Starting phenix.real_space_refine on Tue Jun 10 16:45:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hj4_34832/06_2025/8hj4_34832.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hj4_34832/06_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_34832/06_2025/8hj4_34832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hj4_34832/06_2025/8hj4_34832.map" model { file = "/net/cci-nas-00/data/ceres_data/8hj4_34832/06_2025/8hj4_34832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hj4_34832/06_2025/8hj4_34832.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 5, 'GLU:plan': 8, 'ASN:plan1': 2, 'ARG:plan': 9, 'ASP:plan': 5} 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: 7.61, per 1000 atoms: 0.65 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: 2.82 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 4.29 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: 5.98 Time building geometry restraints manager: 3.38 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: 0.730 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 34.170 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.470 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (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 TRP 0.009 0.001 TRP A 127 HIS 0.004 0.001 HIS A1024 PHE 0.017 0.001 PHE A 797 TYR 0.009 0.001 TYR C 70 ARG 0.006 0.000 ARG A 638 Details of bonding type rmsd hydrogen bonds : bond 0.19664 ( 444) hydrogen bonds : angle 8.14703 ( 1227) covalent geometry : bond 0.00331 (12107) covalent geometry : angle 0.60039 (16869) *********************** 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 : 1.075 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: 0.6794 (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: 0.2814 time to fit residues: 44.2252 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 : 1.038 ------------------------------------------------------------------------------- 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 107 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 0.0980 chunk 32 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 38 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 422 GLN ** 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 = 0.4898 r_free = 0.4898 target = 0.195028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.155586 restraints weight = 18963.133| |-----------------------------------------------------------------------------| r_work (start): 0.4445 rms_B_bonded: 2.11 r_work: 0.4281 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.4148 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12107 Z= 0.130 Angle : 0.602 9.087 16869 Z= 0.307 Chirality : 0.039 0.224 1944 Planarity : 0.005 0.044 1776 Dihedral : 19.505 100.915 3029 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.07 % Favored : 93.84 % Rotamer: Outliers : 1.14 % Allowed : 8.32 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.25), residues: 1153 helix: 0.63 (0.24), residues: 501 sheet: -1.81 (0.51), residues: 104 loop : -1.25 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 127 HIS 0.004 0.001 HIS A 133 PHE 0.019 0.001 PHE C 124 TYR 0.011 0.001 TYR C 11 ARG 0.003 0.000 ARG A 721 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 444) hydrogen bonds : angle 5.13541 ( 1227) covalent geometry : bond 0.00276 (12107) covalent geometry : angle 0.60243 (16869) *********************** 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 106 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 748 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.6682 (pttt) REVERT: A 908 TYR cc_start: 0.7850 (m-80) cc_final: 0.7596 (m-80) REVERT: C 89 LYS cc_start: 0.7931 (tmtt) cc_final: 0.7214 (tmtt) outliers start: 11 outliers final: 6 residues processed: 102 average time/residue: 0.3058 time to fit residues: 43.6556 Evaluate side-chains 92 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR 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 1012 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 113 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 ** 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 = 0.4855 r_free = 0.4855 target = 0.191083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.145372 restraints weight = 19047.710| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 2.24 r_work: 0.4209 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.4068 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12107 Z= 0.210 Angle : 0.637 8.958 16869 Z= 0.326 Chirality : 0.041 0.178 1944 Planarity : 0.005 0.047 1776 Dihedral : 19.446 108.276 3026 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.94 % Favored : 92.97 % Rotamer: Outliers : 2.19 % Allowed : 13.01 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.25), residues: 1153 helix: 0.63 (0.23), residues: 488 sheet: -2.04 (0.50), residues: 104 loop : -1.35 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 46 HIS 0.004 0.001 HIS A1024 PHE 0.020 0.002 PHE C 124 TYR 0.019 0.002 TYR C 11 ARG 0.003 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.04465 ( 444) hydrogen bonds : angle 4.94793 ( 1227) covalent geometry : bond 0.00472 (12107) covalent geometry : angle 0.63743 (16869) *********************** 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 105 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 748 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.6638 (pttt) REVERT: C 89 LYS cc_start: 0.7823 (tmtt) cc_final: 0.7164 (tmtt) outliers start: 21 outliers final: 12 residues processed: 98 average time/residue: 0.2694 time to fit residues: 36.9455 Evaluate side-chains 88 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 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 748 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain C residue 101 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 15 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 62 optimal weight: 0.0270 chunk 80 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 99 optimal weight: 0.0170 chunk 35 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 121 optimal weight: 1.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- 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 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 = 0.4918 r_free = 0.4918 target = 0.197160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.158004 restraints weight = 19056.565| |-----------------------------------------------------------------------------| r_work (start): 0.4470 rms_B_bonded: 2.12 r_work: 0.4305 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.4173 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12107 Z= 0.110 Angle : 0.548 8.570 16869 Z= 0.282 Chirality : 0.038 0.193 1944 Planarity : 0.004 0.050 1776 Dihedral : 19.389 110.112 3026 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.94 % Favored : 94.97 % Rotamer: Outliers : 1.77 % Allowed : 14.78 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.25), residues: 1153 helix: 0.93 (0.24), residues: 496 sheet: -1.96 (0.50), residues: 107 loop : -1.30 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 127 HIS 0.003 0.001 HIS A 354 PHE 0.020 0.001 PHE C 124 TYR 0.015 0.001 TYR C 70 ARG 0.003 0.000 ARG A 522 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 444) hydrogen bonds : angle 4.61913 ( 1227) covalent geometry : bond 0.00227 (12107) covalent geometry : angle 0.54837 (16869) *********************** 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 107 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.7117 (OUTLIER) cc_final: 0.6339 (tp) REVERT: A 306 MET cc_start: 0.8252 (tmm) cc_final: 0.8027 (tmm) REVERT: A 632 TRP cc_start: 0.6964 (t-100) cc_final: 0.6011 (t-100) REVERT: A 706 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7661 (mt) REVERT: A 748 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.6687 (pttt) REVERT: A 812 GLU cc_start: 0.7370 (pp20) cc_final: 0.7021 (pt0) REVERT: C 50 LEU cc_start: 0.8334 (mt) cc_final: 0.8035 (mt) REVERT: C 89 LYS cc_start: 0.7607 (tmtt) cc_final: 0.7102 (tmtt) outliers start: 17 outliers final: 11 residues processed: 100 average time/residue: 0.4758 time to fit residues: 65.2662 Evaluate side-chains 92 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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 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 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 60 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 32 optimal weight: 40.0000 chunk 99 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 92 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 = 0.4679 r_free = 0.4679 target = 0.180285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.141113 restraints weight = 18353.849| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 2.03 r_work: 0.3968 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12107 Z= 0.198 Angle : 0.611 8.534 16869 Z= 0.313 Chirality : 0.040 0.184 1944 Planarity : 0.005 0.049 1776 Dihedral : 19.348 110.752 3026 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.39 % Allowed : 16.86 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.25), residues: 1153 helix: 0.78 (0.24), residues: 497 sheet: -1.81 (0.53), residues: 94 loop : -1.43 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 46 HIS 0.004 0.001 HIS A1024 PHE 0.019 0.002 PHE C 124 TYR 0.017 0.001 TYR C 11 ARG 0.005 0.000 ARG A1015 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 444) hydrogen bonds : angle 4.72522 ( 1227) covalent geometry : bond 0.00446 (12107) covalent geometry : angle 0.61111 (16869) *********************** 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 105 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7216 (mt) REVERT: A 306 MET cc_start: 0.8307 (tmm) cc_final: 0.8069 (tmm) REVERT: A 552 ASP cc_start: 0.8534 (p0) cc_final: 0.8132 (p0) REVERT: A 706 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7680 (mt) REVERT: A 748 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.6863 (pttt) REVERT: A 812 GLU cc_start: 0.7259 (pp20) cc_final: 0.7016 (pt0) REVERT: C 89 LYS cc_start: 0.7562 (tmtt) cc_final: 0.7174 (tmtt) outliers start: 23 outliers final: 14 residues processed: 100 average time/residue: 0.3194 time to fit residues: 45.1652 Evaluate side-chains 98 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 1.566 ------------------------------------------------------------------------------- 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 409 GLU Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain A residue 1027 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 77 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 71 optimal weight: 0.1980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.3980 chunk 78 optimal weight: 0.7980 overall best weight: 0.5582 ------------------------------------------------------------------------------- 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 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 = 0.4736 r_free = 0.4736 target = 0.185805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.141440 restraints weight = 18677.802| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 2.01 r_work: 0.4068 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3919 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12107 Z= 0.112 Angle : 0.550 8.423 16869 Z= 0.281 Chirality : 0.037 0.183 1944 Planarity : 0.004 0.052 1776 Dihedral : 19.337 109.878 3026 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.77 % Allowed : 17.17 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.25), residues: 1153 helix: 1.03 (0.24), residues: 497 sheet: -1.94 (0.50), residues: 106 loop : -1.31 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 127 HIS 0.003 0.001 HIS A 354 PHE 0.020 0.001 PHE C 124 TYR 0.017 0.001 TYR C 120 ARG 0.005 0.000 ARG A1015 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 444) hydrogen bonds : angle 4.53174 ( 1227) covalent geometry : bond 0.00237 (12107) covalent geometry : angle 0.54957 (16869) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 552 ASP cc_start: 0.8539 (p0) cc_final: 0.8141 (p0) REVERT: A 632 TRP cc_start: 0.6903 (t-100) cc_final: 0.5981 (t-100) REVERT: A 669 ASP cc_start: 0.7825 (t0) cc_final: 0.7481 (t70) REVERT: A 706 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7638 (mt) REVERT: A 748 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.6756 (pttt) REVERT: A 812 GLU cc_start: 0.7332 (pp20) cc_final: 0.7038 (pt0) REVERT: A 1038 ASP cc_start: 0.8237 (t0) cc_final: 0.7979 (t0) REVERT: C 87 LEU cc_start: 0.8427 (tt) cc_final: 0.7499 (mt) REVERT: C 89 LYS cc_start: 0.7453 (tmtt) cc_final: 0.7100 (tmtt) outliers start: 17 outliers final: 10 residues processed: 107 average time/residue: 0.3843 time to fit residues: 61.3133 Evaluate side-chains 101 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR 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 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 29 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 102 optimal weight: 0.4980 chunk 14 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 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 = 0.4691 r_free = 0.4691 target = 0.181591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.135814 restraints weight = 18678.352| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 2.10 r_work: 0.3991 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3837 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12107 Z= 0.185 Angle : 0.619 11.507 16869 Z= 0.316 Chirality : 0.039 0.185 1944 Planarity : 0.004 0.050 1776 Dihedral : 19.302 109.568 3026 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.29 % Allowed : 18.00 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.25), residues: 1153 helix: 0.87 (0.24), residues: 495 sheet: -2.07 (0.49), residues: 107 loop : -1.37 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 46 HIS 0.004 0.001 HIS A1024 PHE 0.023 0.002 PHE A 185 TYR 0.015 0.001 TYR C 120 ARG 0.004 0.000 ARG A1015 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 444) hydrogen bonds : angle 4.65849 ( 1227) covalent geometry : bond 0.00416 (12107) covalent geometry : angle 0.61861 (16869) *********************** 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 109 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 552 ASP cc_start: 0.8598 (p0) cc_final: 0.8181 (p0) REVERT: A 706 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7727 (mt) REVERT: A 748 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.6820 (pttt) REVERT: A 812 GLU cc_start: 0.7315 (pp20) cc_final: 0.6966 (pt0) REVERT: A 886 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.6050 (mp0) REVERT: A 908 TYR cc_start: 0.7840 (m-80) cc_final: 0.7091 (m-80) REVERT: A 1038 ASP cc_start: 0.8353 (t0) cc_final: 0.8096 (t0) REVERT: C 89 LYS cc_start: 0.7547 (tmtt) cc_final: 0.7102 (tmtt) outliers start: 22 outliers final: 16 residues processed: 103 average time/residue: 0.2839 time to fit residues: 40.8569 Evaluate side-chains 102 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 886 GLU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain A residue 1016 MET Chi-restraints excluded: chain A residue 1027 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 4 optimal weight: 0.7980 chunk 39 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 17 optimal weight: 0.0010 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- 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 ** 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 = 0.4711 r_free = 0.4711 target = 0.183416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.139088 restraints weight = 18673.254| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 2.25 r_work: 0.4004 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12107 Z= 0.145 Angle : 0.583 10.567 16869 Z= 0.298 Chirality : 0.038 0.178 1944 Planarity : 0.004 0.054 1776 Dihedral : 19.287 108.599 3026 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.19 % Allowed : 18.00 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1153 helix: 0.92 (0.24), residues: 496 sheet: -2.03 (0.49), residues: 107 loop : -1.34 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 24 HIS 0.003 0.001 HIS A1024 PHE 0.023 0.001 PHE C 124 TYR 0.015 0.001 TYR C 120 ARG 0.003 0.000 ARG A 916 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 444) hydrogen bonds : angle 4.58117 ( 1227) covalent geometry : bond 0.00322 (12107) covalent geometry : angle 0.58317 (16869) *********************** 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 107 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 MET cc_start: 0.5178 (mmp) cc_final: 0.4960 (mmp) REVERT: A 552 ASP cc_start: 0.8602 (p0) cc_final: 0.8211 (p0) REVERT: A 632 TRP cc_start: 0.6865 (t-100) cc_final: 0.5966 (t-100) REVERT: A 706 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7622 (mt) REVERT: A 748 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.6831 (pttt) REVERT: A 812 GLU cc_start: 0.7180 (pp20) cc_final: 0.6910 (pt0) REVERT: A 886 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.5733 (mp0) REVERT: A 1038 ASP cc_start: 0.8282 (t0) cc_final: 0.8054 (t0) REVERT: C 89 LYS cc_start: 0.7341 (tmtt) cc_final: 0.7030 (tmtt) outliers start: 21 outliers final: 14 residues processed: 102 average time/residue: 0.2911 time to fit residues: 41.9830 Evaluate side-chains 102 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 9 optimal weight: 0.3980 chunk 124 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 = 0.4671 r_free = 0.4671 target = 0.179682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.134772 restraints weight = 18677.191| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 2.02 r_work: 0.3972 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12107 Z= 0.229 Angle : 0.657 10.070 16869 Z= 0.335 Chirality : 0.041 0.177 1944 Planarity : 0.005 0.051 1776 Dihedral : 19.302 108.537 3026 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.19 % Allowed : 18.42 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.25), residues: 1153 helix: 0.66 (0.23), residues: 501 sheet: -2.21 (0.49), residues: 107 loop : -1.45 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 24 HIS 0.006 0.001 HIS A1024 PHE 0.019 0.002 PHE C 124 TYR 0.015 0.002 TYR C 120 ARG 0.005 0.000 ARG A1015 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 444) hydrogen bonds : angle 4.73313 ( 1227) covalent geometry : bond 0.00516 (12107) covalent geometry : angle 0.65683 (16869) *********************** 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 106 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 MET cc_start: 0.5286 (mmp) cc_final: 0.5038 (mmp) REVERT: A 552 ASP cc_start: 0.8530 (p0) cc_final: 0.8118 (p0) REVERT: A 706 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7759 (mt) REVERT: A 748 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.6867 (pttt) REVERT: A 812 GLU cc_start: 0.7483 (pp20) cc_final: 0.7046 (pt0) REVERT: A 886 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6071 (mp0) REVERT: C 89 LYS cc_start: 0.7398 (tmtt) cc_final: 0.7020 (tmtt) outliers start: 21 outliers final: 16 residues processed: 100 average time/residue: 0.2634 time to fit residues: 36.8992 Evaluate side-chains 102 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 594 ARG 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 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 113 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4715 r_free = 0.4715 target = 0.183756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.138880 restraints weight = 18491.243| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 2.08 r_work: 0.4041 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3901 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2688 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= 0.124 Angle : 0.577 10.215 16869 Z= 0.295 Chirality : 0.037 0.175 1944 Planarity : 0.004 0.055 1776 Dihedral : 19.230 107.533 3026 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.87 % Allowed : 19.04 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.25), residues: 1153 helix: 0.89 (0.23), residues: 500 sheet: -2.02 (0.49), residues: 107 loop : -1.34 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 127 HIS 0.002 0.001 HIS A 354 PHE 0.025 0.001 PHE C 124 TYR 0.017 0.001 TYR C 120 ARG 0.005 0.000 ARG A1015 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 444) hydrogen bonds : angle 4.55727 ( 1227) covalent geometry : bond 0.00266 (12107) covalent geometry : angle 0.57706 (16869) ********************** 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 108 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 PHE cc_start: 0.2728 (m-10) cc_final: 0.2404 (m-80) REVERT: A 552 ASP cc_start: 0.8558 (p0) cc_final: 0.8167 (p0) REVERT: A 632 TRP cc_start: 0.6873 (t-100) cc_final: 0.6045 (t-100) REVERT: A 706 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7704 (mt) REVERT: A 748 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.6916 (pttt) REVERT: A 812 GLU cc_start: 0.7359 (pp20) cc_final: 0.7035 (pt0) REVERT: C 89 LYS cc_start: 0.7447 (tmtt) cc_final: 0.7084 (tmtt) outliers start: 18 outliers final: 15 residues processed: 102 average time/residue: 0.2901 time to fit residues: 41.2419 Evaluate side-chains 103 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 594 ARG 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 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 19 optimal weight: 6.9990 chunk 35 optimal weight: 0.0770 chunk 8 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 chunk 104 optimal weight: 4.9990 chunk 4 optimal weight: 0.4980 chunk 114 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 overall best weight: 1.3742 ------------------------------------------------------------------------------- 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 = 0.4699 r_free = 0.4699 target = 0.182264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.137248 restraints weight = 18593.785| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 2.04 r_work: 0.4011 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3869 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12107 Z= 0.163 Angle : 0.608 9.786 16869 Z= 0.309 Chirality : 0.038 0.174 1944 Planarity : 0.004 0.052 1776 Dihedral : 19.147 107.370 3026 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.98 % Allowed : 18.94 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.25), residues: 1153 helix: 0.86 (0.23), residues: 500 sheet: -2.05 (0.49), residues: 107 loop : -1.39 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 46 HIS 0.004 0.001 HIS A1024 PHE 0.025 0.002 PHE C 124 TYR 0.017 0.001 TYR C 120 ARG 0.004 0.000 ARG A1015 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 444) hydrogen bonds : angle 4.60177 ( 1227) covalent geometry : bond 0.00366 (12107) covalent geometry : angle 0.60764 (16869) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8574.32 seconds wall clock time: 151 minutes 41.14 seconds (9101.14 seconds total)