Starting phenix.real_space_refine on Fri Aug 22 20:32:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywg_39632/08_2025/8ywg_39632.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywg_39632/08_2025/8ywg_39632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ywg_39632/08_2025/8ywg_39632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywg_39632/08_2025/8ywg_39632.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ywg_39632/08_2025/8ywg_39632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywg_39632/08_2025/8ywg_39632.map" } resolution = 3.28 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= 0.001 sd= 0.028 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: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 4946 2.51 5 N 1291 2.21 5 O 1421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 7707 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 7707 Classifications: {'peptide': 963} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 919} Chain breaks: 2 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 4, 'ASP:plan': 4, 'GLN:plan1': 3, 'TRP:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 101 Time building chain proxies: 1.94, per 1000 atoms: 0.25 Number of scatterers: 7707 At special positions: 0 Unit cell: (79.35, 111.78, 111.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 1421 8.00 N 1291 7.00 C 4946 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: 0.53 Conformation dependent library (CDL) restraints added in 346.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1842 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 7 sheets defined 48.4% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 6 through 15 Processing helix chain 'A' and resid 15 through 27 Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 128 through 143 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 271 through 287 Processing helix chain 'A' and resid 300 through 312 Processing helix chain 'A' and resid 313 through 322 Processing helix chain 'A' and resid 328 through 335 Processing helix chain 'A' and resid 365 through 374 Processing helix chain 'A' and resid 381 through 390 Processing helix chain 'A' and resid 398 through 409 removed outlier: 3.510A pdb=" N MET A 402 " --> pdb=" O PRO A 398 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 436 removed outlier: 3.626A pdb=" N ILE A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N CYS A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 449 removed outlier: 3.938A pdb=" N ASP A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 458 Processing helix chain 'A' and resid 460 through 474 removed outlier: 3.746A pdb=" N HIS A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 530 Processing helix chain 'A' and resid 532 through 534 No H-bonds generated for 'chain 'A' and resid 532 through 534' Processing helix chain 'A' and resid 539 through 550 Processing helix chain 'A' and resid 580 through 608 Processing helix chain 'A' and resid 616 through 646 removed outlier: 3.796A pdb=" N LEU A 620 " --> pdb=" O GLY A 616 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N TYR A 642 " --> pdb=" O MET A 638 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY A 643 " --> pdb=" O ASN A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 679 removed outlier: 3.517A pdb=" N ALA A 658 " --> pdb=" O LEU A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 699 removed outlier: 3.634A pdb=" N LEU A 699 " --> pdb=" O PRO A 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 696 through 699' Processing helix chain 'A' and resid 700 through 709 removed outlier: 3.612A pdb=" N ALA A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR A 707 " --> pdb=" O VAL A 703 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 708 " --> pdb=" O THR A 704 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 709 " --> pdb=" O ASP A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 748 removed outlier: 3.619A pdb=" N THR A 734 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 816 removed outlier: 3.722A pdb=" N THR A 805 " --> pdb=" O LYS A 801 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 816 " --> pdb=" O GLU A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 840 Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 864 through 878 removed outlier: 3.773A pdb=" N PHE A 868 " --> pdb=" O ALA A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 957 removed outlier: 4.052A pdb=" N TYR A 943 " --> pdb=" O ASP A 939 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LEU A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N GLY A 950 " --> pdb=" O ASN A 946 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 951 " --> pdb=" O TYR A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 963 removed outlier: 3.592A pdb=" N PHE A 962 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 991 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 180 removed outlier: 7.373A pdb=" N LYS A 60 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N PHE A 186 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU A 62 " --> pdb=" O PHE A 186 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL A 188 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG A 64 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N PHE A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ILE A 39 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TYR A 52 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 105 removed outlier: 3.572A pdb=" N ALA A 147 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 268 removed outlier: 7.190A pdb=" N SER A 250 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N ILE A 267 " --> pdb=" O SER A 250 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N CYS A 252 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 249 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL A 232 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N TYR A 215 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 344 removed outlier: 5.383A pdb=" N LYS A 339 " --> pdb=" O PHE A 355 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N PHE A 355 " --> pdb=" O LYS A 339 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 508 Processing sheet with id=AA6, first strand: chain 'A' and resid 682 through 687 removed outlier: 6.163A pdb=" N ILE A 683 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR A 694 " --> pdb=" O ILE A 683 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N THR A 513 " --> pdb=" O VAL A 759 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL A 759 " --> pdb=" O THR A 513 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N GLY A 515 " --> pdb=" O GLU A 757 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU A 757 " --> pdb=" O GLY A 515 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 536 through 537 398 hydrogen bonds defined for protein. 1146 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 0.72 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: 2474 1.34 - 1.46: 1587 1.46 - 1.58: 3753 1.58 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 7892 Sorted by residual: bond pdb=" N ARG A 185 " pdb=" CA ARG A 185 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.25e-02 6.40e+03 5.49e+00 bond pdb=" N LYS A 60 " pdb=" CA LYS A 60 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.33e-02 5.65e+03 4.68e+00 bond pdb=" N PHE A 78 " pdb=" CA PHE A 78 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.50e-02 4.44e+03 3.69e+00 bond pdb=" CA ILE A 956 " pdb=" C ILE A 956 " ideal model delta sigma weight residual 1.520 1.535 -0.015 1.23e-02 6.61e+03 1.53e+00 bond pdb=" C LYS A 60 " pdb=" O LYS A 60 " ideal model delta sigma weight residual 1.234 1.247 -0.013 1.22e-02 6.72e+03 1.12e+00 ... (remaining 7887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 10290 1.56 - 3.13: 338 3.13 - 4.69: 48 4.69 - 6.26: 13 6.26 - 7.82: 5 Bond angle restraints: 10694 Sorted by residual: angle pdb=" N PHE A 78 " pdb=" CA PHE A 78 " pdb=" C PHE A 78 " ideal model delta sigma weight residual 114.39 108.47 5.92 1.45e+00 4.76e-01 1.67e+01 angle pdb=" C ASN A 141 " pdb=" N MET A 142 " pdb=" CA MET A 142 " ideal model delta sigma weight residual 121.58 116.31 5.27 1.95e+00 2.63e-01 7.32e+00 angle pdb=" CA TYR A 974 " pdb=" CB TYR A 974 " pdb=" CG TYR A 974 " ideal model delta sigma weight residual 113.90 118.70 -4.80 1.80e+00 3.09e-01 7.11e+00 angle pdb=" CB MET A 402 " pdb=" CG MET A 402 " pdb=" SD MET A 402 " ideal model delta sigma weight residual 112.70 120.35 -7.65 3.00e+00 1.11e-01 6.51e+00 angle pdb=" CA LYS A 60 " pdb=" C LYS A 60 " pdb=" O LYS A 60 " ideal model delta sigma weight residual 120.92 118.11 2.81 1.15e+00 7.56e-01 5.99e+00 ... (remaining 10689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4277 17.76 - 35.51: 375 35.51 - 53.27: 80 53.27 - 71.02: 12 71.02 - 88.78: 7 Dihedral angle restraints: 4751 sinusoidal: 1893 harmonic: 2858 Sorted by residual: dihedral pdb=" CA GLN A 844 " pdb=" C GLN A 844 " pdb=" N TRP A 845 " pdb=" CA TRP A 845 " ideal model delta harmonic sigma weight residual 180.00 161.06 18.94 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA GLU A 757 " pdb=" C GLU A 757 " pdb=" N GLU A 758 " pdb=" CA GLU A 758 " ideal model delta harmonic sigma weight residual -180.00 -163.54 -16.46 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CB GLU A 599 " pdb=" CG GLU A 599 " pdb=" CD GLU A 599 " pdb=" OE1 GLU A 599 " ideal model delta sinusoidal sigma weight residual 0.00 -88.78 88.78 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 4748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 767 0.034 - 0.067: 274 0.067 - 0.101: 91 0.101 - 0.134: 39 0.134 - 0.168: 3 Chirality restraints: 1174 Sorted by residual: chirality pdb=" CA ILE A 789 " pdb=" N ILE A 789 " pdb=" C ILE A 789 " pdb=" CB ILE A 789 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" CA MET A 402 " pdb=" N MET A 402 " pdb=" C MET A 402 " pdb=" CB MET A 402 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ARG A 978 " pdb=" N ARG A 978 " pdb=" C ARG A 978 " pdb=" CB ARG A 978 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 1171 not shown) Planarity restraints: 1369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 164 " 0.056 5.00e-02 4.00e+02 8.57e-02 1.17e+01 pdb=" N PRO A 165 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 403 " 0.019 2.00e-02 2.50e+03 1.86e-02 8.62e+00 pdb=" CG TRP A 403 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 403 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 403 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 403 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 403 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 403 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 403 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 403 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 403 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 77 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C GLU A 77 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU A 77 " -0.016 2.00e-02 2.50e+03 pdb=" N PHE A 78 " -0.014 2.00e-02 2.50e+03 ... (remaining 1366 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1638 2.78 - 3.31: 7183 3.31 - 3.84: 11861 3.84 - 4.37: 12641 4.37 - 4.90: 22758 Nonbonded interactions: 56081 Sorted by model distance: nonbonded pdb=" O SER A 244 " pdb=" NE2 GLN A 429 " model vdw 2.255 3.120 nonbonded pdb=" OG1 THR A 146 " pdb=" OD2 ASP A 149 " model vdw 2.315 3.040 nonbonded pdb=" OG SER A 270 " pdb=" OD1 ASN A 274 " model vdw 2.324 3.040 nonbonded pdb=" O TYR A 700 " pdb=" OG1 THR A 704 " model vdw 2.345 3.040 nonbonded pdb=" O ASP A 510 " pdb=" NZ LYS A 724 " model vdw 2.350 3.120 ... (remaining 56076 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.360 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 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 0.043 7892 Z= 0.157 Angle : 0.663 7.822 10694 Z= 0.364 Chirality : 0.042 0.168 1174 Planarity : 0.005 0.086 1369 Dihedral : 14.300 88.778 2909 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.70 % Favored : 95.19 % Rotamer: Outliers : 0.24 % Allowed : 0.48 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.59 (0.28), residues: 957 helix: 1.95 (0.26), residues: 424 sheet: 0.35 (0.46), residues: 140 loop : -1.40 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 819 TYR 0.029 0.001 TYR A 974 PHE 0.019 0.001 PHE A 986 TRP 0.050 0.003 TRP A 403 HIS 0.005 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7892) covalent geometry : angle 0.66272 (10694) hydrogen bonds : bond 0.13830 ( 398) hydrogen bonds : angle 5.13522 ( 1146) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 230 time to evaluate : 0.300 Fit side-chains REVERT: A 9 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7526 (mp0) REVERT: A 20 GLN cc_start: 0.7978 (tp-100) cc_final: 0.7573 (tp-100) REVERT: A 39 ILE cc_start: 0.8526 (mp) cc_final: 0.8324 (mt) REVERT: A 163 LYS cc_start: 0.8297 (mttm) cc_final: 0.8037 (mttp) REVERT: A 212 ILE cc_start: 0.8121 (tt) cc_final: 0.7441 (tt) REVERT: A 213 GLU cc_start: 0.6533 (mm-30) cc_final: 0.6205 (mm-30) REVERT: A 251 THR cc_start: 0.7685 (m) cc_final: 0.7266 (m) REVERT: A 255 MET cc_start: 0.7555 (tpp) cc_final: 0.7328 (tpt) REVERT: A 272 GLU cc_start: 0.7306 (tp30) cc_final: 0.6716 (tp30) REVERT: A 339 LYS cc_start: 0.8365 (ptpp) cc_final: 0.8061 (ptpp) REVERT: A 344 LYS cc_start: 0.8230 (ttmm) cc_final: 0.8013 (ttmm) REVERT: A 402 MET cc_start: 0.7298 (mpp) cc_final: 0.6968 (mpp) REVERT: A 598 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7981 (tm-30) REVERT: A 632 LYS cc_start: 0.8419 (ttmt) cc_final: 0.8201 (ttmt) REVERT: A 703 VAL cc_start: 0.8852 (p) cc_final: 0.8557 (p) REVERT: A 728 SER cc_start: 0.8199 (t) cc_final: 0.7917 (m) REVERT: A 730 LYS cc_start: 0.8628 (tppt) cc_final: 0.8360 (ttmm) REVERT: A 749 THR cc_start: 0.7750 (p) cc_final: 0.7509 (t) REVERT: A 805 THR cc_start: 0.7610 (p) cc_final: 0.7370 (t) REVERT: A 816 LYS cc_start: 0.8199 (tttt) cc_final: 0.7989 (ttpp) REVERT: A 836 LYS cc_start: 0.8474 (pptt) cc_final: 0.8249 (pptt) REVERT: A 869 MET cc_start: 0.7330 (tpp) cc_final: 0.6850 (tpp) REVERT: A 941 LEU cc_start: 0.8800 (mt) cc_final: 0.8586 (mt) outliers start: 2 outliers final: 0 residues processed: 232 average time/residue: 0.1015 time to fit residues: 30.9597 Evaluate side-chains 206 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 140 ASN A 282 GLN ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.142201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.112904 restraints weight = 12770.906| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 3.07 r_work: 0.3286 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7892 Z= 0.255 Angle : 0.658 7.476 10694 Z= 0.347 Chirality : 0.045 0.159 1174 Planarity : 0.005 0.061 1369 Dihedral : 4.311 18.004 1057 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.43 % Favored : 94.46 % Rotamer: Outliers : 1.69 % Allowed : 11.20 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.50 (0.27), residues: 957 helix: 1.85 (0.25), residues: 430 sheet: 0.44 (0.45), residues: 141 loop : -1.53 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 285 TYR 0.020 0.002 TYR A 138 PHE 0.024 0.002 PHE A 675 TRP 0.028 0.002 TRP A 403 HIS 0.009 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00588 ( 7892) covalent geometry : angle 0.65816 (10694) hydrogen bonds : bond 0.07136 ( 398) hydrogen bonds : angle 4.52953 ( 1146) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 225 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7938 (mp0) REVERT: A 20 GLN cc_start: 0.8400 (tp-100) cc_final: 0.8022 (tp-100) REVERT: A 39 ILE cc_start: 0.8651 (mp) cc_final: 0.8446 (mt) REVERT: A 114 LYS cc_start: 0.8404 (tppt) cc_final: 0.8199 (tppt) REVERT: A 163 LYS cc_start: 0.8468 (mttm) cc_final: 0.8231 (mttp) REVERT: A 182 LEU cc_start: 0.8704 (tp) cc_final: 0.8414 (tt) REVERT: A 192 ASP cc_start: 0.8260 (m-30) cc_final: 0.8058 (m-30) REVERT: A 255 MET cc_start: 0.7625 (tpp) cc_final: 0.7372 (tpt) REVERT: A 272 GLU cc_start: 0.7790 (tp30) cc_final: 0.7122 (tp30) REVERT: A 303 PHE cc_start: 0.8627 (t80) cc_final: 0.8274 (t80) REVERT: A 304 ILE cc_start: 0.8630 (tt) cc_final: 0.8423 (tt) REVERT: A 369 MET cc_start: 0.8023 (mmm) cc_final: 0.7742 (mmp) REVERT: A 402 MET cc_start: 0.7577 (mpp) cc_final: 0.7124 (mpp) REVERT: A 477 TYR cc_start: 0.8908 (m-80) cc_final: 0.8682 (m-80) REVERT: A 598 GLN cc_start: 0.8380 (tm-30) cc_final: 0.8130 (tm-30) REVERT: A 704 THR cc_start: 0.8508 (m) cc_final: 0.8234 (p) REVERT: A 723 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7829 (mm-30) REVERT: A 728 SER cc_start: 0.8451 (t) cc_final: 0.8079 (p) REVERT: A 730 LYS cc_start: 0.8861 (tppt) cc_final: 0.8591 (ttmm) REVERT: A 836 LYS cc_start: 0.8735 (pptt) cc_final: 0.8493 (pptt) REVERT: A 957 ASN cc_start: 0.8383 (p0) cc_final: 0.8104 (p0) REVERT: A 976 GLN cc_start: 0.8078 (tp40) cc_final: 0.7876 (tp40) outliers start: 14 outliers final: 11 residues processed: 227 average time/residue: 0.1079 time to fit residues: 32.0310 Evaluate side-chains 222 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 211 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 722 HIS Chi-restraints excluded: chain A residue 768 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN A 319 ASN A 400 HIS ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.143937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.114697 restraints weight = 12690.682| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.08 r_work: 0.3325 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7892 Z= 0.153 Angle : 0.587 7.743 10694 Z= 0.301 Chirality : 0.043 0.146 1174 Planarity : 0.004 0.047 1369 Dihedral : 4.083 16.716 1057 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.64 % Favored : 94.25 % Rotamer: Outliers : 3.01 % Allowed : 15.42 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.61 (0.27), residues: 957 helix: 2.00 (0.25), residues: 430 sheet: 0.60 (0.46), residues: 135 loop : -1.58 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 285 TYR 0.014 0.001 TYR A 667 PHE 0.016 0.002 PHE A 85 TRP 0.013 0.001 TRP A 403 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 7892) covalent geometry : angle 0.58653 (10694) hydrogen bonds : bond 0.05721 ( 398) hydrogen bonds : angle 4.29968 ( 1146) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 219 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7883 (mp0) REVERT: A 20 GLN cc_start: 0.8358 (tp-100) cc_final: 0.7856 (tp-100) REVERT: A 22 VAL cc_start: 0.8732 (t) cc_final: 0.8507 (t) REVERT: A 24 ASN cc_start: 0.8280 (m110) cc_final: 0.7961 (m-40) REVERT: A 39 ILE cc_start: 0.8662 (mp) cc_final: 0.8458 (mt) REVERT: A 114 LYS cc_start: 0.8398 (tppt) cc_final: 0.8139 (tppt) REVERT: A 115 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8136 (tp30) REVERT: A 163 LYS cc_start: 0.8443 (mttm) cc_final: 0.8205 (mttp) REVERT: A 182 LEU cc_start: 0.8687 (tp) cc_final: 0.8384 (tt) REVERT: A 255 MET cc_start: 0.7509 (tpp) cc_final: 0.7222 (tpp) REVERT: A 303 PHE cc_start: 0.8596 (t80) cc_final: 0.8163 (t80) REVERT: A 304 ILE cc_start: 0.8604 (tt) cc_final: 0.8398 (tt) REVERT: A 369 MET cc_start: 0.8056 (mmm) cc_final: 0.7802 (mmp) REVERT: A 402 MET cc_start: 0.7544 (mpp) cc_final: 0.7098 (mpp) REVERT: A 458 TYR cc_start: 0.8141 (m-10) cc_final: 0.7916 (m-10) REVERT: A 598 GLN cc_start: 0.8381 (tm-30) cc_final: 0.8124 (tm-30) REVERT: A 702 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7675 (tm-30) REVERT: A 704 THR cc_start: 0.8503 (m) cc_final: 0.8236 (p) REVERT: A 728 SER cc_start: 0.8346 (t) cc_final: 0.7973 (p) REVERT: A 730 LYS cc_start: 0.8835 (tppt) cc_final: 0.8570 (ttmm) REVERT: A 836 LYS cc_start: 0.8760 (pptt) cc_final: 0.8490 (pptt) REVERT: A 956 ILE cc_start: 0.8965 (tp) cc_final: 0.8756 (tp) outliers start: 25 outliers final: 17 residues processed: 226 average time/residue: 0.1088 time to fit residues: 32.2371 Evaluate side-chains 229 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 212 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 517 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 722 HIS Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 805 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 12 optimal weight: 0.7980 chunk 52 optimal weight: 0.3980 chunk 38 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 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 319 ASN ** A 509 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 = 0.3890 r_free = 0.3890 target = 0.144914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.115738 restraints weight = 12866.128| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.11 r_work: 0.3331 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7892 Z= 0.135 Angle : 0.574 7.896 10694 Z= 0.293 Chirality : 0.042 0.170 1174 Planarity : 0.004 0.046 1369 Dihedral : 3.992 16.695 1057 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.77 % Allowed : 18.67 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.68 (0.27), residues: 957 helix: 2.05 (0.25), residues: 430 sheet: 0.66 (0.46), residues: 135 loop : -1.52 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 185 TYR 0.013 0.001 TYR A 667 PHE 0.018 0.002 PHE A 71 TRP 0.010 0.001 TRP A 845 HIS 0.004 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 7892) covalent geometry : angle 0.57447 (10694) hydrogen bonds : bond 0.05278 ( 398) hydrogen bonds : angle 4.21826 ( 1146) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 218 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 20 GLN cc_start: 0.8363 (tp-100) cc_final: 0.7831 (tp-100) REVERT: A 22 VAL cc_start: 0.8713 (t) cc_final: 0.8475 (t) REVERT: A 24 ASN cc_start: 0.8276 (m110) cc_final: 0.7917 (m-40) REVERT: A 39 ILE cc_start: 0.8674 (mp) cc_final: 0.8411 (mm) REVERT: A 41 GLU cc_start: 0.8153 (pt0) cc_final: 0.7758 (pt0) REVERT: A 93 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8414 (mt-10) REVERT: A 114 LYS cc_start: 0.8368 (tppt) cc_final: 0.8117 (tppt) REVERT: A 142 MET cc_start: 0.8635 (tpp) cc_final: 0.7981 (mtt) REVERT: A 161 GLU cc_start: 0.8570 (tp30) cc_final: 0.8141 (tp30) REVERT: A 163 LYS cc_start: 0.8452 (mttm) cc_final: 0.8206 (mttp) REVERT: A 182 LEU cc_start: 0.8699 (tp) cc_final: 0.8411 (tt) REVERT: A 255 MET cc_start: 0.7481 (tpp) cc_final: 0.7210 (tpp) REVERT: A 281 GLU cc_start: 0.8223 (tp30) cc_final: 0.7576 (tp30) REVERT: A 303 PHE cc_start: 0.8544 (t80) cc_final: 0.8088 (t80) REVERT: A 320 LYS cc_start: 0.8910 (mmtp) cc_final: 0.8442 (tptm) REVERT: A 402 MET cc_start: 0.7586 (mpp) cc_final: 0.7100 (mpp) REVERT: A 443 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7760 (mm-30) REVERT: A 598 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8091 (tm-30) REVERT: A 635 LYS cc_start: 0.8492 (ttmt) cc_final: 0.8125 (ttmt) REVERT: A 702 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7608 (tm-30) REVERT: A 704 THR cc_start: 0.8500 (m) cc_final: 0.8226 (p) REVERT: A 728 SER cc_start: 0.8285 (t) cc_final: 0.7980 (m) REVERT: A 730 LYS cc_start: 0.8810 (tppt) cc_final: 0.8542 (ttmm) REVERT: A 741 GLU cc_start: 0.8494 (tp30) cc_final: 0.8177 (tp30) REVERT: A 749 THR cc_start: 0.8320 (t) cc_final: 0.8107 (p) REVERT: A 816 LYS cc_start: 0.8231 (ttpp) cc_final: 0.8029 (ttpp) REVERT: A 836 LYS cc_start: 0.8785 (pptt) cc_final: 0.8502 (pptt) REVERT: A 956 ILE cc_start: 0.8927 (tp) cc_final: 0.8717 (tp) outliers start: 23 outliers final: 21 residues processed: 224 average time/residue: 0.1119 time to fit residues: 32.5401 Evaluate side-chains 240 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 517 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 722 HIS Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 805 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 25 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN A 319 ASN ** A 509 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 = 0.3856 r_free = 0.3856 target = 0.142551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113654 restraints weight = 12778.329| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.18 r_work: 0.3288 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7892 Z= 0.172 Angle : 0.596 7.582 10694 Z= 0.307 Chirality : 0.043 0.177 1174 Planarity : 0.004 0.044 1369 Dihedral : 4.062 16.209 1057 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.49 % Allowed : 19.16 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.68 (0.27), residues: 957 helix: 2.03 (0.25), residues: 430 sheet: 0.60 (0.46), residues: 141 loop : -1.51 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 593 TYR 0.014 0.001 TYR A 667 PHE 0.017 0.002 PHE A 71 TRP 0.010 0.001 TRP A 845 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 7892) covalent geometry : angle 0.59630 (10694) hydrogen bonds : bond 0.05925 ( 398) hydrogen bonds : angle 4.29370 ( 1146) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 230 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 20 GLN cc_start: 0.8384 (tp-100) cc_final: 0.7843 (tp-100) REVERT: A 22 VAL cc_start: 0.8712 (t) cc_final: 0.8506 (t) REVERT: A 24 ASN cc_start: 0.8316 (m110) cc_final: 0.7951 (m-40) REVERT: A 39 ILE cc_start: 0.8656 (mp) cc_final: 0.8392 (mm) REVERT: A 41 GLU cc_start: 0.8234 (pt0) cc_final: 0.7833 (pt0) REVERT: A 114 LYS cc_start: 0.8422 (tppt) cc_final: 0.8148 (tppt) REVERT: A 142 MET cc_start: 0.8694 (tpp) cc_final: 0.8360 (ttm) REVERT: A 161 GLU cc_start: 0.8642 (tp30) cc_final: 0.8168 (tp30) REVERT: A 163 LYS cc_start: 0.8495 (mttm) cc_final: 0.8228 (mttp) REVERT: A 182 LEU cc_start: 0.8760 (tp) cc_final: 0.8453 (tt) REVERT: A 237 MET cc_start: 0.8317 (mtt) cc_final: 0.7964 (mtp) REVERT: A 251 THR cc_start: 0.7903 (m) cc_final: 0.7652 (m) REVERT: A 255 MET cc_start: 0.7499 (tpp) cc_final: 0.7205 (tpp) REVERT: A 281 GLU cc_start: 0.8251 (tp30) cc_final: 0.7604 (tp30) REVERT: A 303 PHE cc_start: 0.8623 (t80) cc_final: 0.8179 (t80) REVERT: A 320 LYS cc_start: 0.8932 (mmtp) cc_final: 0.8444 (tptm) REVERT: A 402 MET cc_start: 0.7669 (mpp) cc_final: 0.7152 (mpp) REVERT: A 443 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7604 (mm-30) REVERT: A 542 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: A 598 GLN cc_start: 0.8381 (tm-30) cc_final: 0.8091 (tm-30) REVERT: A 635 LYS cc_start: 0.8426 (ttmt) cc_final: 0.8039 (ttmt) REVERT: A 678 ASN cc_start: 0.8785 (t0) cc_final: 0.8482 (t0) REVERT: A 702 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7711 (tm-30) REVERT: A 704 THR cc_start: 0.8528 (m) cc_final: 0.8211 (p) REVERT: A 705 ASP cc_start: 0.7572 (m-30) cc_final: 0.7360 (m-30) REVERT: A 728 SER cc_start: 0.8375 (t) cc_final: 0.8046 (m) REVERT: A 730 LYS cc_start: 0.8868 (tppt) cc_final: 0.8599 (ttmm) REVERT: A 741 GLU cc_start: 0.8482 (tp30) cc_final: 0.8158 (tp30) REVERT: A 816 LYS cc_start: 0.8261 (ttpp) cc_final: 0.8058 (ttpp) REVERT: A 836 LYS cc_start: 0.8820 (pptt) cc_final: 0.8524 (pptt) REVERT: A 983 LEU cc_start: 0.9107 (tp) cc_final: 0.8897 (tp) outliers start: 29 outliers final: 23 residues processed: 237 average time/residue: 0.1083 time to fit residues: 33.7326 Evaluate side-chains 248 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 517 ASP Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 722 HIS Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 805 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 84 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN A 319 ASN ** A 509 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 = 0.3877 r_free = 0.3877 target = 0.144248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115528 restraints weight = 12897.171| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.18 r_work: 0.3322 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7892 Z= 0.131 Angle : 0.586 8.182 10694 Z= 0.295 Chirality : 0.042 0.165 1174 Planarity : 0.004 0.042 1369 Dihedral : 3.941 16.501 1057 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.01 % Allowed : 20.36 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.74 (0.27), residues: 957 helix: 2.10 (0.25), residues: 429 sheet: 0.69 (0.46), residues: 135 loop : -1.49 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 819 TYR 0.013 0.001 TYR A 667 PHE 0.028 0.002 PHE A 126 TRP 0.008 0.001 TRP A 241 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7892) covalent geometry : angle 0.58629 (10694) hydrogen bonds : bond 0.05060 ( 398) hydrogen bonds : angle 4.19393 ( 1146) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 223 time to evaluate : 0.313 Fit side-chains REVERT: A 20 GLN cc_start: 0.8320 (tp-100) cc_final: 0.7911 (tp-100) REVERT: A 22 VAL cc_start: 0.8654 (t) cc_final: 0.8413 (t) REVERT: A 24 ASN cc_start: 0.8268 (m110) cc_final: 0.7768 (m-40) REVERT: A 39 ILE cc_start: 0.8664 (mp) cc_final: 0.8394 (mm) REVERT: A 41 GLU cc_start: 0.8233 (pt0) cc_final: 0.7803 (pt0) REVERT: A 114 LYS cc_start: 0.8368 (tppt) cc_final: 0.8081 (tppt) REVERT: A 142 MET cc_start: 0.8686 (tpp) cc_final: 0.8307 (ttm) REVERT: A 161 GLU cc_start: 0.8627 (tp30) cc_final: 0.8161 (tp30) REVERT: A 163 LYS cc_start: 0.8483 (mttm) cc_final: 0.8206 (mttp) REVERT: A 182 LEU cc_start: 0.8758 (tp) cc_final: 0.8457 (tt) REVERT: A 251 THR cc_start: 0.7739 (m) cc_final: 0.7527 (m) REVERT: A 281 GLU cc_start: 0.8231 (tp30) cc_final: 0.7899 (tp30) REVERT: A 303 PHE cc_start: 0.8568 (t80) cc_final: 0.8089 (t80) REVERT: A 367 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7562 (ptp90) REVERT: A 369 MET cc_start: 0.8031 (mmm) cc_final: 0.7661 (mmp) REVERT: A 402 MET cc_start: 0.7690 (mpp) cc_final: 0.7164 (mpp) REVERT: A 443 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7725 (mm-30) REVERT: A 517 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7411 (m-30) REVERT: A 598 GLN cc_start: 0.8351 (tm-30) cc_final: 0.8060 (tm-30) REVERT: A 635 LYS cc_start: 0.8375 (ttmt) cc_final: 0.7983 (ttmt) REVERT: A 678 ASN cc_start: 0.8769 (t0) cc_final: 0.8463 (t0) REVERT: A 702 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7718 (tm-30) REVERT: A 704 THR cc_start: 0.8538 (m) cc_final: 0.8223 (p) REVERT: A 705 ASP cc_start: 0.7586 (m-30) cc_final: 0.7356 (m-30) REVERT: A 711 GLN cc_start: 0.8354 (tp40) cc_final: 0.8004 (tp40) REVERT: A 730 LYS cc_start: 0.8828 (tppt) cc_final: 0.8548 (ttmm) REVERT: A 741 GLU cc_start: 0.8463 (tp30) cc_final: 0.8144 (tp30) REVERT: A 749 THR cc_start: 0.8354 (t) cc_final: 0.8128 (p) REVERT: A 771 TYR cc_start: 0.8417 (p90) cc_final: 0.8116 (p90) REVERT: A 836 LYS cc_start: 0.8795 (pptt) cc_final: 0.8518 (pptt) REVERT: A 934 LYS cc_start: 0.4817 (OUTLIER) cc_final: 0.4209 (tptt) REVERT: A 983 LEU cc_start: 0.9117 (tp) cc_final: 0.8899 (tp) outliers start: 25 outliers final: 18 residues processed: 233 average time/residue: 0.1075 time to fit residues: 32.5897 Evaluate side-chains 243 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 222 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 517 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 934 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 93 optimal weight: 0.2980 chunk 81 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.144639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115733 restraints weight = 12990.910| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.18 r_work: 0.3325 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7892 Z= 0.137 Angle : 0.587 8.606 10694 Z= 0.297 Chirality : 0.043 0.168 1174 Planarity : 0.004 0.041 1369 Dihedral : 3.897 16.055 1057 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.37 % Allowed : 21.57 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.79 (0.27), residues: 957 helix: 2.14 (0.25), residues: 429 sheet: 0.58 (0.45), residues: 146 loop : -1.47 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 185 TYR 0.014 0.001 TYR A 943 PHE 0.028 0.002 PHE A 126 TRP 0.009 0.001 TRP A 845 HIS 0.002 0.001 HIS A 572 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7892) covalent geometry : angle 0.58668 (10694) hydrogen bonds : bond 0.05112 ( 398) hydrogen bonds : angle 4.16280 ( 1146) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 231 time to evaluate : 0.325 Fit side-chains REVERT: A 20 GLN cc_start: 0.8326 (tp-100) cc_final: 0.8099 (tp-100) REVERT: A 22 VAL cc_start: 0.8678 (t) cc_final: 0.8454 (t) REVERT: A 24 ASN cc_start: 0.8288 (m110) cc_final: 0.7987 (m-40) REVERT: A 39 ILE cc_start: 0.8675 (mp) cc_final: 0.8410 (mm) REVERT: A 41 GLU cc_start: 0.8212 (pt0) cc_final: 0.7781 (pt0) REVERT: A 93 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8563 (mt-10) REVERT: A 114 LYS cc_start: 0.8354 (tppt) cc_final: 0.8074 (tppt) REVERT: A 142 MET cc_start: 0.8712 (tpp) cc_final: 0.8324 (ttm) REVERT: A 161 GLU cc_start: 0.8609 (tp30) cc_final: 0.8137 (tp30) REVERT: A 163 LYS cc_start: 0.8481 (mttm) cc_final: 0.8166 (mttp) REVERT: A 182 LEU cc_start: 0.8752 (tp) cc_final: 0.8447 (tt) REVERT: A 251 THR cc_start: 0.7797 (m) cc_final: 0.7555 (m) REVERT: A 255 MET cc_start: 0.7250 (tpp) cc_final: 0.7047 (tpp) REVERT: A 267 ILE cc_start: 0.8993 (tp) cc_final: 0.8662 (pt) REVERT: A 281 GLU cc_start: 0.8262 (tp30) cc_final: 0.7966 (tp30) REVERT: A 303 PHE cc_start: 0.8557 (t80) cc_final: 0.8098 (t80) REVERT: A 369 MET cc_start: 0.8051 (mmm) cc_final: 0.7695 (mmp) REVERT: A 402 MET cc_start: 0.7695 (mpp) cc_final: 0.7170 (mpp) REVERT: A 443 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7650 (mm-30) REVERT: A 517 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7432 (m-30) REVERT: A 579 MET cc_start: 0.8306 (mtp) cc_final: 0.8069 (ttm) REVERT: A 598 GLN cc_start: 0.8315 (tm-30) cc_final: 0.8023 (tm-30) REVERT: A 635 LYS cc_start: 0.8378 (ttmt) cc_final: 0.7997 (ttmt) REVERT: A 678 ASN cc_start: 0.8772 (t0) cc_final: 0.8473 (t0) REVERT: A 702 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7687 (tm-30) REVERT: A 704 THR cc_start: 0.8521 (m) cc_final: 0.8234 (p) REVERT: A 711 GLN cc_start: 0.8355 (tp40) cc_final: 0.8003 (tp40) REVERT: A 728 SER cc_start: 0.8333 (t) cc_final: 0.7995 (m) REVERT: A 730 LYS cc_start: 0.8818 (tppt) cc_final: 0.8527 (ttmm) REVERT: A 738 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: A 741 GLU cc_start: 0.8468 (tp30) cc_final: 0.8239 (tp30) REVERT: A 749 THR cc_start: 0.8383 (t) cc_final: 0.8152 (p) REVERT: A 771 TYR cc_start: 0.8416 (p90) cc_final: 0.8125 (p90) REVERT: A 836 LYS cc_start: 0.8804 (pptt) cc_final: 0.8522 (pptt) REVERT: A 934 LYS cc_start: 0.4966 (OUTLIER) cc_final: 0.4351 (tptt) REVERT: A 983 LEU cc_start: 0.9123 (tp) cc_final: 0.8914 (tp) outliers start: 28 outliers final: 21 residues processed: 241 average time/residue: 0.1057 time to fit residues: 33.4706 Evaluate side-chains 254 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 230 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 517 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 722 HIS Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 934 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.8682 > 50: distance: 52 - 73: 18.288 distance: 55 - 70: 5.189 distance: 63 - 70: 4.028 distance: 70 - 71: 3.813 distance: 71 - 72: 20.080 distance: 71 - 74: 11.549 distance: 72 - 73: 17.011 distance: 74 - 75: 7.624 distance: 75 - 76: 4.178 distance: 75 - 77: 16.946 distance: 76 - 78: 8.532 distance: 77 - 79: 6.261 distance: 78 - 80: 12.094 distance: 79 - 80: 10.584 distance: 80 - 81: 5.825 distance: 82 - 83: 14.564 distance: 82 - 176: 20.784 distance: 83 - 84: 13.933 distance: 84 - 85: 11.753 distance: 84 - 86: 13.217 distance: 85 - 173: 27.428 distance: 86 - 87: 5.552 distance: 87 - 88: 27.649 distance: 87 - 90: 12.364 distance: 88 - 89: 20.487 distance: 88 - 94: 20.017 distance: 90 - 91: 28.780 distance: 90 - 92: 35.386 distance: 91 - 93: 46.293 distance: 94 - 95: 10.250 distance: 95 - 96: 32.527 distance: 95 - 98: 11.786 distance: 96 - 99: 27.491 distance: 100 - 101: 6.389 distance: 100 - 103: 18.778 distance: 101 - 109: 24.263 distance: 103 - 104: 25.740 distance: 104 - 105: 26.500 distance: 104 - 106: 19.882 distance: 105 - 107: 12.722 distance: 106 - 108: 45.978 distance: 107 - 108: 8.850 distance: 109 - 110: 26.495 distance: 110 - 111: 6.324 distance: 110 - 113: 29.177 distance: 111 - 112: 43.173 distance: 111 - 116: 7.293 distance: 113 - 114: 15.560 distance: 113 - 115: 8.124 distance: 116 - 117: 9.963 distance: 117 - 118: 39.352 distance: 117 - 120: 17.457 distance: 118 - 119: 11.915 distance: 118 - 124: 44.859 distance: 120 - 121: 26.601 distance: 121 - 122: 28.646 distance: 121 - 123: 14.180 distance: 124 - 125: 26.808 distance: 125 - 126: 31.816 distance: 125 - 128: 42.699 distance: 126 - 127: 18.633 distance: 126 - 131: 21.385 distance: 128 - 129: 28.850 distance: 128 - 130: 31.218 distance: 131 - 132: 17.071 distance: 131 - 137: 17.709 distance: 132 - 133: 15.156 distance: 132 - 135: 13.452 distance: 133 - 134: 3.135 distance: 133 - 138: 5.114 distance: 135 - 136: 18.781 distance: 136 - 137: 21.026 distance: 138 - 139: 4.999 distance: 139 - 140: 8.447 distance: 139 - 142: 16.222 distance: 140 - 141: 10.165 distance: 140 - 146: 27.138 distance: 142 - 143: 9.080 distance: 143 - 144: 4.187 distance: 143 - 145: 21.625