Starting phenix.real_space_refine on Wed Mar 12 10:39:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywg_39632/03_2025/8ywg_39632.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywg_39632/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ywg_39632/03_2025/8ywg_39632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywg_39632/03_2025/8ywg_39632.map" model { file = "/net/cci-nas-00/data/ceres_data/8ywg_39632/03_2025/8ywg_39632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywg_39632/03_2025/8ywg_39632.cif" } resolution = 3.28 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= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 101 Time building chain proxies: 5.29, per 1000 atoms: 0.69 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: 1.98 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.97 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: 2.35 Time building geometry restraints manager: 2.27 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: 3.010 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.880 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.410 ------------------------------------------------------------------------------- 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= 0.204 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 : 5.39 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 (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: 0.59 (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 TRP 0.050 0.003 TRP A 403 HIS 0.005 0.001 HIS A 722 PHE 0.019 0.001 PHE A 986 TYR 0.029 0.001 TYR A 974 ARG 0.009 0.001 ARG A 819 *********************** 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 : 0.885 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: 0.2229 time to fit residues: 67.7582 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 : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.145255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.115909 restraints weight = 12669.599| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 3.06 r_work: 0.3339 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7892 Z= 0.242 Angle : 0.594 7.625 10694 Z= 0.307 Chirality : 0.042 0.151 1174 Planarity : 0.005 0.062 1369 Dihedral : 4.023 16.809 1057 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.30 % Rotamer: Outliers : 1.33 % Allowed : 10.48 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.69 (0.27), residues: 957 helix: 2.09 (0.25), residues: 428 sheet: 0.57 (0.46), residues: 135 loop : -1.52 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 403 HIS 0.006 0.001 HIS A 326 PHE 0.015 0.002 PHE A 675 TYR 0.020 0.001 TYR A 138 ARG 0.005 0.001 ARG A 285 *********************** 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 221 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 210 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7890 (mp0) REVERT: A 20 GLN cc_start: 0.8315 (tp-100) cc_final: 0.7928 (tp-100) REVERT: A 163 LYS cc_start: 0.8440 (mttm) cc_final: 0.8221 (mttp) REVERT: A 182 LEU cc_start: 0.8592 (tp) cc_final: 0.8302 (tt) REVERT: A 192 ASP cc_start: 0.8199 (m-30) cc_final: 0.7947 (m-30) REVERT: A 255 MET cc_start: 0.7589 (tpp) cc_final: 0.7345 (tpt) REVERT: A 276 LEU cc_start: 0.8801 (mm) cc_final: 0.8580 (mt) REVERT: A 303 PHE cc_start: 0.8569 (t80) cc_final: 0.8151 (t80) REVERT: A 339 LYS cc_start: 0.8550 (ptpp) cc_final: 0.8320 (ptpp) REVERT: A 369 MET cc_start: 0.7961 (mmm) cc_final: 0.7667 (mmp) REVERT: A 402 MET cc_start: 0.7528 (mpp) cc_final: 0.7106 (mpp) REVERT: A 598 GLN cc_start: 0.8354 (tm-30) cc_final: 0.8093 (tm-30) REVERT: A 702 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7707 (tm-30) REVERT: A 704 THR cc_start: 0.8470 (m) cc_final: 0.8264 (p) REVERT: A 728 SER cc_start: 0.8355 (t) cc_final: 0.8083 (m) REVERT: A 730 LYS cc_start: 0.8843 (tppt) cc_final: 0.8587 (ttmm) REVERT: A 836 LYS cc_start: 0.8692 (pptt) cc_final: 0.8456 (pptt) REVERT: A 957 ASN cc_start: 0.8284 (p0) cc_final: 0.8003 (p0) outliers start: 11 outliers final: 10 residues processed: 211 average time/residue: 0.2407 time to fit residues: 65.5268 Evaluate side-chains 216 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 206 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 546 LEU 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 768 LYS Chi-restraints excluded: chain A residue 785 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 60 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.145510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.116207 restraints weight = 12875.122| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.09 r_work: 0.3336 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7892 Z= 0.213 Angle : 0.573 7.418 10694 Z= 0.294 Chirality : 0.042 0.150 1174 Planarity : 0.004 0.047 1369 Dihedral : 3.946 16.261 1057 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.43 % Favored : 94.46 % Rotamer: Outliers : 3.13 % Allowed : 14.46 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.69 (0.27), residues: 957 helix: 2.08 (0.25), residues: 429 sheet: 0.61 (0.46), residues: 135 loop : -1.54 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 845 HIS 0.005 0.001 HIS A 326 PHE 0.015 0.001 PHE A 85 TYR 0.013 0.001 TYR A 667 ARG 0.006 0.001 ARG A 490 *********************** 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 248 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 222 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.8332 (tp-100) cc_final: 0.7956 (tp-100) REVERT: A 41 GLU cc_start: 0.8165 (pt0) cc_final: 0.7813 (pt0) REVERT: A 114 LYS cc_start: 0.8232 (tppt) cc_final: 0.7990 (tppt) REVERT: A 161 GLU cc_start: 0.8543 (tp30) cc_final: 0.8108 (tp30) REVERT: A 163 LYS cc_start: 0.8414 (mttm) cc_final: 0.8202 (mttp) REVERT: A 182 LEU cc_start: 0.8612 (tp) cc_final: 0.8323 (tt) REVERT: A 192 ASP cc_start: 0.8226 (m-30) cc_final: 0.8004 (m-30) REVERT: A 213 GLU cc_start: 0.6923 (mm-30) cc_final: 0.6573 (mm-30) REVERT: A 255 MET cc_start: 0.7554 (tpp) cc_final: 0.7275 (tpp) REVERT: A 281 GLU cc_start: 0.8132 (tp30) cc_final: 0.7746 (tp30) REVERT: A 303 PHE cc_start: 0.8539 (t80) cc_final: 0.8101 (t80) REVERT: A 304 ILE cc_start: 0.8594 (tt) cc_final: 0.8386 (tt) REVERT: A 339 LYS cc_start: 0.8598 (ptpp) cc_final: 0.8357 (ptpp) REVERT: A 369 MET cc_start: 0.8051 (mmm) cc_final: 0.7800 (mmp) REVERT: A 402 MET cc_start: 0.7537 (mpp) cc_final: 0.7112 (mpp) REVERT: A 443 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7789 (mm-30) REVERT: A 454 ASP cc_start: 0.8162 (m-30) cc_final: 0.7859 (t0) REVERT: A 458 TYR cc_start: 0.8140 (m-10) cc_final: 0.7835 (m-10) REVERT: A 598 GLN cc_start: 0.8360 (tm-30) cc_final: 0.8089 (tm-30) REVERT: A 702 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7655 (tm-30) REVERT: A 703 VAL cc_start: 0.9002 (OUTLIER) cc_final: 0.8458 (t) REVERT: A 704 THR cc_start: 0.8499 (m) cc_final: 0.8205 (p) REVERT: A 728 SER cc_start: 0.8340 (t) cc_final: 0.8057 (m) REVERT: A 730 LYS cc_start: 0.8839 (tppt) cc_final: 0.8568 (ttmm) REVERT: A 741 GLU cc_start: 0.8509 (tp30) cc_final: 0.8209 (tp30) REVERT: A 821 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7633 (mm-30) REVERT: A 836 LYS cc_start: 0.8724 (pptt) cc_final: 0.8471 (pptt) REVERT: A 956 ILE cc_start: 0.8924 (tp) cc_final: 0.8692 (tp) REVERT: A 957 ASN cc_start: 0.8264 (p0) cc_final: 0.7976 (p0) outliers start: 26 outliers final: 20 residues processed: 227 average time/residue: 0.2329 time to fit residues: 68.6060 Evaluate side-chains 237 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 216 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 350 SER 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 677 ILE Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 703 VAL 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 763 VAL Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 770 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 30 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.144605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.115459 restraints weight = 12674.540| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.08 r_work: 0.3330 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7892 Z= 0.224 Angle : 0.572 7.325 10694 Z= 0.294 Chirality : 0.043 0.173 1174 Planarity : 0.004 0.045 1369 Dihedral : 3.947 15.829 1057 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.01 % Allowed : 17.47 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.69 (0.27), residues: 957 helix: 2.08 (0.25), residues: 430 sheet: 0.64 (0.46), residues: 134 loop : -1.55 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 845 HIS 0.007 0.001 HIS A 474 PHE 0.020 0.002 PHE A 71 TYR 0.013 0.001 TYR A 667 ARG 0.004 0.000 ARG A 593 *********************** 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 246 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: A 20 GLN cc_start: 0.8381 (tp-100) cc_final: 0.7997 (tp-100) REVERT: A 22 VAL cc_start: 0.8719 (t) cc_final: 0.8488 (t) REVERT: A 62 GLU cc_start: 0.8050 (tt0) cc_final: 0.7775 (tt0) REVERT: A 114 LYS cc_start: 0.8217 (tppt) cc_final: 0.7953 (tppt) REVERT: A 142 MET cc_start: 0.8675 (tpp) cc_final: 0.8051 (mtt) REVERT: A 161 GLU cc_start: 0.8576 (tp30) cc_final: 0.8158 (tp30) REVERT: A 163 LYS cc_start: 0.8443 (mttm) cc_final: 0.8222 (mttp) REVERT: A 182 LEU cc_start: 0.8652 (tp) cc_final: 0.8352 (tt) REVERT: A 192 ASP cc_start: 0.8236 (m-30) cc_final: 0.8023 (m-30) REVERT: A 213 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6638 (mm-30) REVERT: A 255 MET cc_start: 0.7542 (tpp) cc_final: 0.7264 (tpp) REVERT: A 281 GLU cc_start: 0.8179 (tp30) cc_final: 0.7843 (tp30) REVERT: A 282 GLN cc_start: 0.8879 (tp-100) cc_final: 0.8637 (tp-100) REVERT: A 303 PHE cc_start: 0.8555 (t80) cc_final: 0.8090 (t80) REVERT: A 339 LYS cc_start: 0.8635 (ptpp) cc_final: 0.8377 (ptpp) REVERT: A 402 MET cc_start: 0.7576 (mpp) cc_final: 0.7094 (mpp) REVERT: A 443 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7635 (mm-30) REVERT: A 458 TYR cc_start: 0.8075 (m-10) cc_final: 0.7782 (m-10) REVERT: A 579 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8142 (mtp) REVERT: A 598 GLN cc_start: 0.8368 (tm-30) cc_final: 0.8101 (tm-30) REVERT: A 635 LYS cc_start: 0.8488 (ttmt) cc_final: 0.8115 (ttmt) REVERT: A 702 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7614 (tm-30) REVERT: A 703 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.8468 (t) REVERT: A 704 THR cc_start: 0.8534 (m) cc_final: 0.8240 (p) REVERT: A 728 SER cc_start: 0.8321 (t) cc_final: 0.8025 (m) REVERT: A 730 LYS cc_start: 0.8820 (tppt) cc_final: 0.8546 (ttmm) REVERT: A 741 GLU cc_start: 0.8502 (tp30) cc_final: 0.8183 (tp30) REVERT: A 836 LYS cc_start: 0.8770 (pptt) cc_final: 0.8487 (pptt) outliers start: 25 outliers final: 20 residues processed: 225 average time/residue: 0.2191 time to fit residues: 64.2671 Evaluate side-chains 241 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 219 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET 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 350 SER Chi-restraints excluded: chain A residue 482 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 579 MET Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 703 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 84 optimal weight: 0.0770 chunk 46 optimal weight: 0.5980 chunk 86 optimal weight: 7.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3901 r_free = 0.3901 target = 0.145626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.116496 restraints weight = 12612.136| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.06 r_work: 0.3343 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7892 Z= 0.198 Angle : 0.569 7.664 10694 Z= 0.290 Chirality : 0.042 0.173 1174 Planarity : 0.004 0.042 1369 Dihedral : 3.902 15.943 1057 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.65 % Allowed : 19.64 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 (0.27), residues: 957 helix: 2.12 (0.25), residues: 429 sheet: 0.63 (0.46), residues: 139 loop : -1.52 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 845 HIS 0.004 0.001 HIS A 474 PHE 0.015 0.001 PHE A 126 TYR 0.012 0.001 TYR A 667 ARG 0.004 0.000 ARG A 185 *********************** 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 247 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 225 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 20 GLN cc_start: 0.8363 (tp-100) cc_final: 0.8027 (tp-100) REVERT: A 22 VAL cc_start: 0.8715 (t) cc_final: 0.8473 (t) REVERT: A 41 GLU cc_start: 0.8149 (pt0) cc_final: 0.7771 (pt0) REVERT: A 93 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8372 (mt-10) REVERT: A 114 LYS cc_start: 0.8222 (tppt) cc_final: 0.7937 (tppt) REVERT: A 142 MET cc_start: 0.8665 (tpp) cc_final: 0.8426 (tpp) REVERT: A 161 GLU cc_start: 0.8591 (tp30) cc_final: 0.8177 (tp30) REVERT: A 163 LYS cc_start: 0.8453 (mttm) cc_final: 0.8236 (mttp) REVERT: A 182 LEU cc_start: 0.8661 (tp) cc_final: 0.8361 (tt) REVERT: A 191 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7624 (tm-30) REVERT: A 192 ASP cc_start: 0.8240 (m-30) cc_final: 0.7912 (m-30) REVERT: A 213 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6636 (mm-30) REVERT: A 255 MET cc_start: 0.7516 (tpp) cc_final: 0.7209 (tpp) REVERT: A 281 GLU cc_start: 0.8182 (tp30) cc_final: 0.7618 (tp30) REVERT: A 303 PHE cc_start: 0.8586 (t80) cc_final: 0.8120 (t80) REVERT: A 320 LYS cc_start: 0.8914 (mmtp) cc_final: 0.8474 (tptm) REVERT: A 339 LYS cc_start: 0.8650 (ptpp) cc_final: 0.8369 (ptpp) REVERT: A 369 MET cc_start: 0.8081 (mmm) cc_final: 0.7722 (mmp) REVERT: A 402 MET cc_start: 0.7603 (mpp) cc_final: 0.7105 (mpp) REVERT: A 443 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7707 (mm-30) REVERT: A 579 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8110 (mtp) REVERT: A 598 GLN cc_start: 0.8383 (tm-30) cc_final: 0.8101 (tm-30) REVERT: A 635 LYS cc_start: 0.8461 (ttmt) cc_final: 0.8089 (ttmt) REVERT: A 702 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7662 (tm-30) REVERT: A 704 THR cc_start: 0.8529 (m) cc_final: 0.8255 (p) REVERT: A 728 SER cc_start: 0.8300 (t) cc_final: 0.8000 (m) REVERT: A 730 LYS cc_start: 0.8805 (tppt) cc_final: 0.8526 (ttmm) REVERT: A 741 GLU cc_start: 0.8514 (tp30) cc_final: 0.8301 (tp30) REVERT: A 836 LYS cc_start: 0.8781 (pptt) cc_final: 0.8498 (pptt) REVERT: A 983 LEU cc_start: 0.9084 (tp) cc_final: 0.8866 (tp) outliers start: 22 outliers final: 18 residues processed: 231 average time/residue: 0.2235 time to fit residues: 67.0512 Evaluate side-chains 240 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 221 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 501 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 579 MET 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 785 LYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 831 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 88 optimal weight: 20.0000 chunk 5 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 65 optimal weight: 0.0870 chunk 68 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 82 optimal weight: 0.4980 chunk 39 optimal weight: 30.0000 chunk 30 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN ** A 474 HIS ** 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 = 0.3905 r_free = 0.3905 target = 0.146129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.117163 restraints weight = 12622.236| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.07 r_work: 0.3353 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7892 Z= 0.186 Angle : 0.564 7.513 10694 Z= 0.287 Chirality : 0.042 0.165 1174 Planarity : 0.004 0.040 1369 Dihedral : 3.823 15.708 1057 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.13 % Allowed : 20.24 % 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 (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: 0.76 (0.27), residues: 957 helix: 2.11 (0.25), residues: 429 sheet: 0.56 (0.45), residues: 145 loop : -1.47 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 845 HIS 0.003 0.001 HIS A 474 PHE 0.019 0.001 PHE A 85 TYR 0.011 0.001 TYR A 772 ARG 0.006 0.000 ARG A 185 *********************** 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 251 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8387 (tp30) cc_final: 0.8133 (tp30) REVERT: A 20 GLN cc_start: 0.8341 (tp-100) cc_final: 0.7928 (tp-100) REVERT: A 22 VAL cc_start: 0.8710 (t) cc_final: 0.8469 (t) REVERT: A 24 ASN cc_start: 0.8294 (m-40) cc_final: 0.7795 (m-40) REVERT: A 41 GLU cc_start: 0.8126 (pt0) cc_final: 0.7750 (pt0) REVERT: A 114 LYS cc_start: 0.8197 (tppt) cc_final: 0.7941 (tppt) REVERT: A 142 MET cc_start: 0.8668 (tpp) cc_final: 0.8337 (tpp) REVERT: A 161 GLU cc_start: 0.8586 (tp30) cc_final: 0.8107 (tp30) REVERT: A 163 LYS cc_start: 0.8475 (mttm) cc_final: 0.8259 (mttp) REVERT: A 182 LEU cc_start: 0.8643 (tp) cc_final: 0.8357 (tt) REVERT: A 191 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7590 (tm-30) REVERT: A 192 ASP cc_start: 0.8218 (m-30) cc_final: 0.7881 (m-30) REVERT: A 213 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6556 (mm-30) REVERT: A 237 MET cc_start: 0.8184 (mtt) cc_final: 0.7853 (mtp) REVERT: A 281 GLU cc_start: 0.8185 (tp30) cc_final: 0.7646 (tp30) REVERT: A 303 PHE cc_start: 0.8567 (t80) cc_final: 0.8089 (t80) REVERT: A 320 LYS cc_start: 0.8927 (mmtp) cc_final: 0.8475 (tptm) REVERT: A 339 LYS cc_start: 0.8648 (ptpp) cc_final: 0.8357 (ptpp) REVERT: A 369 MET cc_start: 0.8081 (mmm) cc_final: 0.7721 (mmp) REVERT: A 402 MET cc_start: 0.7590 (mpp) cc_final: 0.7087 (mpp) REVERT: A 443 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7650 (mm-30) REVERT: A 579 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8103 (mtp) REVERT: A 598 GLN cc_start: 0.8370 (tm-30) cc_final: 0.8096 (tm-30) REVERT: A 635 LYS cc_start: 0.8436 (ttmt) cc_final: 0.8060 (ttmt) REVERT: A 702 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7601 (tm-30) REVERT: A 703 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.8512 (t) REVERT: A 704 THR cc_start: 0.8494 (m) cc_final: 0.8188 (p) REVERT: A 728 SER cc_start: 0.8255 (t) cc_final: 0.7947 (m) REVERT: A 730 LYS cc_start: 0.8776 (tppt) cc_final: 0.8492 (ttmm) REVERT: A 741 GLU cc_start: 0.8506 (tp30) cc_final: 0.8201 (tp30) REVERT: A 836 LYS cc_start: 0.8774 (pptt) cc_final: 0.8500 (pptt) REVERT: A 946 ASN cc_start: 0.7886 (OUTLIER) cc_final: 0.7612 (m110) REVERT: A 983 LEU cc_start: 0.9102 (tp) cc_final: 0.8885 (tp) outliers start: 26 outliers final: 23 residues processed: 233 average time/residue: 0.2380 time to fit residues: 72.6254 Evaluate side-chains 247 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET 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 542 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 703 VAL 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 Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 946 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 47 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 90 optimal weight: 0.0770 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 946 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.145701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.116939 restraints weight = 12762.253| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 3.05 r_work: 0.3345 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7892 Z= 0.193 Angle : 0.566 8.170 10694 Z= 0.287 Chirality : 0.042 0.168 1174 Planarity : 0.004 0.040 1369 Dihedral : 3.834 16.225 1057 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.61 % Allowed : 19.76 % 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 (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: 0.78 (0.27), residues: 957 helix: 2.11 (0.25), residues: 429 sheet: 0.58 (0.45), residues: 145 loop : -1.45 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 845 HIS 0.003 0.001 HIS A 474 PHE 0.017 0.001 PHE A 85 TYR 0.013 0.001 TYR A 555 ARG 0.006 0.000 ARG A 185 *********************** 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 254 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.8351 (tp-100) cc_final: 0.7936 (tp-100) REVERT: A 22 VAL cc_start: 0.8718 (t) cc_final: 0.8465 (t) REVERT: A 24 ASN cc_start: 0.8298 (m-40) cc_final: 0.7791 (m-40) REVERT: A 41 GLU cc_start: 0.8109 (pt0) cc_final: 0.7734 (pt0) REVERT: A 93 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8345 (mt-10) REVERT: A 114 LYS cc_start: 0.8218 (tppt) cc_final: 0.7955 (tppt) REVERT: A 142 MET cc_start: 0.8673 (tpp) cc_final: 0.8227 (ttm) REVERT: A 161 GLU cc_start: 0.8581 (tp30) cc_final: 0.8179 (tp30) REVERT: A 163 LYS cc_start: 0.8490 (mttm) cc_final: 0.8267 (mttp) REVERT: A 182 LEU cc_start: 0.8645 (tp) cc_final: 0.8357 (tt) REVERT: A 191 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7562 (tm-30) REVERT: A 192 ASP cc_start: 0.8223 (m-30) cc_final: 0.7889 (m-30) REVERT: A 213 GLU cc_start: 0.6959 (mm-30) cc_final: 0.6510 (mm-30) REVERT: A 281 GLU cc_start: 0.8202 (tp30) cc_final: 0.7615 (tp30) REVERT: A 303 PHE cc_start: 0.8566 (t80) cc_final: 0.8088 (t80) REVERT: A 320 LYS cc_start: 0.8932 (mmtp) cc_final: 0.8454 (tptm) REVERT: A 339 LYS cc_start: 0.8649 (ptpp) cc_final: 0.8351 (ptpp) REVERT: A 402 MET cc_start: 0.7611 (mpp) cc_final: 0.7104 (mpp) REVERT: A 443 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7799 (mm-30) REVERT: A 579 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8111 (mtp) REVERT: A 598 GLN cc_start: 0.8386 (tm-30) cc_final: 0.8111 (tm-30) REVERT: A 635 LYS cc_start: 0.8445 (ttmt) cc_final: 0.8065 (ttmt) REVERT: A 702 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 703 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.8511 (t) REVERT: A 704 THR cc_start: 0.8494 (m) cc_final: 0.8187 (p) REVERT: A 730 LYS cc_start: 0.8777 (tppt) cc_final: 0.8505 (ttmm) REVERT: A 741 GLU cc_start: 0.8508 (tp30) cc_final: 0.8209 (tp30) REVERT: A 836 LYS cc_start: 0.8781 (pptt) cc_final: 0.8487 (pptt) REVERT: A 946 ASN cc_start: 0.7909 (OUTLIER) cc_final: 0.7617 (m110) REVERT: A 983 LEU cc_start: 0.9113 (tp) cc_final: 0.8904 (tp) outliers start: 30 outliers final: 24 residues processed: 232 average time/residue: 0.2675 time to fit residues: 81.8482 Evaluate side-chains 248 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 221 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET 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 482 CYS Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 703 VAL 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 756 TYR 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 946 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 0.0670 chunk 83 optimal weight: 2.9990 chunk 86 optimal weight: 0.0870 chunk 87 optimal weight: 4.9990 chunk 84 optimal weight: 0.0050 chunk 71 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 30.0000 chunk 5 optimal weight: 2.9990 overall best weight: 0.3710 ------------------------------------------------------------------------------- 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** A 946 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.146248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.117782 restraints weight = 12947.983| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.14 r_work: 0.3357 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7892 Z= 0.165 Angle : 0.564 8.488 10694 Z= 0.284 Chirality : 0.042 0.174 1174 Planarity : 0.004 0.038 1369 Dihedral : 3.770 16.008 1057 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.89 % Allowed : 20.60 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.82 (0.27), residues: 957 helix: 2.14 (0.25), residues: 428 sheet: 0.56 (0.45), residues: 144 loop : -1.39 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 241 HIS 0.003 0.001 HIS A 474 PHE 0.015 0.001 PHE A 71 TYR 0.012 0.001 TYR A 772 ARG 0.007 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 8 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: 24 poor density : 220 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.8269 (tp-100) cc_final: 0.8034 (tp-100) REVERT: A 22 VAL cc_start: 0.8632 (t) cc_final: 0.8364 (t) REVERT: A 41 GLU cc_start: 0.8166 (pt0) cc_final: 0.7769 (pt0) REVERT: A 142 MET cc_start: 0.8669 (tpp) cc_final: 0.8233 (ttm) REVERT: A 161 GLU cc_start: 0.8576 (tp30) cc_final: 0.8128 (tp30) REVERT: A 163 LYS cc_start: 0.8470 (mttm) cc_final: 0.8241 (mttp) REVERT: A 182 LEU cc_start: 0.8658 (tp) cc_final: 0.8376 (tt) REVERT: A 191 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7533 (tm-30) REVERT: A 192 ASP cc_start: 0.8281 (m-30) cc_final: 0.7894 (m-30) REVERT: A 213 GLU cc_start: 0.6926 (mm-30) cc_final: 0.6469 (mm-30) REVERT: A 237 MET cc_start: 0.8255 (mtt) cc_final: 0.7860 (mtp) REVERT: A 267 ILE cc_start: 0.8957 (tp) cc_final: 0.8667 (pt) REVERT: A 281 GLU cc_start: 0.8212 (tp30) cc_final: 0.7952 (tp30) REVERT: A 282 GLN cc_start: 0.8853 (tp40) cc_final: 0.8567 (tp-100) REVERT: A 339 LYS cc_start: 0.8627 (ptpp) cc_final: 0.8327 (ptpp) REVERT: A 402 MET cc_start: 0.7629 (mpp) cc_final: 0.7108 (mpp) REVERT: A 443 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7736 (mm-30) REVERT: A 598 GLN cc_start: 0.8320 (tm-30) cc_final: 0.8031 (tm-30) REVERT: A 635 LYS cc_start: 0.8363 (ttmt) cc_final: 0.7963 (ttmt) REVERT: A 702 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7690 (tm-30) REVERT: A 704 THR cc_start: 0.8493 (m) cc_final: 0.8189 (p) REVERT: A 730 LYS cc_start: 0.8779 (tppt) cc_final: 0.8503 (ttmm) REVERT: A 741 GLU cc_start: 0.8477 (tp30) cc_final: 0.8172 (tp30) REVERT: A 771 TYR cc_start: 0.8389 (p90) cc_final: 0.8064 (p90) REVERT: A 836 LYS cc_start: 0.8764 (pptt) cc_final: 0.8475 (pptt) REVERT: A 946 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.7648 (m110) REVERT: A 983 LEU cc_start: 0.9125 (tp) cc_final: 0.8916 (tp) outliers start: 24 outliers final: 21 residues processed: 227 average time/residue: 0.2345 time to fit residues: 69.5048 Evaluate side-chains 242 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 220 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET 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 319 ASN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 546 LEU 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 756 TYR 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 946 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 59 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 0.0570 chunk 6 optimal weight: 0.9990 overall best weight: 0.7504 ------------------------------------------------------------------------------- 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** A 946 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.144577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115873 restraints weight = 12860.147| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 3.15 r_work: 0.3320 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7892 Z= 0.217 Angle : 0.579 8.727 10694 Z= 0.293 Chirality : 0.043 0.174 1174 Planarity : 0.004 0.041 1369 Dihedral : 3.839 17.227 1057 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.89 % Allowed : 21.08 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.80 (0.27), residues: 957 helix: 2.12 (0.25), residues: 428 sheet: 0.59 (0.45), residues: 145 loop : -1.40 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 845 HIS 0.003 0.001 HIS A 474 PHE 0.025 0.002 PHE A 85 TYR 0.014 0.001 TYR A 772 ARG 0.007 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 9 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 251 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.8280 (tp-100) cc_final: 0.7923 (tp-100) REVERT: A 22 VAL cc_start: 0.8660 (t) cc_final: 0.8415 (t) REVERT: A 41 GLU cc_start: 0.8205 (pt0) cc_final: 0.7816 (pt0) REVERT: A 142 MET cc_start: 0.8715 (tpp) cc_final: 0.8259 (ttm) REVERT: A 161 GLU cc_start: 0.8614 (tp30) cc_final: 0.8163 (tp30) REVERT: A 163 LYS cc_start: 0.8513 (mttm) cc_final: 0.8240 (mttp) REVERT: A 182 LEU cc_start: 0.8684 (tp) cc_final: 0.8407 (tt) REVERT: A 191 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7556 (tm-30) REVERT: A 192 ASP cc_start: 0.8283 (m-30) cc_final: 0.7905 (m-30) REVERT: A 213 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6495 (mm-30) REVERT: A 237 MET cc_start: 0.8315 (mtt) cc_final: 0.7919 (mtp) REVERT: A 267 ILE cc_start: 0.8968 (tp) cc_final: 0.8666 (pt) REVERT: A 281 GLU cc_start: 0.8237 (tp30) cc_final: 0.7978 (tp30) REVERT: A 282 GLN cc_start: 0.8859 (tp40) cc_final: 0.8635 (tp-100) REVERT: A 303 PHE cc_start: 0.8556 (t80) cc_final: 0.8121 (t80) REVERT: A 337 TYR cc_start: 0.8573 (t80) cc_final: 0.8336 (t80) REVERT: A 339 LYS cc_start: 0.8633 (ptpp) cc_final: 0.8359 (ptpp) REVERT: A 342 ARG cc_start: 0.8642 (ttm-80) cc_final: 0.8342 (ttm-80) REVERT: A 369 MET cc_start: 0.7966 (mmm) cc_final: 0.7268 (mmm) REVERT: A 402 MET cc_start: 0.7667 (mpp) cc_final: 0.7140 (mpp) REVERT: A 443 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7750 (mm-30) REVERT: A 598 GLN cc_start: 0.8341 (tm-30) cc_final: 0.8052 (tm-30) REVERT: A 635 LYS cc_start: 0.8369 (ttmt) cc_final: 0.7974 (ttmt) REVERT: A 702 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7737 (tm-30) REVERT: A 704 THR cc_start: 0.8520 (m) cc_final: 0.8199 (p) REVERT: A 730 LYS cc_start: 0.8810 (tppt) cc_final: 0.8538 (ttmm) REVERT: A 741 GLU cc_start: 0.8478 (tp30) cc_final: 0.8200 (tp30) REVERT: A 771 TYR cc_start: 0.8424 (p90) cc_final: 0.8098 (p90) REVERT: A 836 LYS cc_start: 0.8784 (pptt) cc_final: 0.8494 (pptt) REVERT: A 946 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7674 (m110) outliers start: 24 outliers final: 23 residues processed: 234 average time/residue: 0.2391 time to fit residues: 72.3604 Evaluate side-chains 251 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET 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 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 546 LEU Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 703 VAL 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 756 TYR 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 946 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 70 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 52 optimal weight: 0.1980 chunk 38 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 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 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 = 0.3893 r_free = 0.3893 target = 0.145160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116185 restraints weight = 12960.618| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 3.18 r_work: 0.3340 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7892 Z= 0.203 Angle : 0.593 9.721 10694 Z= 0.297 Chirality : 0.043 0.173 1174 Planarity : 0.004 0.039 1369 Dihedral : 3.826 15.997 1057 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.89 % Allowed : 21.45 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.81 (0.27), residues: 957 helix: 2.11 (0.25), residues: 428 sheet: 0.58 (0.45), residues: 145 loop : -1.38 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 845 HIS 0.003 0.001 HIS A 474 PHE 0.017 0.001 PHE A 71 TYR 0.014 0.001 TYR A 138 ARG 0.007 0.000 ARG A 185 ********************** REFINEMENT MACRO_CYCLE 10 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 251 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8670 (t) cc_final: 0.8420 (t) REVERT: A 41 GLU cc_start: 0.8210 (pt0) cc_final: 0.7806 (pt0) REVERT: A 142 MET cc_start: 0.8704 (tpp) cc_final: 0.8212 (ttm) REVERT: A 161 GLU cc_start: 0.8588 (tp30) cc_final: 0.8137 (tp30) REVERT: A 182 LEU cc_start: 0.8680 (tp) cc_final: 0.8402 (tt) REVERT: A 191 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7564 (tm-30) REVERT: A 192 ASP cc_start: 0.8297 (m-30) cc_final: 0.7927 (m-30) REVERT: A 213 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6484 (mm-30) REVERT: A 237 MET cc_start: 0.8337 (mtt) cc_final: 0.7949 (mtp) REVERT: A 267 ILE cc_start: 0.8940 (tp) cc_final: 0.8651 (pt) REVERT: A 281 GLU cc_start: 0.8220 (tp30) cc_final: 0.7961 (tp30) REVERT: A 282 GLN cc_start: 0.8870 (tp40) cc_final: 0.8638 (tp-100) REVERT: A 337 TYR cc_start: 0.8575 (t80) cc_final: 0.8342 (t80) REVERT: A 339 LYS cc_start: 0.8615 (ptpp) cc_final: 0.8345 (ptpp) REVERT: A 342 ARG cc_start: 0.8665 (ttm-80) cc_final: 0.8360 (ttm-80) REVERT: A 369 MET cc_start: 0.7948 (mmm) cc_final: 0.7237 (mmm) REVERT: A 402 MET cc_start: 0.7654 (mpp) cc_final: 0.7121 (mpp) REVERT: A 443 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7711 (mm-30) REVERT: A 598 GLN cc_start: 0.8318 (tm-30) cc_final: 0.8021 (tm-30) REVERT: A 635 LYS cc_start: 0.8360 (ttmt) cc_final: 0.7967 (ttmt) REVERT: A 702 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7706 (tm-30) REVERT: A 704 THR cc_start: 0.8523 (m) cc_final: 0.8187 (p) REVERT: A 730 LYS cc_start: 0.8781 (tppt) cc_final: 0.8477 (ttmm) REVERT: A 771 TYR cc_start: 0.8427 (p90) cc_final: 0.8098 (p90) REVERT: A 836 LYS cc_start: 0.8790 (pptt) cc_final: 0.8508 (pptt) REVERT: A 934 LYS cc_start: 0.5115 (OUTLIER) cc_final: 0.4795 (tptt) outliers start: 24 outliers final: 23 residues processed: 234 average time/residue: 0.2384 time to fit residues: 72.6219 Evaluate side-chains 249 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 225 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET 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 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 546 LEU Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 703 VAL 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 756 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 15 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 51 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3898 r_free = 0.3898 target = 0.145706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116569 restraints weight = 12960.327| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.19 r_work: 0.3346 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7892 Z= 0.186 Angle : 0.591 8.799 10694 Z= 0.298 Chirality : 0.042 0.171 1174 Planarity : 0.004 0.039 1369 Dihedral : 3.817 16.461 1057 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.13 % Allowed : 21.93 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.80 (0.27), residues: 957 helix: 2.14 (0.25), residues: 427 sheet: 0.61 (0.45), residues: 145 loop : -1.43 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 845 HIS 0.004 0.001 HIS A 474 PHE 0.027 0.001 PHE A 85 TYR 0.021 0.001 TYR A 943 ARG 0.008 0.000 ARG A 367 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3894.87 seconds wall clock time: 68 minutes 45.67 seconds (4125.67 seconds total)