Starting phenix.real_space_refine on Sat Jul 4 06:33:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9odz_70381/07_2026/9odz_70381_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9odz_70381/07_2026/9odz_70381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9odz_70381/07_2026/9odz_70381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9odz_70381/07_2026/9odz_70381.map" model { file = "/net/cci-nas-00/data/ceres_data/9odz_70381/07_2026/9odz_70381_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9odz_70381/07_2026/9odz_70381_trim.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 5734 2.51 5 N 1523 2.21 5 O 1665 1.98 5 H 9093 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18071 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 18006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 18006 Classifications: {'peptide': 1150} Link IDs: {'PTRANS': 27, 'TRANS': 1122} Chain breaks: 2 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4, 'water': 1} Link IDs: {None: 4} Time building chain proxies: 3.19, per 1000 atoms: 0.18 Number of scatterers: 18071 At special positions: 0 Unit cell: (70.55, 127.82, 140.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 48 16.00 P 6 15.00 Mg 2 11.99 O 1665 8.00 N 1523 7.00 C 5734 6.00 H 9093 1.00 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: 1.62 Conformation dependent library (CDL) restraints added in 692.4 milliseconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 4 sheets defined 67.9% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 40 through 44 removed outlier: 3.632A pdb=" N LEU A 44 " --> pdb=" O PRO A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 68 Processing helix chain 'A' and resid 72 through 79 Processing helix chain 'A' and resid 119 through 160 Processing helix chain 'A' and resid 164 through 171 removed outlier: 3.690A pdb=" N PHE A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 183 removed outlier: 3.717A pdb=" N LEU A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 191 Processing helix chain 'A' and resid 192 through 215 removed outlier: 3.541A pdb=" N GLY A 196 " --> pdb=" O GLY A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 233 removed outlier: 4.070A pdb=" N THR A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Proline residue: A 228 - end of helix removed outlier: 3.920A pdb=" N GLY A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 245 Processing helix chain 'A' and resid 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'A' and resid 253 through 265 Processing helix chain 'A' and resid 265 through 272 removed outlier: 3.537A pdb=" N VAL A 269 " --> pdb=" O SER A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 323 removed outlier: 3.633A pdb=" N ILE A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 331 through 376 removed outlier: 3.850A pdb=" N MET A 335 " --> pdb=" O TYR A 331 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) Proline residue: A 355 - end of helix removed outlier: 4.293A pdb=" N GLN A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR A 359 " --> pdb=" O PRO A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.842A pdb=" N ILE A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 501 through 512 Processing helix chain 'A' and resid 513 through 519 removed outlier: 4.393A pdb=" N PHE A 517 " --> pdb=" O ASN A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 552 removed outlier: 4.632A pdb=" N ARG A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG A 552 " --> pdb=" O ARG A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 583 removed outlier: 4.124A pdb=" N LEU A 583 " --> pdb=" O ASP A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 599 removed outlier: 4.035A pdb=" N ASN A 599 " --> pdb=" O SER A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 624 removed outlier: 3.619A pdb=" N GLU A 619 " --> pdb=" O GLY A 615 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A 622 " --> pdb=" O ASP A 618 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 637 Processing helix chain 'A' and resid 695 through 703 removed outlier: 3.674A pdb=" N ASN A 703 " --> pdb=" O VAL A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 738 removed outlier: 3.639A pdb=" N MET A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN A 724 " --> pdb=" O ASN A 720 " (cutoff:3.500A) Proline residue: A 725 - end of helix removed outlier: 3.609A pdb=" N ILE A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 797 Processing helix chain 'A' and resid 798 through 803 Processing helix chain 'A' and resid 808 through 819 removed outlier: 4.163A pdb=" N THR A 814 " --> pdb=" O GLY A 810 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 826 Processing helix chain 'A' and resid 828 through 852 removed outlier: 3.586A pdb=" N ASN A 837 " --> pdb=" O THR A 833 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR A 851 " --> pdb=" O ILE A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 900 Proline residue: A 864 - end of helix removed outlier: 4.120A pdb=" N GLN A 890 " --> pdb=" O LYS A 886 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ALA A 891 " --> pdb=" O GLU A 887 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 898 " --> pdb=" O ILE A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 909 removed outlier: 3.832A pdb=" N SER A 907 " --> pdb=" O ARG A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 922 Processing helix chain 'A' and resid 922 through 963 removed outlier: 3.742A pdb=" N HIS A 934 " --> pdb=" O LYS A 930 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 935 " --> pdb=" O LYS A 931 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A 958 " --> pdb=" O CYS A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 992 removed outlier: 3.633A pdb=" N ALA A 983 " --> pdb=" O VAL A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1011 removed outlier: 3.995A pdb=" N ALA A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1082 removed outlier: 3.517A pdb=" N GLU A1082 " --> pdb=" O ILE A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1108 Processing helix chain 'A' and resid 1124 through 1132 Processing helix chain 'A' and resid 1139 through 1150 removed outlier: 3.513A pdb=" N ILE A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1158 removed outlier: 4.012A pdb=" N ASN A1158 " --> pdb=" O SER A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1189 removed outlier: 4.979A pdb=" N ARG A1181 " --> pdb=" O GLY A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1220 removed outlier: 3.668A pdb=" N VAL A1212 " --> pdb=" O SER A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1236 Processing helix chain 'A' and resid 1254 through 1260 Processing helix chain 'A' and resid 1262 through 1273 Processing sheet with id=AA1, first strand: chain 'A' and resid 421 through 422 removed outlier: 4.623A pdb=" N ASN A 401 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 455 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 427 through 429 removed outlier: 6.875A pdb=" N ILE A 428 " --> pdb=" O VAL A 589 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU A 559 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A 478 " --> pdb=" O ASP A 560 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 1058 through 1059 removed outlier: 3.682A pdb=" N VAL A1033 " --> pdb=" O VAL A1058 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A1036 " --> pdb=" O ARG A1091 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A1091 " --> pdb=" O GLU A1036 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1244 through 1245 541 hydrogen bonds defined for protein. 1590 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: 4.25 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 9084 1.06 - 1.28: 1483 1.28 - 1.50: 3776 1.50 - 1.73: 3798 1.73 - 1.95: 85 Bond restraints: 18226 Sorted by residual: bond pdb=" O3B AGS A1304 " pdb=" PB AGS A1304 " ideal model delta sigma weight residual 1.673 1.580 0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" O3B AGS A1303 " pdb=" PB AGS A1303 " ideal model delta sigma weight residual 1.673 1.581 0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" O3A AGS A1304 " pdb=" PA AGS A1304 " ideal model delta sigma weight residual 1.664 1.574 0.090 2.00e-02 2.50e+03 2.05e+01 bond pdb=" O3A AGS A1303 " pdb=" PA AGS A1303 " ideal model delta sigma weight residual 1.664 1.575 0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" O5' AGS A1303 " pdb=" PA AGS A1303 " ideal model delta sigma weight residual 1.634 1.573 0.061 2.00e-02 2.50e+03 9.26e+00 ... (remaining 18221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 32315 2.05 - 4.09: 571 4.09 - 6.14: 64 6.14 - 8.19: 14 8.19 - 10.23: 9 Bond angle restraints: 32973 Sorted by residual: angle pdb=" N TYR A 315 " pdb=" CA TYR A 315 " pdb=" C TYR A 315 " ideal model delta sigma weight residual 111.36 107.30 4.06 1.09e+00 8.42e-01 1.39e+01 angle pdb=" CA LYS A1170 " pdb=" CB LYS A1170 " pdb=" CG LYS A1170 " ideal model delta sigma weight residual 114.10 121.35 -7.25 2.00e+00 2.50e-01 1.32e+01 angle pdb=" CA SER A1260 " pdb=" C SER A1260 " pdb=" O SER A1260 " ideal model delta sigma weight residual 121.87 117.71 4.16 1.16e+00 7.43e-01 1.29e+01 angle pdb=" CB MET A1093 " pdb=" CG MET A1093 " pdb=" SD MET A1093 " ideal model delta sigma weight residual 112.70 122.93 -10.23 3.00e+00 1.11e-01 1.16e+01 angle pdb=" PB AGS A1304 " pdb=" O3B AGS A1304 " pdb=" PG AGS A1304 " ideal model delta sigma weight residual 129.21 119.27 9.94 3.00e+00 1.11e-01 1.10e+01 ... (remaining 32968 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.56: 8158 35.56 - 71.11: 357 71.11 - 106.67: 19 106.67 - 142.23: 1 142.23 - 177.79: 2 Dihedral angle restraints: 8537 sinusoidal: 4694 harmonic: 3843 Sorted by residual: dihedral pdb=" CA GLN A1116 " pdb=" C GLN A1116 " pdb=" N GLU A1117 " pdb=" CA GLU A1117 " ideal model delta harmonic sigma weight residual 180.00 -152.80 -27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA GLY A 530 " pdb=" C GLY A 530 " pdb=" N ASP A 531 " pdb=" CA ASP A 531 " ideal model delta harmonic sigma weight residual 180.00 155.98 24.02 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" O1A AGS A1303 " pdb=" O3A AGS A1303 " pdb=" PA AGS A1303 " pdb=" PB AGS A1303 " ideal model delta sinusoidal sigma weight residual 82.37 -95.42 177.79 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 8534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1206 0.054 - 0.107: 192 0.107 - 0.161: 27 0.161 - 0.214: 0 0.214 - 0.268: 2 Chirality restraints: 1427 Sorted by residual: chirality pdb=" C3' AGS A1304 " pdb=" C2' AGS A1304 " pdb=" C4' AGS A1304 " pdb=" O3' AGS A1304 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C3' AGS A1303 " pdb=" C2' AGS A1303 " pdb=" C4' AGS A1303 " pdb=" O3' AGS A1303 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CG LEU A1268 " pdb=" CB LEU A1268 " pdb=" CD1 LEU A1268 " pdb=" CD2 LEU A1268 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 1424 not shown) Planarity restraints: 2681 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 863 " 0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO A 864 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 864 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 864 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1259 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" C LEU A1259 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU A1259 " 0.011 2.00e-02 2.50e+03 pdb=" N SER A1260 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 227 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.87e+00 pdb=" N PRO A 228 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 228 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 228 " -0.024 5.00e-02 4.00e+02 ... (remaining 2678 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.20: 1204 2.20 - 2.80: 37555 2.80 - 3.40: 50498 3.40 - 4.00: 62844 4.00 - 4.60: 97657 Nonbonded interactions: 249758 Sorted by model distance: nonbonded pdb=" H ALA A 429 " pdb=" O VAL A 602 " model vdw 1.605 2.450 nonbonded pdb=" O GLY A 533 " pdb="HE21 GLN A 535 " model vdw 1.679 2.450 nonbonded pdb=" H GLU A 561 " pdb=" O VAL A 590 " model vdw 1.697 2.450 nonbonded pdb=" O ARG A1231 " pdb=" HG1 THR A1234 " model vdw 1.703 2.450 nonbonded pdb=" O MET A 723 " pdb=" H PHE A 727 " model vdw 1.704 2.450 ... (remaining 249753 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 group one per residue 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: 3.100 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: 0.080 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 17.380 Find NCS groups from input model: 0.040 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 0.005 0.093 9133 Z= 0.240 Angle : 0.825 10.232 12356 Z= 0.421 Chirality : 0.040 0.268 1427 Planarity : 0.004 0.043 1561 Dihedral : 18.848 177.786 3387 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.17 % Favored : 92.57 % Rotamer: Outliers : 1.58 % Allowed : 21.77 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.25), residues: 1144 helix: 0.95 (0.20), residues: 714 sheet: -3.17 (0.98), residues: 22 loop : -2.40 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 494 TYR 0.013 0.001 TYR A 627 PHE 0.027 0.002 PHE A 992 TRP 0.012 0.001 TRP A 853 HIS 0.004 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.24 ( 9133) covalent geometry : angle 0.82457 / 0.42 (12356) hydrogen bonds : bond 0.16201 / 11.23 ( 541) hydrogen bonds : angle 6.14173 / 4.50 ( 1590) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 439 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9101 (mp) REVERT: A 241 MET cc_start: 0.8941 (ppp) cc_final: 0.8495 (ppp) REVERT: A 621 MET cc_start: 0.9219 (tpt) cc_final: 0.8982 (tpt) REVERT: A 635 MET cc_start: 0.9290 (tmm) cc_final: 0.8971 (tpp) outliers start: 15 outliers final: 12 residues processed: 66 average time/residue: 0.1546 time to fit residues: 15.6909 Evaluate side-chains 63 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 806 LYS Chi-restraints excluded: chain A residue 901 ASN Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1268 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.052566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.041060 restraints weight = 149433.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.043046 restraints weight = 59743.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.044371 restraints weight = 34885.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.045262 restraints weight = 24738.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.045856 restraints weight = 19594.904| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9133 Z= 0.263 Angle : 0.602 6.630 12356 Z= 0.338 Chirality : 0.038 0.136 1427 Planarity : 0.004 0.036 1561 Dihedral : 12.547 179.124 1333 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.39 % Favored : 91.43 % Rotamer: Outliers : 2.73 % Allowed : 22.19 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.25), residues: 1144 helix: 1.14 (0.19), residues: 724 sheet: -3.04 (1.06), residues: 22 loop : -2.67 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 785 TYR 0.016 0.002 TYR A 918 PHE 0.016 0.002 PHE A 399 TRP 0.011 0.002 TRP A 217 HIS 0.005 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.26 ( 9133) covalent geometry : angle 0.60206 / 0.34 (12356) hydrogen bonds : bond 0.05113 / 3.61 ( 541) hydrogen bonds : angle 5.09694 / 3.68 ( 1590) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 439 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 49 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9097 (mp) REVERT: A 621 MET cc_start: 0.9215 (tpt) cc_final: 0.8976 (tpt) REVERT: A 635 MET cc_start: 0.9281 (tmm) cc_final: 0.8977 (tpp) outliers start: 26 outliers final: 18 residues processed: 72 average time/residue: 0.1502 time to fit residues: 17.2112 Evaluate side-chains 66 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 901 ASN Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1225 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.053248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.041873 restraints weight = 147883.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.043893 restraints weight = 57799.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.045249 restraints weight = 33429.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.046159 restraints weight = 23460.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.046765 restraints weight = 18426.093| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9133 Z= 0.133 Angle : 0.512 5.373 12356 Z= 0.278 Chirality : 0.036 0.133 1427 Planarity : 0.003 0.038 1561 Dihedral : 11.763 178.147 1323 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.13 % Favored : 91.70 % Rotamer: Outliers : 2.10 % Allowed : 22.61 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.25), residues: 1144 helix: 1.44 (0.20), residues: 732 sheet: -3.23 (1.11), residues: 20 loop : -2.70 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 494 TYR 0.012 0.001 TYR A 627 PHE 0.015 0.001 PHE A 992 TRP 0.015 0.001 TRP A 853 HIS 0.003 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 ( 9133) covalent geometry : angle 0.51227 / 0.28 (12356) hydrogen bonds : bond 0.04758 / 3.37 ( 541) hydrogen bonds : angle 4.64712 / 3.36 ( 1590) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 439 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9076 (mp) REVERT: A 621 MET cc_start: 0.9208 (tpt) cc_final: 0.8999 (tpt) REVERT: A 635 MET cc_start: 0.9295 (tmm) cc_final: 0.8987 (tpp) outliers start: 20 outliers final: 13 residues processed: 68 average time/residue: 0.1649 time to fit residues: 17.7633 Evaluate side-chains 62 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1225 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 107 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN ** A 575 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 = 0.3337 r_free = 0.3337 target = 0.052968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.041496 restraints weight = 148562.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.043513 restraints weight = 58515.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.044872 restraints weight = 34039.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.045761 restraints weight = 24047.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.046324 restraints weight = 19048.293| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9133 Z= 0.155 Angle : 0.504 5.401 12356 Z= 0.277 Chirality : 0.036 0.144 1427 Planarity : 0.003 0.040 1561 Dihedral : 11.250 176.991 1321 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.57 % Favored : 91.26 % Rotamer: Outliers : 1.89 % Allowed : 22.82 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.25), residues: 1144 helix: 1.56 (0.19), residues: 733 sheet: -2.97 (1.13), residues: 22 loop : -2.66 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 494 TYR 0.011 0.001 TYR A 627 PHE 0.015 0.001 PHE A 992 TRP 0.012 0.001 TRP A 853 HIS 0.009 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 ( 9133) covalent geometry : angle 0.50448 / 0.28 (12356) hydrogen bonds : bond 0.04369 / 3.07 ( 541) hydrogen bonds : angle 4.58286 / 3.32 ( 1590) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 439 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9095 (mp) REVERT: A 241 MET cc_start: 0.8949 (ppp) cc_final: 0.8498 (ppp) REVERT: A 621 MET cc_start: 0.9214 (tpt) cc_final: 0.9013 (tpt) REVERT: A 635 MET cc_start: 0.9305 (tmm) cc_final: 0.9004 (tpp) outliers start: 18 outliers final: 16 residues processed: 64 average time/residue: 0.1614 time to fit residues: 16.3464 Evaluate side-chains 65 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1268 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 0.0670 overall best weight: 1.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.052834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.041478 restraints weight = 148392.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.043517 restraints weight = 58581.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.044861 restraints weight = 33924.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.045777 restraints weight = 23874.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.046348 restraints weight = 18758.699| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9133 Z= 0.160 Angle : 0.500 5.365 12356 Z= 0.275 Chirality : 0.036 0.132 1427 Planarity : 0.003 0.041 1561 Dihedral : 10.914 174.922 1321 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.48 % Favored : 91.35 % Rotamer: Outliers : 2.10 % Allowed : 22.61 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.25), residues: 1144 helix: 1.65 (0.20), residues: 731 sheet: -3.31 (1.11), residues: 20 loop : -2.68 (0.27), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 494 TYR 0.011 0.001 TYR A 627 PHE 0.015 0.001 PHE A 992 TRP 0.013 0.001 TRP A 853 HIS 0.007 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 ( 9133) covalent geometry : angle 0.49998 / 0.27 (12356) hydrogen bonds : bond 0.04239 / 2.98 ( 541) hydrogen bonds : angle 4.51677 / 3.27 ( 1590) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 439 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9083 (mp) REVERT: A 635 MET cc_start: 0.9303 (tmm) cc_final: 0.9018 (tpp) outliers start: 20 outliers final: 14 residues processed: 65 average time/residue: 0.1618 time to fit residues: 16.7544 Evaluate side-chains 62 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1268 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.053241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.041965 restraints weight = 146536.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.044005 restraints weight = 58189.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.045354 restraints weight = 33713.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.046249 restraints weight = 23704.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.046849 restraints weight = 18761.281| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9133 Z= 0.116 Angle : 0.483 5.260 12356 Z= 0.260 Chirality : 0.036 0.133 1427 Planarity : 0.003 0.041 1561 Dihedral : 10.503 172.966 1320 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.22 % Favored : 91.61 % Rotamer: Outliers : 2.00 % Allowed : 21.98 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.26), residues: 1144 helix: 1.85 (0.20), residues: 729 sheet: -3.68 (0.87), residues: 30 loop : -2.51 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 494 TYR 0.010 0.001 TYR A 627 PHE 0.016 0.001 PHE A 992 TRP 0.013 0.001 TRP A 853 HIS 0.006 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 ( 9133) covalent geometry : angle 0.48330 / 0.26 (12356) hydrogen bonds : bond 0.04092 / 2.87 ( 541) hydrogen bonds : angle 4.32791 / 3.13 ( 1590) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 439 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9075 (mp) REVERT: A 635 MET cc_start: 0.9298 (tmm) cc_final: 0.9027 (tpp) outliers start: 19 outliers final: 16 residues processed: 66 average time/residue: 0.1630 time to fit residues: 17.1140 Evaluate side-chains 66 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1268 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 41 optimal weight: 0.0970 chunk 98 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.053058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.041685 restraints weight = 148550.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.043729 restraints weight = 59080.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.045081 restraints weight = 34226.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.045985 restraints weight = 24127.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.046589 restraints weight = 19047.639| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9133 Z= 0.131 Angle : 0.484 5.532 12356 Z= 0.261 Chirality : 0.036 0.132 1427 Planarity : 0.003 0.041 1561 Dihedral : 10.241 172.332 1320 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.30 % Favored : 91.43 % Rotamer: Outliers : 1.68 % Allowed : 22.61 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.26), residues: 1144 helix: 1.92 (0.20), residues: 729 sheet: -3.96 (0.83), residues: 28 loop : -2.50 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 494 TYR 0.009 0.001 TYR A 627 PHE 0.016 0.001 PHE A 992 TRP 0.011 0.001 TRP A 853 HIS 0.006 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 9133) covalent geometry : angle 0.48433 / 0.26 (12356) hydrogen bonds : bond 0.03968 / 2.78 ( 541) hydrogen bonds : angle 4.32247 / 3.13 ( 1590) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 439 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9096 (mp) REVERT: A 241 MET cc_start: 0.8920 (ppp) cc_final: 0.8440 (ppp) REVERT: A 519 MET cc_start: 0.9002 (mmm) cc_final: 0.8535 (mmm) REVERT: A 635 MET cc_start: 0.9289 (tmm) cc_final: 0.9022 (tpp) outliers start: 16 outliers final: 14 residues processed: 64 average time/residue: 0.1586 time to fit residues: 16.0050 Evaluate side-chains 64 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1268 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 84 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.052348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.041050 restraints weight = 149409.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.043025 restraints weight = 59820.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.044356 restraints weight = 34863.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.045225 restraints weight = 24619.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.045819 restraints weight = 19488.981| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9133 Z= 0.209 Angle : 0.527 5.810 12356 Z= 0.290 Chirality : 0.036 0.131 1427 Planarity : 0.003 0.041 1561 Dihedral : 10.116 169.123 1320 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.74 % Favored : 91.00 % Rotamer: Outliers : 2.00 % Allowed : 22.40 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.25), residues: 1144 helix: 1.74 (0.19), residues: 729 sheet: -4.01 (0.81), residues: 28 loop : -2.58 (0.27), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 494 TYR 0.010 0.001 TYR A 321 PHE 0.016 0.001 PHE A 992 TRP 0.009 0.001 TRP A 853 HIS 0.005 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.21 ( 9133) covalent geometry : angle 0.52734 / 0.29 (12356) hydrogen bonds : bond 0.04081 / 2.84 ( 541) hydrogen bonds : angle 4.53571 / 3.28 ( 1590) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 439 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 MET cc_start: 0.9054 (mmm) cc_final: 0.8580 (mmm) REVERT: A 1017 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8257 (t70) outliers start: 19 outliers final: 18 residues processed: 66 average time/residue: 0.1642 time to fit residues: 17.2537 Evaluate side-chains 67 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1268 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 70 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 3 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.052709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.041430 restraints weight = 148234.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.043436 restraints weight = 58855.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.044784 restraints weight = 34156.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.045666 restraints weight = 24029.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.046139 restraints weight = 18963.375| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9133 Z= 0.141 Angle : 0.500 6.299 12356 Z= 0.269 Chirality : 0.036 0.132 1427 Planarity : 0.003 0.041 1561 Dihedral : 9.864 165.428 1318 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.30 % Favored : 91.43 % Rotamer: Outliers : 1.79 % Allowed : 22.71 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.26), residues: 1144 helix: 1.88 (0.20), residues: 729 sheet: -3.99 (0.82), residues: 28 loop : -2.52 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 494 TYR 0.010 0.001 TYR A 627 PHE 0.016 0.001 PHE A 992 TRP 0.013 0.001 TRP A 853 HIS 0.007 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 ( 9133) covalent geometry : angle 0.49976 / 0.27 (12356) hydrogen bonds : bond 0.04020 / 2.81 ( 541) hydrogen bonds : angle 4.35855 / 3.14 ( 1590) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 439 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.8915 (ppp) cc_final: 0.8389 (ppp) REVERT: A 519 MET cc_start: 0.9065 (mmm) cc_final: 0.8584 (mmm) REVERT: A 635 MET cc_start: 0.9305 (tmm) cc_final: 0.9051 (tpp) outliers start: 17 outliers final: 16 residues processed: 64 average time/residue: 0.1662 time to fit residues: 16.8391 Evaluate side-chains 64 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1268 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 90 optimal weight: 0.5980 chunk 54 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 105 optimal weight: 0.1980 chunk 72 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.053144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.041782 restraints weight = 147030.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.043820 restraints weight = 58570.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.045181 restraints weight = 33973.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.046087 restraints weight = 23942.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.046695 restraints weight = 18868.506| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9133 Z= 0.113 Angle : 0.487 7.034 12356 Z= 0.259 Chirality : 0.036 0.132 1427 Planarity : 0.003 0.041 1561 Dihedral : 9.613 162.050 1318 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.39 % Favored : 91.35 % Rotamer: Outliers : 1.68 % Allowed : 22.82 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.26), residues: 1144 helix: 2.03 (0.20), residues: 729 sheet: -4.06 (0.81), residues: 28 loop : -2.45 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 494 TYR 0.009 0.001 TYR A 627 PHE 0.016 0.001 PHE A 992 TRP 0.013 0.001 TRP A 853 HIS 0.006 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 9133) covalent geometry : angle 0.48742 / 0.26 (12356) hydrogen bonds : bond 0.03880 / 2.71 ( 541) hydrogen bonds : angle 4.20243 / 3.03 ( 1590) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 439 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.8906 (ppp) cc_final: 0.8380 (ppp) REVERT: A 519 MET cc_start: 0.9100 (mmm) cc_final: 0.8621 (mmm) outliers start: 16 outliers final: 15 residues processed: 65 average time/residue: 0.1409 time to fit residues: 14.7817 Evaluate side-chains 64 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1268 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 54 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.052975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.041600 restraints weight = 148699.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.043623 restraints weight = 59029.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.044980 restraints weight = 34283.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.045858 restraints weight = 24184.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.046466 restraints weight = 19191.615| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9133 Z= 0.134 Angle : 0.500 7.181 12356 Z= 0.268 Chirality : 0.036 0.205 1427 Planarity : 0.003 0.042 1561 Dihedral : 9.568 161.211 1318 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.22 % Favored : 91.52 % Rotamer: Outliers : 1.58 % Allowed : 22.71 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.26), residues: 1144 helix: 2.01 (0.20), residues: 729 sheet: -4.07 (0.81), residues: 28 loop : -2.46 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 494 TYR 0.008 0.001 TYR A1039 PHE 0.016 0.001 PHE A 992 TRP 0.011 0.001 TRP A 853 HIS 0.006 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 ( 9133) covalent geometry : angle 0.49994 / 0.27 (12356) hydrogen bonds : bond 0.03869 / 2.70 ( 541) hydrogen bonds : angle 4.24226 / 3.06 ( 1590) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2845.31 seconds wall clock time: 49 minutes 21.29 seconds (2961.29 seconds total)