 0.4032 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3885 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2800 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= 0.127 Angle : 0.585 9.586 16869 Z= 0.296 Chirality : 0.037 0.175 1944 Planarity : 0.004 0.055 1776 Dihedral : 19.193 107.564 3026 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.07 % Favored : 93.84 % Rotamer: Outliers : 2.29 % Allowed : 19.35 % 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 aren not related in a simple way. whole: -0.75 (0.25), residues: 1153 helix: 0.94 (0.23), residues: 500 sheet: -2.39 (0.46), residues: 115 loop : -1.44 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 916 TYR 0.011 0.001 TYR A 908 PHE 0.027 0.001 PHE A 797 TRP 0.011 0.001 TRP A 127 HIS 0.007 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00280 (12107) covalent geometry : angle 0.58456 (16869) hydrogen bonds : bond 0.03584 ( 444) hydrogen bonds : angle 4.55609 ( 1227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3732.59 seconds wall clock time: 64 minutes 40.39 seconds (3880.39 seconds total)